title: The role of FAM46C in myeloma cells [array]

summary: FAM46C is one of the most recurrently mutated genes in multiple myeloma (MM), however its role in disease pathogenesis is not determined. Here we demonstrate that wild type (WT) FAM46C overexpression induces substantial cytotoxicity in MM cells. In contrast, FAM46C mutations found in MM patients abrogate this cytotoxicity indicating a MM survival advantage conferred by the FAM46C mutant phenotype. WT FAM46C overexpression downregulated IRF4, CEBPB, MYC and upregulated immunoglobulin (Ig) light chain and HSPA5/BIP. Furthermore, pathway analysis suggests that enforced FAM46C expression activates the unfolded protein response (UPR) pathway and induces mitochondrial dysfunction. In contrast, endogenous CRISPR FAM46C depletion enhanced MM cell growth and notably decreasing Ig light chain and BIP expression, activating of ERK and anti-apoptotic signaling and conferring relative resistance to dexamethasone and lenalidomide treatment. The genes altered in FAM46C depleted cells are enriched for signaling pathways regulating estrogen, glucocorticoid, B cell receptor signaling and ATM signaling. Together these results implicate FAM46C in myeloma cell growth and survival. FAM46C mutation contributes to myeloma pathogenesis and disease progression by perturbation in plasma cell differentiation and endoplasmic reticulum homeostasis.

overall_design: To assess the gene expression changes induced by FAM46C depletion, three samples, including OCIMY5 cells harboring, respectively, control, FAM46C gRNA #1 and FAM46C #6 gRNA, were harvested and processed for gene expression analysis.

first: Yuan

middle: X

last: Zhu

first: Chang

last: Shi

first: Esteban

last: Braggio

first: A

middle: K

last: Stewart


title: Differential Expression of Long Non-Coding RNAs in Patients with Tuberculosis Infection

status: Public on Jul 25 2017

city: Shenzhen

first: Dayong

last: Gu

address: 1011, Fuqiang Road, Futian District

department: Central Laboratory of Health quarantine

country: China

institute: Shenzhen Entry-exit Inspection and Quarantine Bureau

summary: The differential expression of the long non-coding RNAs (lncRNAs) in the sputa from patients with Tuberculosis (TB) as (TB positive), community acquired pneumonia (CAP) and healthy individuals (CG) using lncRNA microarray scanning were evaluated. It was found that there were 2116 specific lncRNAs differentially expressed in the TB positive samples (1102 up-regulated and 1014 down-regulated), which accounted for 6.96% of total lncRNAs.

overall_design: In the study presented here, plasma samples from patients diagnosed as TB positive by sputum smear microscopy and sputum culture, patients with CAP and healthy subjects for reference control in Zhuhai Center for Chronic Disease Control during the period from October, 2014 to November, 2015 were collected.

first: Jianan

last: He

first: Qingye

last: Ou

first: Chunxiao

last: Liu

first: Lei

first: Chunzhong

last: Zhao

first: Yunqing

last: Xu

first: Siu

last: Kong

first: Jacky

middle: F

last: Loo

first: Boan

last: Li


title: Genomic profile of CRC Xenosphere and original PDX

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

overall_design: 90 samples of matched Xeno patients and Xenospheres

first: Paolo

last: Luraghi

first: Carla

last: Boccaccio


title: Microarray analyses using bone marrow-derived macrophages from Batf2−/− and wildtype mice that had been stimulated with R848

status: Public on Jul 24 2017

city: Kumamoto

first: Hisashi

last: Kanemaru

state: Kumamoto

address: 1-1-1 Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

summary:
We assessed the role of basic leucine zipper transcription factor ATF-like 2 (Batf2), particularly its positive transcriptional activities via TLR signals.
Because TLR7 agonists are clinically used against tumors and have proven effective as antitumor drugs, we assessed effect of Batf2 on the responses to the TLR7 ligand (R848).

overall_design: We performed microarray analyses using bone marrow-derived macrophages (BMDMs) from Batf2-/- and wildtype (WT) mice that had been stimulated with R848 (100 ng/ml).

first: Shizuo

last: Akira


title: Analysis of the gene expression of the mouse after different heat-induced treatment

city: shanghai

first: Dean

state: shanghai

address: new ring road 138,minghang area

department: Bioinformatics

institute: OE biotech

summary: To detect the gene expression changes in the mouse after different iron treatment to find the affected genes and its pathways

overall_design: 38.5℃ for 1h after waterbath at 37 for 1h, collect blood ,compared with the control to see the genes affected

first: Liwu

last: Zhu

first: Bing

last: Jia


title: Expression data from MNV-specific CD8 T cells

city: Philadelphia

first: Vesselin

middle: T

last: Tomov

state: PA

address: 421 Curie Boulevard

department: Medicine/GI

country: USA

institute: University of Pennsylvania

summary:
Mouse norovirus (MNV) causes acute or chronic infection in immunocompetent hosts, but the CD8 T cell determinants of viral persistence versus clearance are unknown.
We used microarrays to interrogate the transcriptional program on MNV-specific CD8 T cells from the spleen and intestine at days 8, 15, 30 post infection with and acute or chronic strain of MNV.

overall_design: Mice were infected with MNV-CW3 or MNV-CR6fy and tetramer-positive CD8 T cells were sorted from the spleen and intestinal epithelium at day 8, 15, and 30.  Analysis was done on an Affymetrix MoGene 2.0 Micorarrays.

first: John

middle: E

last: Wherry


title: Genomics-enabled analysis of the emergent disease cotton bacterial blight

city: St Louis

first: Rebecca

last: Bart

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

type: Expression profiling by high throughput sequencing

summary: Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Analysis of cotton variety planting statistics indicates a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen  Xcm isolates. These genomes, along with 4 previously published Xcm genomes, encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes  a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different class III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars.

overall_design: The cotton varieties Acala Maxxa and DES56 were syringe inoculated with two strains of Xcm (MS14003 and AR81009) and a mock treatment. Tissue was collected in three biological replicates 24 and 48 hours after inoculation.

first: Anne

middle: Z

last: Phillips

first: Jeffrey

middle: C

last: Berry

first: Mark

last: Wilson

first: Anupama

last: Vijayaraghavan

first: Jillian

last: Burke

first: J

middle: I

last: Bunn

first: Tom

middle: W

last: Allen

first: Terry

last: Wheeler


title: Expression data from KSRP knockdown lung cancer cell

status: Public on Jul 26 2017

city: Taipei

first: Kuo-Tai

last: Hua

address: No. 1, Sec. 1, Jen-Ai Rd.

country: Taiwan

institute: National Taiwan University

summary:
KSRP depleted CL1-0 cells were used to identify genes regulated by KSRP
We used microarrays to detail the global programme of gene expression underlying metastasis and identified distinct classes of KSRP-regulated genes during this process.

overall_design: CL1-0 cells stablely depleted KSRP expression were analyzed compare to scramble control cells


title: ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells treated with cycloheximide

status: Public on Jul 23 2017

city: San Francsico

first: Miguel

last: Ramalho-Santos

state: California

address: 35 Medical Center Way, RMB 912D

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells before and after treatment with cycloheximide (CHX, 1 ug/ml) for 3 hours.

first: Aydan

last: Bulut-Karslioglu

first: Trisha

middle: A

last: Macrae


title: Genomic profiling of H3K27ac and transcription factor binding in ERG-overexpressing prostate cancer

city: Toronto

first: Ken

last: Kron

state: ON

address: 101 College Street, TMDT, 11th floor, room 11-601B

country: Canada

institute: University Health Network

summary: Structural rearrangements leading to the TMPRSS2:ERG (T2E) fusion typify ~50% of prostate tumors and result in overexpression of the ERG transcription factor. Using T2E and non-T2E primary prostate tumors, we assessed the impact of ERG overexpression on chromatin by integrating ChIP-seq against H3K27ac, a chromatin modification found at active cis-regulatory elements, with paired genomic and expression data. We show that T2E tumors have a consistent and distinct cis-regulatory landscape to non-T2E tumors which drives their unique transcriptional profile. The T2E-specific cis-regulatory landscape is driven by ERG-mediated co-option of prostate master transcription factors HOXB13 and FOXA1 and is typified by Cluster Of Regulatory Elements (COREs)  including one spreading into the ERG locus of the structurally rearranged allele. This gives rise to a cis-regulatory element within the rearranged ERG gene that contributes to ERG overexpression. The unique cis-regulatory landscape in T2E primary prostate tumors also reveals the activation of the NOTCH signalling pathway. Accordingly, chemical NOTCH pathway inhibition limited the invasive nature of T2E prostate cancer cells, revealing an actionable vulnerability against T2E prostate tumors. Taken together, our work delineates the role of ERG over-expression in co-opting master transcription factors to deploy a unique cis-regulatory landscape inducing a dependency on NOTCH signaling in T2E prostate tumors.

overall_design: Genomic profiles of H3K27ac in ERG overexpressing prostate cancer and prostate cancer without ERG overexpression. Genomic binding of AR, FOXA1, HOXB13 in 22Rv1 prostate cells and of HOXB13 in LNCaP prostate cells. Genomic binding of FOXA1 and HOXB13, as well as H3K27ac profiles, upon knockdown of ERG in VCaP prostate cells.

first: Mathieu

last: Lupien

first: Kenneth


title: Genome-wide mapping of PRDM15 binding in pluripotent mouse Embryonic Stem Cells (mESCs)

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

overall_design: Examination of PRDM15 binding targets in WT vs. Prdm15 KO mESCs in SL or 2i conditions

first: Slim

last: Mzoughi

first: Heike

last: Wollmann


title: PRDM15 safeguards naïve pluripotency by transcriptionally regulating WNT and MAPK/ERK signaling

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

overall_design: Refer to individual Series


title: The LncRNA MetaLnc9 is Transcriptionally controlled by NONO/CRTC Complex and Facilitates Lung Cancer Metastasis through PGK1-Activated AKT/mTOR Pathway

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: We discovered that elevated LINC00963, termed MetaLnc9 (Metastasis Associated LncRNA in chromosome 9q34), expression in NSCLC tissues correlated with poor prognosis and promoted NSCLC cell migration and invasion in vitro and lung metastasis formation in vivo

overall_design: We identified a lncRNA signature associated with non-small cell lung cancer (NSCLC) cell metastasis by comparing the lncRNA expression profiles between SPC-A-1sci (highly metastatic) and SPC-A-1 (weakly metastatic) cells

first: Tao

last: Yu

first: Ming

last: Yao


title: SMC progressively aligns chromosomal arms in Caulobacter crescentus but is antagonized by convergent transcription

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

summary: The Structural Maintenance of Chromosomes (SMC) complex plays an important role in chromosome organization and segregation in most living organisms. In Caulobacter crescentus, SMC is required to align the left and the right arms of the chromosome that run in parallel down the long axis of the cell. However, the mechanism of SMC-mediated alignment of chromosomal arms remains elusive. Here, using genome-wide methods and microscopy of single cells, we show that Caulobacter SMC is recruited to the centromeric parS site and that SMC-mediated arm alignment depends on the chromosome partitioning protein ParB. We provide evidence that SMC likely tethers the parS-proximal regions of the chromosomal arms together, promoting arm alignment. Furthermore, we show that highly-transcribed genes near parS that are oriented against SMC translocation disrupt arm alignment, suggesting that head-on transcription interferes with SMC translocation. Our results demonstrate a tight interdependence of bacterial chromosome organization and global patterns of transcription.

overall_design: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290). After synchronization, swarmer cells were fixed formadehyde for chromosome conformation capture and Hi-C analysis. For antibiotic treatments, swarmer cells were incubated with 25 ug/mL rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

first: T

middle: B

first: N

last: Tran

first: M

last: Laub


title: RXR mediated neurogenesis (ChIP-Seq)

status: Public on Jul 22 2017

city: Orlando

first: Laszlo

last: Nagy

state: Hungary

address: Sanger Road

institute: Sandford Burnham Prebys Institute

summary: A growing number of pieces of evidence suggest the importance of Retinoid X Receptor (RXR)-mediated pathways in neurogenesis and the dysregulation of this signaling in neurodegenerative disorders, such as Alzheimer`s or Amyotrophic Lateral Sclerosis. The data presented here identify the RAR:RXR and LXR:RXR-mediated transcriptional program in embryonic stem cells, neural progenitors and terminally differentiated neurons.

overall_design: LG268, and GW3965 treatments

first: Zoltan

last: Simandi


title: Comparing RNA expression profiles of KALori and KANSL mouse lungs

city: Frederick

first: Zane

last: Gray

state: MD

address: 1050 Boyles Street

department: Cancer and Inflammation Program

institute: National Cancer Institute

summary:
We have reported that pulmonary infiltrating macrophages, which highly express inducible nitric-oxide synthase (iNOS/NOS2), play a critical role for driving spontaneous lung SCC development in a new mouse model (L-Ikka KA/KA; KA/KA) that mimics human lung SCC development. However, the role of NOS2 in lung SCC development is unknown.
Our data suggests deletion of the gene iNOS prevents tumorogenesis in this mouse model. We use microarray data to compare levels of expression of genes associated with lung tumor development and prevention.

overall_design: At 14 weeks of age, lungs were isolated from mice of each background, KALori and KANSL, to generate four total samples. RNA was then isolated by Trizol method and prepared for Microarray Affymetrix  performed by NCI-Genomics lab.

first: Yinling

last: Hu


title: Expression microarray analysis of mycobacteria-specific CD4 T cells

city: Bronx

first: Shajo

last: Kunnath Velayudhan

state: New York

address: 1300 Morris Park Avenue

department: M&I

institute: Albert Einstein College of Medicine

summary: Live antigen-specific CD4 T cells are identified typically by tetramer staining or by staining of cytokines captured on the cell surface by bi-functional antibodies.  We attempted identification of mycobacteria specific CD4 T cells using CD154 staining.  In this method, splenocytes were stimulated with appropriate antigens in the presence of monensin and fluorochrome-conjugated anti-CD154 antibody.  Antigen-specific cells will be stained positive for CD154.  We performed microarrays with CD154 positive and negative CD4 T cells.

overall_design: Splencoytes from M. bovis BCG vaccinated mice were stimulated in vitro with M. tuberculoiss lysate in the presence of monensin and anti-CD154-PE antibody.  Next, they were stained for dead cells, CD4, and CD44.  All sorted cells were live and positive for CD4, and CD44 and two microarray groups were distinguished based on the status of CD154 staining (positive or negative).

first: Steven

last: Porcelli


title: Expression data of lncRNA from MCF7 cells treated or not treated with TGF-β

city: Xi'an

first: Lei

last: Wang

address: 169 Changle West Road

department: Department of Biochemistry and Molecular Biology

institute: Fourth Military Medical University

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

summary:
TGF-β is a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors and other classes of genes
We used microarrays to detail the global programme of gene expression underlying TGF-β-induced EMT and identified distinct classes of TGF-β-regulated lncRNAs during this process.

overall_design: MCF7 cells were treated with TGF-β continuously for 4 days for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain lncRNAs that are differentially regulated by TGF-β. To that end, MCF7 cells were treated with 10 ng/ml of recombinant TGF-β1 for 4 days. TGF-β1 was replenished every 2 days with a fresh medium change.

first: Guoyin


title: RNA-seq data of two half-leaf seedlings under salt treatment and control condition

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

institute: China Agricultural University

summary: Purpose: Genome-wide expression analysis for introgression line 9L136 and indica variety 93-11 under salt reatment and control to identify specifically differentially expressed in 9L136 under salt stress. Methods: Roots of two-half leaf seedlings of 9L136 and 93-11 were  sequenced using an Illumina HiSeq2500 Sequencer; high-quality paired-end reads were mapped to the Nipponbare reference genome (MSU Rice Genome Annotation Project Release 7) using the spliced read mapper TopHat version 2.0.12, and Significant differentially expressed genes (DEGs) were determined based on a threshold of 2-fold expression change and false discovery rate (FDR) < 0.05 using Cuffdiff, one module of Cufflinks. qRT-PCR analysis were performed using SYBR Green Master Mix on  CFX96 Real Time System. Results: 1388 genes which specifically differentilly expressed in 9L136 under salt stress were identified, and expression profile of 18 genes randomely selected was confirmed by qRT-PCR.

overall_design: RNA-seq data of roots of two half-leaf seedlings under salt treatment and control condition were generated using Illumina HiSeq2500 Sequencer, in triplicate for each sample.

first: Fengxia

last: Liu


title: Mbd3-null and control lymphoid progenitor cells

city: Cambridge

first: Stephen

middle: John

last: Loughran

address: Wellcome Trust/MRC building, Addenbrooke's Hospital

department: Haematology

institute: University of Cambridge


title: Genome-wide identification and characterization of novel lncRNAs in Arabidopsis thaliana

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the overall long noncoding RNA (lncRNA) involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (4 rosette leaves>1mm, 14 rosette leaves>1mm, rosette growth complete, first flower buds visible, flourishing florescence, first silique shattered, senescence) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 28.8 Gb raw data and identified 156 novel lncRNAs (unreported in all public plant lncRNA databases) . We also categorized the novel lncRNAs as intergenic, intronic, antisense, overlapped with perhaps pseudogenes and mRNA based on their location on the Arabidopsis genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Arabidopsis, and provide a rich resource for further research on the function of these novel lncRNAs.

overall_design: RNA-sequencing of whole plants at 7 developmental stages (pooled sample).

first: Zhaogeng

last: Lu


title: ATAC-seq analysis of chromatin accessibility in Mbd3-null and control lymphoid progenitor cells

summary: To determine the role of Mbd3/NuRD in lymphopoiesis, chromatin accessbility was analysed in purified populations of Mbd3-deleted and control lymphoid progenitor cells using the assay for transposase-accessible chromatin using sequencing (ATAC-seq).

overall_design: Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow and thymus by flow cytometry, including all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs), pro-B cells and DN3b thymocytes. ATAC-seq was performed as previously described (Buenrostro et al (2013) Nat. Methods 10:1213) on two or three biologically independent samples of 500 cells. Chromatin accessibility scores were determined based on the density of reads across the genome.

middle: J


title: Transcriptomic analysis of a novel Saccharomyces cerevisiae strain with improved xylose fermentation ability under heat and acid co-stress

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

summary: Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.

overall_design: Total RNA extracted from three Saccharomyces cerevisiae strains (Sun049T-Z, Sun224T-K, and Hyb-8) was used for the transcriptomic analysis by Agilent microarray.  Each microarray sample was analyzed in triplicate resulting in total of 9 samples.

first: Kentaro

last: Inokuma

first: Ryo

last: Iwamoto

first: Tomohisa

last: Hasunuma


title: Generation and characterisation of two D2A1 mammary cancer sublines to model spontaneous and experimental metastasis in a syngeneic BALB/c host

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

summary: In vivo and in vitro analyses revealed distinct and shared characteristics of the metastatic D2A1-m1 and D2A1-m2 sublines. In particular, D2A1-m1 cells are more aggressive in experimental metastasis assays, while D2A1-m2 cells are more efficient at disseminating from the primary tumour in spontaneous metastasis assays. Surprisingly, classical metastasis-associated in vitro phenotypes such as enhanced proliferation, migration and invasion are reduced in the sublines compared to the parental cell line. Further, evasion of immune control cannot fully explain their enhanced metastatic properties. By contrast, both sublines show increased resistance to apoptosis when cultured in non-adherent conditions and, for the D2A1-m2 subline, increased 3D tumour spheroid growth. Moreover, the enhanced spontaneous metastatic phenotype of the D2A1-m2 sublines is associated with the ability to recruit an activated tumour stroma and promote directional migration of fibroblasts. Gene expression profiling revealed that the two metastatic sublines are distinct but more closely related to each other than the parental D2A1 cells.

overall_design: Two syngeneic spontaneously metastatic sublines, D2A1-m1 and D2A1-m2, were generated from the poorly metastasising BALB/c-derived D2A1 cell line by serial in vivo passaging. Functional and molecular characterisation of the parental D2A1 cells and the D2A1-m1 and D2A1-m2 sublines was undertaken using spontaneous and experimental in vivo metastasis assays, in vitro cell-based assays and gene expression profiling.

first: Qiong

first: Ute

last: Jungwirth

first: Clare

middle: M

last: Isacke


title: Human bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells from young and elderly patients

status: Public on Jul 21 2017

city: Hirakata

first: Ryusuke

last: Nakatsuka

state: Osaka

address: 2-5-1 Shin-machi

department: Stem Cell Biology

institute: Kansai medical University

summary: Global gene expressions of human bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells from young and elderly patients were analyzed. Results provide an insight into the molecular mechanisms of aging and cellular senescence.

overall_design: Cultured human bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells from young (28 to 31years old) and elderly (80 to 91 years old) patients were analyzed.

first: Hiroshi

last: Kawamura

first: Yoshikazu

last: Matsuoka

first: Keisuke

last: Sumide

first: Tatsuya

last: Fujioka

first: Hiroaki

last: Asano

first: Hirokazu

last: Iida

first: Yoshiaki

last: Sonoda


title: Identification of GLYMA.06G314400 and GLYMA.13G317000 binding sites in soybean early maturation embryos

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.06G314400 and GLYMA.13G317000 in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.06G314400 and GLYMA.13G317000 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 6 samples were sequenced using the Illumina HiSeq2500 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Leonardo

last: Jo

first: Min

last: Chen

first: Robert

last: Golberg


title: BRCA1-mimetic compound NSC35446.HCl inhits IKKB expression by reducing estrogen receptor alpha occupancy in the IKKB promoter and inhibts NF-κB activity in anti-estrogen resitant human breast cells

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

institute: Georgetown University Medical Center

summary: We previously identified small molecules that fit into a BRCA1-binding pocket within estrogen receptor-alpha (ER), mimic the ability of BRCA1 to inhibit ER activity (“BRCA1-mimetics”), and overcome antiestrogen resistance. One such compound, the hydrochloride salt of NSC35446 (“NSC35446.HCl”), also inhibited growth of antiestrogen-resistant LCC9 tumor xenografts. The purpose of this study was to investigate the down-stream effects of NSC35446.HCl and its mechanism of action. Methods: Here, we studied antiestrogen-resistant (LCC9, T47DCO, MCF-7/RR, LY2), ER-negative (MDA-MB-231, HCC1806, MDA-MB-468), and antiestrogen-sensitive (MCF-7) cell lines. Techniques utilized include RNA-seq, qRT-PCR, cell growth analysis, cell-cycle analysis, Western blotting, luciferase reporter assays, TUNEL assays, in-silico analysis of the IKKB gene, and ChIP assays.   Results: NSC35446.HCl inhibited proliferation and induced apoptosis in antiestrogen resistant LCC9, T47DCO, MCF-7/RR, and LY2 cells but not in ER-negative breast cancer cell lines. IKKB (IKKβ, IKBKB), an upstream activator of NF-B, was identified as a BRCA1-mimetic-regulated gene, based on an RNA-seq analysis; and NSC35446.HCl inhibited IKKB mRNA and protein expression in LCC9 cells. NSC35446.HCl also inhibited NF-B activity and expression of NF-B target genes. In-silico analysis of the IKKB promoter identified nine estrogen response element (ERE) half-sites and one ERE-like full-site. ChIP assays revealed that ER was recruited to the ERE-like full-site and five of the nine half-sites and that ER recruitment was inhibited by NSC35446.HCl in LCC9 and T47DCO cells. Conclusions: These studies identify functional EREs in the IKKB promoter and identify IKKB as an NSC35446.HCl-regulated gene; and they suggest that NF-B and IKKB, which were previously linked to antiestrogen resistance, are targets for NSC35446.HCl in reversing antiestrogen resistance.

overall_design: Examination of mRNA profiles of BRCA1 mimetic treated LCC9 cells: 4 samples Total: 2 Vehicle(DMSO) Control and 2 BRCA1 mimetic (A7) treated LCC9 cells

first: Shyam

last: Nathan

first: Yongxian

last: Ma

first: Eliseau

middle: D

last: Oliveira

first: Milton

last: Brown

first: Eliot

last: Rosen


title: Altered infant T cell differentiation in infection or vaccination reduces lung tissue-resident memory generation

city: New York

first: Donna

middle: L

last: Farber

state: NY

address: 650 West 168th Street, BB1701

department: Surgery

institute: Columbia University

summary: Infants suffer disproportionately from respiratory infections and generate reduced vaccine responses compared to adults, although underlying mechanisms remain unclear. In adult mice, lung-localized, tissue-resident memory T cells (TRM) mediate optimal protection to respiratory pathogens. We hypothesized that reduced protection in infancy was due to impaired T effector localization and/or lung TRM establishment. Using an infant mouse model we demonstrate generation of lung-homing, virus-specific T effectors following influenza infection or live-attenuated vaccination, similar to adults. However, infection during infancy generated markedly fewer lung TRM and heterosubtypic protection was reduced compared to adults. Impaired TRM establishment was infant-T cell-intrinsic and infant effectors displayed distinct transcriptional profiles enriched for T-bet-regulated genes. Notably, mouse and human infant T cells exhibited increased T-bet expression following activation and reducing T-bet levels in infant mice enhanced lung TRM establishment. Our findings reveal that infant T cells are intrinsically programmed for short-term responses and targeting key regulators could promote long-term, tissue-targeted protection at this critical life stage.

overall_design: Transcriptional profiling by RNA-seq of infant and adult flu-specific mouse CD4 T cells. Project includes three biological replicates of both sample types.

first: Kyra

last: Zens


title: PRDM1 inhibits proliferation of human colon cancer organoids

first: Changlong

last: Liu

state: Shanghai

address: 518 Ziyue Road, Minhang

institute: Shanghai Veterinary Research Institute

summary: We reports the transcript landscape of PR Domain Containing 1, with ZNF domain (PRDM1)  in RKO colon cancer cells. We show that PRDM1 alpha and PRDM1 beta transcript isoforms repress and activate a largely overlapping suite of genes, many of which belong to the embryonic stem cell core transcript program.

overall_design: To evaluate the roles of PRDM1 in colon cancer cells,  we generated PRDM1 knock out derivatives in RKO colon cancer cells by employing CRISPR/Cas9 technology and PRDM1α and PRDM1β overexpressing derivatives of RKO colon cancer cells. mRNA profile of these RKO derivatives were generated by deep sequencing, in replicate, using Illumina NextSeq 500

first: Phillip

last: Buckhaults


title: Affymetrix SNP array data for beak deformity and normal Beijing-You Chickens

first: Hao

last: Bai

address: Yuanmingyuan West Road No. 2, Haidian District

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Beak deformities (BD) of different forms have been documented in many wild birds. The phenomenon is termed as “the largest epizootic of gross abnormalities ever recorded among wild bird populations.” Frequencies of 1% to 3% of BD (crossed beaks) were found in several indigenous chickens including Silkies, Qingyuan Partridge, Huxu, and the Beijing-You (BJY) chickens (studied here). Birds with deformed beaks have poor production performance and induce higher mortality. Therefore, BD represents an economic as well as a welfare problem. Our lab have focused and performed studies on this complex trait/disease for 7 years. Therefore, we performed a single SNP, a pathways-based genome-wide association study (GWAS), and a genome-wide CNV detection with the genotype data of 48 BD (case) and 48 normal (control) birds from Affymetrix 600K HD genotyping arrays, using ROADTRIPS, SNP ratio test (SRT) and PennCNV, respectively. To the best of our knowledge, this is the first GWAS and CNV study to investigate the mutations and genomic structural variations in the deformed and normal beaks of chickens. The findings herein are worth of further functional characterization for better understanding the genetic mechanisms of BD in chickens and wild birds as well.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.
GWAS and Copy number analysis of Affymetrix 600K chicken SNP arrays were performed for all the samples.

first: Yanyan

last: Sun

first: Jilan


title: Shared αβ T Cell Receptor Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome [ePCR]

city: Aurora

first: Andrew

middle: P

last: Fontenot

state: Colorado

department: Dept. of Medicine

institute: University of Colorado Denver

summary: Expansions of CD4+ T cells utilizing TRAV12-1/TRBV2 were found exclusively in HLA-DR3+ LS patients. These TCRs shared CDR3 homology, suggesting that these T cells are responsible for recognizing sarcoidosis-associated antigen(s) and are involved in the local alveolitis.

overall_design: Analysis of TCR sequences from 12 sarcoidosis and 3 control patient blood and/or lung samples.

first: Angela

last: Mitchell

first: Ylva

last: Kaiser

first: Michael

last: Falta

first: Daniel

last: Munson

first: Anders

last: Eklund

first: Jill

last: Slansky

first: Johan

last: Grunewald


title: Shared αβ T Cell Receptor Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome [scPCR]

summary: Expansions of CD4+ T cells utilizing TRAV12-1 and TRBV2 were found exclusively in HLA-DR3+ LS patients. These TCRs shared CDR3 homology, suggesting that these T cells are responsible for recognizing sarcoidosis-associated antigen(s) and are involved in the local alveolitis.

overall_design: Analysis of TCR sequences from 13 sarcoidosis and 3 control patient blood and/or lung samples.


title: Genome-wide identification of Grainy head targets in Drosophila [ChIP-seq]

status: Public on Aug 12 2017

city: Stockholm

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

summary: Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, we identified embryonic Grh targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. In the airways, Grh repressed genes encode key TFs involved in branching and cell differentiation. Reduction of the POU-domain TF, Vvl, (ventral veins lacking) largely ameliorates the airway morphogenesis defects of grh mutants. Vvl and Grh proteins additionally interact with each other and regulate a set of common enhancers during epithelial morphogenesis. We conclude that Grh and Vvl participate in a regulatory network controlling epithelial maturation.

overall_design: ChIP seq of one transcription factor using two different antibodies and an IgG control.

first: Liqun

last: Yao

first: Shenqiu

last: Wang

first: Jakub

middle: O

last: Westholm


title: Shared αβ T Cell Receptor Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome [iRepertoire]

middle: T


title: Shared αβ T Cell Receptor Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome

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

overall_design: Refer to individual Series


title: Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma [expression]

city: Singapore

first: Shumei

last: Chia

state: Singapore

institute: Genome Institute of Singapore

summary: Gene expression analysis of patient metastatic tumor derived cell lines.

overall_design: Total RNA obtained from cell lines derived from tumors of head and neck squamous cell carcinoma patients.

first: Chia

last: Shumei


title: UHRF2 regulates local 5-methylcytosine and suppresses spontaneous seizures [MeDIP-Seq, hMeDIP-Seq]

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (5mC) regulates multiple cellular processes and is faithfully maintained following DNA replication. Ubiquitin-like PHD and ring finger domain-containing protein 1 (UHRF1) plays an important role in the maintenance of 5mC levels. Interestingly, UHRF1 has a paralog UHRF2 that has similar sequence and domain architecture, but the biological function of UHRF2 is not clear. Here, we have generated Uhrf2 knockout mice and characterized the role of UHRF2 in vivo. Uhrf2 knockout mice are viable, but the adult mice develop frequent spontaneous seizures and display abnormal electrical activities in brain. To explore possible mechanism beyond these phenomenon, we utilized high-throughput sequencing to identify global expression changes in Uhrf2 knockout mice brains. In addition, we explored genome-wide 5mc profiles in these samples to examine if UHRF2 regulates 5mc levels in specific genome loci.

overall_design: Analysis of genome-wide distribution of 5-methylcytosine and 5-hydroxymethylcytosine in wild type and Uhrf2 knockout mice by MeDIP-Seq and hMeDIP-Seq.

first: Lin

middle: Y

first: Xiaochun

last: Yu


title: UHRF2 regulates local 5-methylcytosine and suppresses spontaneous seizures


title: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration

city: New Haven

first: Yangfei

last: Xiang

state: CT

address: 10 Amistad St. Room 214J

department: Genetics

institute: Yale University


title: Nascent RNA profiles from immortalized human cell lines

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

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

country: Finland

institute: University of Eastern Finland

summary: GRO-Seq libraries were performed from immortalized human cell lines to study nascent RNA profiles including non-coding RNA expression and transcriptional pausing.

overall_design: GRO-Seq

first: Maria

last: Bouvy-Liivrand

first: Merja

last: Heinäniemi


title: O-glcnAc reprograms cellular energetics

status: Public on Jul 20 2017

city: Kansas City

first: Stefan

middle: Hannes

last: Graw

address: 3901 Rainbow Blvd

department: Biostatistics

institute: University of Kansas Medical Center

summary: Dysfunctional mitochondria and generation of reactive oxygen species (ROS) promote chronic diseases, which have spurred interest in the molecular mechanisms underlying these conditions. Previously, we have demonstrated that disruption of post-translational modification of proteins with β-linked N-acetylglucosamine (O- glcnAcylation) via overexpression of the O-glcnAc–regulating enzymes O- glcnAc transferase (OGT) or O- glcnAcase (OGA) impairs mitochondrial function. Here, we report that sustained alterations in O- glcnAcylation either by pharmacological or genetic manipulation also alters metabolic function. Sustained O-glcnAc elevation in SH-SY5Y neuroblastoma cells increased OGA expression and reduced cellular respiration and ROS generation. Cells with elevated O-glcnAc levels had elongated mitochondria and increased mitochondrial membrane potential, and RNA-Seq in SH-SY5Y cells indicated transcriptome reprogramming and down regulation of the NRF2-mediated antioxidant response. Sustained O-glcnAcylation in mice brain and liver validated the metabolic phenotypes observed in the cells, and OGT knockdown in the liver elevated ROS levels, impaired respiration, and increased the NRF2 antioxidant response. Moreover, elevated O-glcnAc levels promoted weight loss and lowered respiration in mice and skewed the mice toward carbohydrate-dependent metabolism as determined by indirect calorimetry. In summary, sustained elevation in O-glcnAcylation coupled with increased OGA expression reprograms energy metabolism, a finding that has potential implications for the etiology, development, and management of metabolic diseases.

overall_design: SY5Y cells were adapted to long term O-glcnAcase (OGA) inhibition using the specific OGA inhibitor Thiamet-G (tmg) or glucosamine treatment for 3 weeks. After adaptation to the growth conditions, cells were harvest and RNA isolated for Next Generation RNA sequencing. Briefly, cDNA library was prepared using Illumina TruSeq Stranded mRNA sample preparation kit (Illumina) as manufacturer’s instruction. Total RNA was isolated using the same method as previously described and 800 ng of the total RNA per reaction was used to initiate the protocol. The quality of RNA sequencing results was first assessed using FastQC (0.11.2). RSEM (1.2.22) was utilized to align the reads to the human reference genome HG38 and to calculate gene expression values. EdgeR (3.14.0) was then used to normalize the expression values using the TMM-method (weighted trimmed mean of M-values), and for differential expression analyses. First, the negative binomial conditional common likelihood was maximized to estimate a common dispersion value across all genes (estimateCommonDisp). Next, tagwise dispersion values were estimated by an empirical Bayes method based on weighted conditional maximum likelihood (estimateTagwiseDisp). Finally, the differentially gene expression was calculated by computing genewise exact tests for differences in the means between two groups of negative-binomially distributed counts. Hierarchical clustering analysis was determined using Euclidean distance. The following R-packages were utilized for calculations and visualizations: plots and edgeR.

first: Ee

last: Tan

first: Devin

middle: C

last: Koestler

first: Chad

last: Slawson


title: Global Regulation of Alternative RNA Splicing by the SR-Rich Protein RBM39 CLIP-seq

first: Mai

last: Sanyue

address: 27 Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

summary: RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65.

overall_design: Genome-wide RBM39-RNA interactions were mapped via cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq) in wild-type MCF-7 cells.


title: SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio


title: Identification of GLYMA.08G357600 binding sites in soybean early maturation embryos.

first: John

last: Harada

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.08G357600 in early maturation embryos using ChIP-seq.

overall_design: Identification of Glyma.08G357600 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Leonardo

last: Jo

first: Min

last: Chen

first: Robert

last: Golberg


title: Identification of GLYMA.13G317000 binding sites in soybean mid-maturation embryos

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.13G317000 in mid-maturation embryos using ChIP-seq.

overall_design: Identification of Glyma.13G317000 binding sites in soybean embryos at the mid-maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.


title: Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma

first: Shumei

last: Chia

type: Genome variation profiling by genome tiling array


title: Effects of Propofol Treatment in Neural Progenitors Derived from Human Induced Pluripotent Stem Cells

city: Houston

first: Ying

last: Liu

address: 1825 Pressler

institute: UTHealth

summary: Propofol is an intravenous anesthetic that has been widely used in the clinical setting. Besides its anesthetic effects, propofol has been reported to influence the regulation of autonomic system. Controversies exist with regards to whether propofol exposure is safe for pregnant women and young children. The recent emergence of human induced pluripotent stem cells (hiPSCs) has provided a promising and theoretically inexhaustible source of neural progenitor cells (NPCs) for drug testing, which could be extended to in vitro experiments for anesthetics such as propofol. NPCs derived from three hiPSC lines, NES-GFP (a NESTIN-GFP reporter), USCK7 (iPSCs derived from urine derived cells), and ND2-0 (NIH), were treated with propofol at different concentrations (20, 50, 100 and 300 µM) for 6 h or 24 h. Early and late cell injury, cell proliferation and apoptosis were evaluated. Comparison of genome-wide gene expression profiles was performed for propofol-treated and untreated control iPSC-NPCs. Propofol treatment of NPCs for 6 h at the clinically relevant concentration (20 or 50 µM) did not affect cell viability, apoptosis, or proliferation, while propofol at higher concentration (100 or 300 µM) decreased NPC viability and induced apoptosis. Prolonged treatment of propofol for 24 h significantly decreased cell viability. In addition, 20 µM propofol treatment for 6 h did not alter global gene expression. Higher concentration of propofol exerted potential cytotoxicity via multiple cellular mechanisms. In summary, propofol treatment at commonly practiced clinical doses for 6 h did not have adverse effects on hiPSC-derived NPCs. In contrast, longer exposure and/or higher concentration of propofol treatment could decrease NPC viability and induce apoptosis.

overall_design: Zero µM, 20 µM and 300 µM of propofol treatment in human Nestin reporter iPSC-derived NPCs for 6 hours were chosen for  comparison and analysis.

first: Shenglan

last: Li


title: DNA Methylation alterations following binge-like developmental ethanol exposure assessed in 21 day-old mice

first: Shiva

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

institute: Western University

summary: This experiment is an application of MeDIP-seq on hippocampus in a mouse model of fetal alcohol spectrum disorder (FASD). Here, we investigate genome-wide changes in DNA methylation in six C57BL/6 mice (3 ethanol-exposed and 3 saline-exposed). Mice were injected with either ethanol or saline on postnatal days 4 and 7, with hippocampal DNA methylation assessed on postnatal day 21. Across the six mice, there are 151,911 MeDIP peaks mapped to “intergenic”, “gene body”, or “promoter” based on the DNAm peaks proximity to a gene. Of these locations, 18,992 regions (16,374 intergenic, 1,887 gene body, 661 promoter) were common in all six mice (113,532 total) and can be combined for further analysis.

overall_design: Matched male littermates were injected with either ethanol or saline on postnatal day 4 and 7, hippocampal DNA was isolated on postnatal day 21. DNA methylation was assessed for 3 ethanol-treated and 3 control mice via MeDIP-Seq by Arraystar Inc. Methylated DNA was immunoprecipitated, and fragments were sequenced by running 150 cycles on Illumina HiSeq 2000. Reads were aligned to the mouse genome (mm10) using Bowtie. MeDIP enriched regions (peaks) were identified by MASC v2 using a q-value threshold of 10^-4.

first: Eric

last: Chater-Diehl

first: Dustin

last: Sokolowski

first: Bonnie

last: Alberry


title: Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

city: Shanghai

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University

summary: Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.

sample_organism:
Psilotum nudum
Pteris vittata
Lygodium japonicum
Cibotium barometz
Diplazium esculentum
Trichomanes striatum
Asplenium nidus
Odontosoria chinensis
Salvinia cucullata
Microlepia platyphylla
Azolla caroliniana
Ophioglossum vulgatum
Palhinhaea cernua
Selaginella moellendorffii
Plenasium vachellii
Salvinia molesta
Microsorum cuspidatum
Equisetum ramosissimum
Alsophila spinulosa
Cyrtomium fortunei
Isoetes sinensis
Selaginella uncinata
Angiopteris fokiensis
Dicranopteris pedata
Diplopterygium chinense

overall_design: Examine the 19-26 nt small RNA in 25 samples from 4 lycophytes and 21 ferns, and the degradome of S. moellendorffii fronds.

first: Xuemei


title: Expression profiling of mouse ILCreg cells

city: Beijing

first: Shuo

last: Wang

state: Beijing

address: 15 DaTun Road,Chaoyang District,Beijing

department: Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Investigation of global gene expression levels of ILCreg cells

overall_design: Gene expression profiling using sorted ILCreg cells from IL-10-GFP knockin mice in C57BL/6 background. Purity of cells was over 95% that was determined by post sorting analysis with flow cytometry. Total RNA was extracted from ILCregs using standard RNA extraction protocol, followed by DNase incubation to remove nuclear DNA. RNA quality was monitored by NanoDrop ND-1000 and RNA integrity was tested by agarose gel electrophoresis. Total RNA was amplified with Whole Transcript (WT) Pico Reagent Kit (Affymetrix). The sample preparation and microarray hybridization were performed based on the Affymetrix’s standard protocols.

first: Pengyan

last: Xia

first: Zusen

last: Fan


title: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary:
High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in several of the reaction steps of Quartz-Seq2 allow us to effectively convert initial reads to UMI counts (at a rate of 30%–50%). To demonstrate the power of Quartz-Seq2, we analyzed transcriptomes from a cell population of in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of sequence reads.

Preprint: http://www.biorxiv.org/content/early/2017/07/21/159384

overall_design: Technical validation of high-throughput single-cell RNA-seq methods using 10 pg total RNA. Demonstration of Quartz-Seq2 using 4,484 single-cells of embryonic stem cell and 1,052 single-cells of stromal vascular fraction (SVF).

first: Hiroki

last: Danno

first: Yohei

last: Sasagawa

last: Nikaido


title: Expression profiling of human ILCreg cells

summary: Investigation of global gene expression levels of human ILCreg cells

overall_design: Gene expression profiling using sorted human ILCreg cells. For human ILCregs, lymphocytes were isolated from human normal intestinal tissues from resected small intestines and Lin-CD45+ cells were then enriched by MACS (Lin=CD2, CD3, CD14, CD16, CD19, CD56, CD235a). Enriched cells were stained with Lineage cocktail, anti-CD45, and anti-CD127 antibodies followed by intracellular staining of IL-10. Lin-CD45+CD127+IL-10+ cells were isolated and subjected to RNA extraction.


title: Regulatory innate lymphoid cells control innate intestinal inflammation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: High-Throughput Sequencing Reveals Differential Expression of miRNAs in respiratory tree from the sea cucumber Apostichopus japonicus Under Hypoxia Stress

city: Qingdao

first: Da

last: HUO

address: No. 7 Nanhai Road, Qingdao, China

institute: Institute of Oceanology,Chinese Academy of Science

summary: The present study identified and characterized miRNAs, which may play a major role in stress resistance. we applied high-throughput sequencing to investigate the alterations of miRNAs expression of sea cucumber under hypoxia stress(DO2_1,DO2_2,DO2_3),slight hypoxia stress(DO4_1,DO4_2,DO4_3) and normal condition(DO8_1,DO8_2,DO8_3). These results will provide a basis for future studies of miRNA regulation in sea cucumbers under hypoxia stress.

overall_design: 9 individuals (3 biological replicates×3 sea cucumbers per biological replicate) under hypoxia stress (DO 2mg/L) last for three days were used for our experiments (3 biological replicates: DO2_1,DO2_2,DO2_3). 9 individuals (3 biological replicates×3 sea cucumbers per biological replicate) under slight hypoxia stress (DO 4mg/L) last for three days were used for our experiments (3 biological replicates: DO4_1,DO4_2,DO4_3).9 sea cucumbers  under normal condition (DO 8mg/L) (3 biological replicates×3 sea cucumbers per biological replicate) served as the control (3 biological replicates:DO8_1,DO8_2,DO8_3).

last: Huo

first: Lina

last: Sun

first: Hongsheng

last: Yang


title: Whole genome expression analysis of clinical bone metastasis samples

status: Public on Jul 19 2017

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

summary: Total RNA from clinical bone metastasis samples were analyzed using whole genome expression bead arrays and the Illumina platform with the objective to identify molecular subgroups of potential clinical relevance.

overall_design: Fresh-frozen bone metastasis samples from men with castration-resistant prostate cancer (CRPC, n = 40), untreated prostate cancer (n = 8) or other malignancies (n = 12) were characterized using whole-genome expression profiling followed by multivariate principal component analysis (PCA) and functional enrichment analysis. The CRPC samples were defined as androgen receptor (AR) driven or non-AR driven based on expression of AR and AR-regulated genes (AR activity), please see Ylitalo et al, Eur Urol. 2017 May;71(5):776-787 (PMID 27497761) for further description.

first: E

last: Bovinder Ylitalo

last: Thysell

last: Jernberg

first: M

last: Lundholm

first: S

last: Crnalic

first: L

last: Egevad

first: P

last: Stattin

first: A

last: Widmark

last: Bergh


title: Profiling circular RNA expression in lung cancer

city: Nanjing

first: Mantang

last: Qiu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

summary: Circular RNAs (circRNAs) are a kind of novel non-coding RNAs. Recent evidence has known that circRNAs play important roles in various diseases; however, few circRNAs have been well characterized in lung cancer. Understanding the expression profile of circRNAs and protein-coding genes is critical to discover the pathogenesis of lung cancer.

overall_design: Five female lung adenocarcinoma patients with no smoking history were selected to profile circular RNA expression with microarrays. Paired tumor tissues and adjacent non-tumor tissues were collected and confirmed by pathologists.

first: Rong

last: Yin

first: Lin

last: Xu


title: Tumor-associated neutrophils display a distinct N1 profile following TGFβ modulation: A transcriptomics analysis of pro- vs. antitumor TANs

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: It is becoming increasingly clear that tumor-associated neutrophils (TANs) play an important role in cancer biology, through direct impact on tumor growth and by recruitment of other cells types into the tumor. The function of neutrophils in cancer has been the subject of seemingly contradicting reports, pointing toward a dual role played by TANs in tumor progression. The existence of multiple neutrophil subsets, as well as phenotypic modulation of the neutrophils by various factors in the tumor microenvironment, has been shown. TGFβ plays a significant role in the determination of neutrophils' phenotype, by shifting the balance from an antitumor (N1) toward a more permissive (N2) phenotype. The full range of mechanisms responsible for the pro- vs. antitumor effects of TANs has not yet been elucidated. Therefore, the ability to identify the different neutrophil subpopulations in the tumor is critical in order to understand TANs evolution and contribution throughout tumor progression. Using a transcriptomic approach, we identified alternations in gene expression profile following TGFβ inhibition. We show that N1 and N2 TANs represent distinct subpopulations with different transcriptional signatures and both differ from naive bone marrow neutrophils. The analysis highlights a clear difference in pathways involved in neutrophil function such as cytoskeletal organization and antigen presentation, as well as alterations in chemokine profile, eventually affecting their effect on tumor cells and tumor growth. These data highlights several potential new pathways and mechanisms by which neutrophils can influence both the tumor cells and the adaptive immune system.

overall_design:
Tumor immunosuppression is modulated via secretion of inhibitory cytokines as well as the recruitment of specific cell types to the tumor microenvironment. The phenotype of the myeloid cells (neutrophils and macrophages), which represent a key part of this immunosuppressive network, may be altered by the tumor microenvironment to support tumor growth. Despite growing evidence for the presence of multiple neutrophils subpopulations in cancer, the role of neutrophils in tumor growth and metastatic progression has not yet been fully elucidated. Whereas several studies have provided evidence for neutrophils with pro-tumor functions such as promoting tumor angiogenesis, tumor cell dissemination, and metastatic seeding in distant organs, others have shown the existence of neutrophils with antitumor and anti-metastatic functions. These seemingly conflicting reports over the function of neutrophils in cancer is likely due to the existence of multiple neutrophil subsets; a tumor promoting or N2 phenotype and an tumor-inhibitory or N1 phenotype. Interestingly, it has been proposed that there can be phenotypic or functional plasticity, where neutrophils infiltrating a tumor are modulated by cues present in the tumor environment. This has been well exemplified by recent works showing that TANs can be modulated and polarized toward an N1 phenotype by type-1 interferons or a pro-tumorigenic (N2) phenotype by the presence of TGFβ as demonstrated by the observation that systemic inhibition of TGFβ using a specific Alk5 kinase inhibitor called SM16 in mice caused a shift toward a pro-inflammatory and antitumor phenotype (N1).
Similarly to tumor-associated macrophages (TAMs), N2 TANs can exert their effect by secreting pro-tumor factors and by affecting other cells of the immune system in an immunosuppressive manner, for example, by inducing T-cell tolerance. Accordingly, depletion of N2-polarized TANs inhibits tumor growth and metastasis and reduces the level of immunosuppression in the tumor microenvironment, allowing for increased activity of CD8+ cytotoxic T-lymphocytes (CTL). In contrast, in the presence of type-I IFNs or absence of TGFβ, TANs display an antitumor N1 phenotype with increased tumor cytotoxicity, high neutrophil extracellular traps (NETs) expression, high ICAM1, and TNF-α expression.
Using transcriptomic analysis, we have previously shown that N2-polarized TANs display a dramatically different transcriptomic profile than both myeloid-derived suppressor cells (G-MDSCs) and naive bone marrow neutrophils (BMN), including the expression of a wide range of cytokines (CCL17, CCL2, CCL5). By secreting CCL17, TANs were further shown to recruit regulatory T-cells to the tumor site, thus inducing immunologic self-tolerance and impaired immune response to tumor cells. Conversely, inhibition of TGFβ-driven N2-polarization was shown to promote TANs' expression of cytokines such as CCL3 and TNFα, further attracting CD8+ T cells to the tumor site.
Since no definitive markers discriminating between pro-tumor (N2) and antitumor (N1) neutrophils have yet been established, the identification of neutrophils subsets in the tumor remains a challenge, limiting our understanding of the evolution TANs and their specific contribution throughout tumor progression. The purpose of this study was to gain a deeper understanding of N1 and N2 TANs' polarization states using a transcriptomics approach and to identify the genes and pathways modified following their polarization, resulting into their opposite anti or pro-tumor effect. We examined which pathways and gene-groups varied among these two populations of neutrophils and performed a detailed analysis of pathways related to the main functions of neutrophils, such as phagocytosis, antigen presentation, and specific immune effects, as well as response to stress and structural genes. Our data reveal a significant difference in chemokine/cytokine signature between N2 and N1 TANs, which might further help understanding the chemotaxis forces and role of neutrophils in tumor. Finally, we examined the differential functional effects of N1 and N2 neutrophils on tumor growth, finding that the overall N1 signature is cytotoxic to tumor cells, whereas N2 neutrophils contribute to tumor growth.

first: Merav

middle: E

last: Shaul

first: Liran

last: Levy

first: Jing

first: Inbal

last: Mishalian

first: Sunil

last: Singhal

first: Veena

last: Kapoor

first: Wenhwai

last: Horng

first: Gil

last: Fridlender

first: Steven

last: Albelda

first: Zvi

middle: G


title: Antagonistic BMP–cWNT signaling in the cnidarian Nematostella vectensis reveals insight into the evolution of mesoderm

city: St. Augustine

first: david

middle: k

last: Simmons

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

summary: Using forward transcriptomics, we show that beta-catenin/Tcf signaling and BMP2/4 signaling provide differential inputs into the cnidarian endomesodermal gene regulatory network (GRN) at the onset of gastrulation (24 h postfertilization) in N. vectensis. Surprisingly, beta-catenin/Tcf signaling and BMP2/4 signaling regulate a subset of common downstream target genes in the GRN in opposite ways, leading to the spatial and temporal differentiation of fields of cells in the developing embryo. Thus, we show that regulatory interactions between beta-catenin/Tcf signaling and BMP2/4 signaling are required for the specification and determination of different embryonic regions and the patterning of the oral?aboral axis in Nematostella.

overall_design: Three biological replicates for two experimental conditions (Morpholino knockdown of NvBMP2/4, and RNA injection of the dominant negative form of NvTCF) and control dextran injection samples taken at 24 Hours past fertilization.

first: Naveen

last: Wijesena

first: David

middle: K

last: Simmon

first: Mark

middle: Q

last: Martindale


title: Elucidation of transcription alteration in peripheral blood of SCA12 patients

city: Delhi

first: Mohammed

last: Faruq

address: Mall Road

department: Genomics and Molecular Medicine

country: India

institute: CSIR-IGIB

summary: Analysis of altered level of transcripts in cases of SCA12 patients from peripheral blood samples

overall_design: RNA isolated from cases and controls of SCA12 patients and healthy individuals were analyzed for differential expression of genes.


title: The role of histone demethylase KDM5C in super-enhancer activation

city: wuhan

first: xiaohua

last: chen

address: donghu road 185

department: medical genetics

institute: wuhan university

summary: This SuperSeries is composed of the SubSeries listed below

overall_design: Examination of 3 different histone modifications in CaSki-Vector and CaSki-KDM5C cells

first: Feng

last: Li

first: Xiaohua

last: Chen


title: Comparison of non-coding RNAs in exosomes and functional efficacy of human embryonic stem cell- versus induced pluripotent stem cell-derived cardiomyocytes

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

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

summary: To understand the exosomal secretome of ESC-CMs and iPSC-CMs, samples were analyzed using the Human LncRNA Array v4.0 (8 x 60K, Arraystar)

overall_design: Two independent lines for both ESC-CMs and iPSC-CMs were used, with two replicates (from two different differentiations) per line. Exosomes were collected from media from both cell types at 36 hours, and isolated using Total Exosome Isolation Reagent (Life Technologies)

first: Ning-Yi

last: Shao

first: Sang-Ging

last: Ong


title: MicroRNAs-143 and -145 induce epithelial to mesenchymal transition by enhancing TGF-β signaling and modulating the expression of junction proteins

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary:
Transforming growth factor (TGF)-β is one of the major inducers of epithelial to mesenchymal transition (EMT), a crucial program that plays a critical role in promoting carcinoma’s metastasis formation. MicroRNAs-143 and -145, which are both TGF-β direct transcriptional targets, are essential for the differentiation of vascular smooth muscle cells (VSMC) during embryogenesis, a TGF-β-dependent process reminiscent of EMT. Their role in adult tissues is however less well defined and even ambiguous, since their expression was correlated both positively and negatively with tumor progression.  Here we show that high expression of both miRs-143 and -145 in mouse mammary tumor cells expressing constitutively active STAT3 (S3C) is involved in mediating their disrupted cell-cell junctions. Additionally, miR-143 appears to play a unique role in tumorigenesis by enhancing cell migration in vitro and extravasation in vivo while impairing anchorage-independent
growth, which may explain the contradictory reports about its role in tumors.   Accordingly, we demonstrate that overexpression of either miRNA in the non-transformed mammary epithelial NMuMG cells leads to upregulation of EMT markers and of several endogenous TGF-β targets, downmodulation of several junction proteins and increased motility. This correlates with enhanced basal and TGF-β-induced activity of SMAD transcription factors, suggesting that miR-143 and -145 can help promoting TGF-β mediated EMT via a positive feedback loop. Moreover, pervasive transcriptome perturbation consistent with the described phenotype was observed. In particular, the expression of several transcription factors involved in the mitogenic responses, of MAPK family members and, importantly, of several tight junction proteins and the SMAD co-repressor TGIF was significantly reduced.   Our results provide important mechanistic insight into the non-redundant role played by miRs-143 and -145 in EMT-related processes in both transformed and non-transformed cells, and suggest that their expression must be finely coordinated to warrant optimal migration/invasion while not interfering with cell growth.

overall_design: Transcriptome profiling by high-throughput sequencing

first: Lidia

last: Avalle

first: Aurora

last: Savino

first: Marta

last: Gai

first: Francesca

last: Marino

first: Sara

last: Pensa

first: Isaia

last: Barbieri

first: Michael

middle: B

last: Stadler

first: Paolo

last: Provero

first: Salvatore

last: Oliviero

first: Valeria

last: Poli


title: RXR mediated neurogenesis (RNA-Seq I)

status: Public on Jul 18 2017

city: Orlando

first: Laszlo

last: Nagy

state: Hungary

address: Sanger Road

institute: Sandford Burnham Prebys Institute

summary: A growing number of pieces of evidence suggest the importance of Retinoid X Receptor (RXR)-mediated pathways in neurogenesis and the dysregulation of this signaling in neurodegenerative disorders, such as Alzheimer`s or Amyotrophic Lateral Sclerosis. The data presented here identify the RAR:RXR and LXR:RXR-mediated transcriptional program in embryonic stem cells, neural progenitors and terminally differentiated neurons.

overall_design: ATRA treatment

first: Zoltan

last: Simandi


title: Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [RNA-seq]

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling revealed a set of common genes regulated by all five transcription factors, which we propose as connective tissue core expression set. This common core was enriched in genes associated with axon guidance and myofibroblast signature, including fibrosis-related genes. In addition, each transcription factor regulated a specific set of signalling molecules and extracellular matrix components. This suggests a concept whereby local molecular niches can be created via the expression of specific transcription factors impinging on the specification of local microenvironments. The regulatory network established here identifies common and distinct molecular signatures of limb connective tissue subtypes, provides novel insight into the signalling pathways governing connective tissue specification, and serves as a resource for connective tissue development.

overall_design: Gene expression profiling of mesenchymal cells extracted from limb buds of E4.5 chick embryos and overexpressing connective tissue-associated transcription factors.

first: Stefan

last: Börno

first: Bernd

last: Timmermann

first: Jochen

last: Hecht

first: Delphine

last: Duprez

first: Sigmar

last: Stricker


title: Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition [SNP array]

city: Valencia

first: Jaime

last: Font de Mora

address: Avenida Fernando Abril Martorell, 106; Torre A,  5-07

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

summary: SNP arrays were combined with next generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma aetiology. We assessed PARP inhibitor olaparib in combination with other chemotherapy medications using both in vitro and in vivo models.

overall_design: CytoScan HD arrays (Affymetrix) were performed according to the manufacturer's directions on DNA extracted from 17 neuroblastoma tumor samples and 7 neuroblastoma cell lines.

first: Elena

last: Sanmartín


title: RXR mediated neurogenesis (RNA-Seq II)

overall_design: LG268, and  GW3965 treatments


title: Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data

city: Wageningen

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

institute: Wageningen University & Research

summary: Normalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides.

overall_design: RNA isolated from two biological replicates for Col-0 floral buds, Col-0 leaves and dcl234 floral buds was used to generate mRNA-Seq and sRNA-Seq libraries

last: Lutzmayer


title: Genome-wide inhibition of pro-atherogenic gene expression by multi-STAT targeting compounds as a novel treatment strategy of CVD

city: Poznan

first: Martyna

last: Plens Gałąska

state: Wielkopolska

address: Umultowska 89

department: Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz Univerity

summary: Cardiovascular diseases (CVD), including atherosclerosis, are globally the leading cause of death. Key factors contributing to onset and progression of atherosclerosis and plaque development include the pro-infslammatory cytokines Interferon (IFN)α and IFNγ and the Pattern Recognition Receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger activation of members of the Signal Transducer and Activator of Transcription (STAT) family. Searches for STAT3-targeting compounds, exploring the pTyr-SH2 interaction area of STAT3, yielded many small molecules, including STATTIC and STX-0119. However, many of these inhibitors do not seem STAT-specific. We hypothesized that non-specific STAT-inhibitors that simultaneously block STAT1, STAT2 and STAT3 activity and pro-inflammatory target gene expression may be a promising avenue for the treatment of CVD.  We developed a pipeline approach combining comparative in silico docking of multiple STAT-SH2 models on multi-million Clean Lead and Clean Drug-Like libraries with in vitro STAT inhibition validation, as a novel STAT-inhibitory selection strategy. This approach allowed us to identify a new type of non-specific STAT inhibitor, C01L_F03 targeting the SH2 domain of STAT1, 2 and 3 with equal affinity. Moreover we observed a similar STAT cross-binding mechanism for STATTIC and STX-0119, leading to genome-wide inhibition of pro-atherogenic gene expression. Consequently, a multi-STAT inhibitory strategy was applied to inhibit endothelial cell (EC) migration, leukocyte adhesion to ECs and impairment of aortic ring contractility under inflammatory conditions.   Together, this implicates that multi-STAT inhibition could provide a powerfull approach for the success of combating vascular inflammation in CVD

overall_design: RNA obtained from HMEC treated with inhibitory compounds and IFNγ+LPS was compared to RNA isolated from untreated HMEC.

last: Plens-Galaska

first: Malgorzata

last: Szelag

first: Aida

last: Colladoc

first: Patrice

last: Marquesc

first: Susana

last: Vallejoe

first: Mariella

last: Ramos-Gonzáleze

first: Joanna

last: Wesoly

first: Maria

middle: J

last: Sanz

first: Concepción

last: Peiró

first: Hans

middle: A

last: Bluyssen


title: Arginine-dependent gene regulation in Streptococcus gordonii ahrC regulator knockout

city: Newcastle upon Tyne

first: Nicholas

middle: S

last: Jakubovics

address: Framlington Place

department: School of Dental Sciences

institute: Newcastle University

summary: We have previously shown that responses of the oral bacterium Streptococcus gordonii to arginine are co-ordinated by three paralogous regulators: ArcR, ArgR and AhrC. This set of experiments was designed to assess the effects of the AhrC gene regulator on global gene expression in Streptococcus gordonii under high arginine or following a shift to no arginine.

overall_design: Single colour microarrays were used to measure gene expression in four biological replicates of S. gordonii cells cultured, with and without arginine restriction. One replicate of 'arg+' was identified as an outlier and was not processed for normalised data. The raw data text file for this data set (US92200305_254184610003_S01_GE1_107_Sep09_1_2.txt) has been included in the supplementary files.

first: John

last: Casement


title: Arginine-dependent gene regulation in Streptococcus gordonii arcR regulator knockout

summary: We have previously shown that responses of the oral bacterium Streptococcus gordonii to arginine are co-ordinated by three paralogous regulators: ArcR, ArgR and AhrC. This set of experiments was designed to assess the effects of the ArcR gene regulator on global gene expression in Streptococcus gordonii under high arginine or following a shift to no arginine.

overall_design: Single colour microarrays were used to measure gene expression in four biological replicates of S. gordonii cells cultured, with and without arginine restriction.


title: microRNA expression profiling in human colon cancer

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

institute: Hainan Medical university

summary:
Using the highly sensitive miRCURY LNA™ microRNA array, we screened 3100 microRNAs abundant in the human colon cancer and Adjacent normal gastric mucosa tissues, and the function of differentially expressed microRNAs were analyzed by bioinformatics. The enrichment results indicated that these microRNAs perhaps participated in the occurrence and development process of colon cancer.
In this study, three cases of colon cancer were used to acquire the microRNA expression profiling, and qPCR was employed to confirm the results of microRNA chip. The function of the differentially expressed microRNA were analyzed by bioinformatic methods.Finally,compared with the adjacent normal mucosa tissues，the expression of 2 microRNAs were up regulated in colon cancer. qPCR results showed an expression pattern consistent with that of the chip analysis.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

first: YouSheng

last: Xie


title: Arginine-dependent gene regulation in Streptococcus gordonii ArgR regulator knockout

summary: We have previously shown that responses of the oral bacterium Streptococcus gordonii to arginine are co-ordinated by three paralogous regulators: ArgR, ArgR and AhrC. This set of experiments was designed to assess the effects of the ArgR gene regulator on global gene expression in Streptococcus gordonii under high arginine or following a shift to no arginine.


title: Stapled peptide inhibitors of RAB25 target context-specific phenotypes in cancer

city: Houston

first: Funda

last: Meric-Bernstam

address: 1400 Pressler St.

department: Invest. Cancer Therapeutics

institute: The University of Texas MD Anderson Cancer Center

summary: The Ras-family small GTPase RAB25 is involved in numerous aspects of endosomal protein trafficking and cell polarity. Recent evidence has established a role for RAB25, as well as related RAB-family and effector proteins, in oncogenic signaling, highlighting the need for chemical probes targeting this class of proteins. Here we report the development of all-hydrocarbon stabilized peptides targeting RAB25 derived from the RAB-binding FIP-family of proteins. Relative to unmodified FIP peptides, optimized stapled peptides show markedly increased structural stability, binding affinity, cell permeability and inhibition of RAB25:FIP complex formation. RAB25 expression has been shown to promote both pro- and anti-oncogenic phenotypes in specific cellular contexts. Stapled peptide RFP14 treatment of breast and ovarian cancer cell lines, in which RAB25 is pro-oncogenic, inhibited migration and proliferation in a RAB25-dependent manner. In contrast, treatment of a triple-negative breast cancer cell line in which RAB25 is tumor suppressive augmented proliferation and migration. Gene expression (RNA Seq) profiling identified significantly altered transcripts in response to RAB25 expression in ovarian cancer cells, and treatment with the optimized stapled peptide RFP14 reversed this expression profile. These data validate first-in-class chemical probes targeting RAB-family proteins and support the role of RAB25 in regulating context-specific oncogenic phenotypes.

overall_design: Hey ovarian cancer cells with stable overexpression of RAB25 (10 cm plate, 70-80% confluent) were treated with stapled peptide RFP14 (10 μM) or the equivalent amount of DMSO in serum free media  (RPMI) overnight, followed by stimulation with 5% FBS for 8 hours. pcDNA3 mock vector expressing HEY ovarian cancer cells labelled as HeyCont were similarly treated with DMSO overnight and stimulated with 5% FBS for 8 hours in parallel. Individual biological replicates performed on different days were used for RNAseq studies. Therefore, combining the two replicate experiments (experiment 1 and experiment 2), RNA samples analyzed included Hey Cont DMSO, Hey RAB25 DMSO, and Hey RAB25 RFP14, totalling six samples.

first: Shreya

last: Mitra

first: Jeffery

last: Montgomery

first: Mathew

last: Kolar

first: Gang

last: Li

first: Kang

last: Jeong

first: Bo

last: Peng

first: Gregory

middle: L

last: Verdine

first: Gordon

last: Mills

first: Raymond

last: Moellering


title: miRNA expression of Tubulocystic Renal Cell Carcinoma (TC-RCC) cases

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

institute: University of Oxford

summary:
Eleven TC-RCC cases were selected on the basis of the criteria defined by the 2012 Vancouver Classification of Renal Neoplasia and WHO 2016 classification criteria, and re-reviewed by a panel of expert renal pathologists. Two of these cases, TC-RCC#9 and #10, had a mixed tubulocystic and papillary histology and were macro-dissected into separate PRCC and TC-RCC components.
The molecular basis of TC-RCC, and miRNA expression profile, is unknown. We therefore used Affymetrix miRNA v.2. arrays to elucidate the expression of these samples

overall_design: Samples were extracted from macrodisected FFPE slides and purified using the Recoverall kit from Ambion

first: Charles

middle: H

last: Lawrie


title: The Yersinia pestis NlpD Lipoprotein is important for iron assimilation and is functionally linked to the twin-arginine translocation system

city: Ness-Ziona

first: Avital

last: Tidhar

department: Biochemistry and molecular Genetics

country: Israel

institute: Israel Institute for Biological Research

summary: Cultures of Y. pestis Kimberley53 (Kim53) virulent strain and Kim53∆nlpD were grown in heart infusion broth supplemented with 0.2% xylose and 2.5 mM CaCl2 for 5 h at 37°C, 200rpm. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP and Cy5-CTP). cRNA of two independent samples from each strain were labeled and hybridized to custom made Agilent 8x15K slide. Goal: Identifing alterations in gene expression profile between the wild-type Kim53 virulent strain and Kim53∆nlpD. Those altered mRNA transcrips will be used for better understanding of the cause for Kim53∆nlpD attenuation.

overall_design:
Y. perstis two independent biological replicates were performed. Extracted total RNA were used for cRNA synthesis and labeling with Cy3/Cy5-CTP, hybridized to Agilent custom-made 8x15K slide format.
For bacterial total RNA preparation, bacterial colonies were grown on BHIA plats for 48 h at 28°C , harvested and diluted in heart infusion broth (HIB) supplemented with 0.2% xylose and 2.5 mM CaCl2 to an OD660 of 0.01 and grown over night at 28°C in a shaker (200 rpm). The resulting cultures were diluted in fresh broth to an OD660 of 0.05 and allowed to grow for 5 h at 37°C. Aliquots of ~5×108 cfu were collected by centrifugation and cells were used for RNA preperation from Y. pestis Kimberley53 (Kim53) virulent strain and Kim53∆nlpD (fully attenuated) strain. Differential expression was  evaluate using linear models for designed microarray experiments. Genes with differences corresponding to P<0.05 in either the high or the low photomultiplicator scans and that had signal to control or control to signal ratios ³2.0 were considered to be differentially regulated.

first: Yinon

last: Levy

first: Ayelet

last: Zauberman

first: Yaron

last: Vagima

first: David

last: Gur

first: Moshe

last: Aftalion

first: Ofir

last: Israeli

first: Theodor

last: Chitlaru

first: Naomi

last: Ariel

first: Yehuda

last: Flashner

first: Avigdor

last: Shafferman

first: Anat

last: Zvi

first: Emanuelle

last: Mamroud


title: Gene expression profile of CD141+DNGR-1+ dendritic cells (cDC1s) derived in vitro from multipotent lymphoid progenitors (MLP) or common myeloid progenitors (CMP)

city: London

first: Julie

last: Helft

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

summary:
CD141+DNGR-1+ cDC1 have a dual origin. Both MLP and CMP can differentiate in CD141+DNGR-1+ cDC1s.
Using Affymetrix microarrays (GeneChip Human Gene 2.0 ST) we compared gene expression of CD141+DNGR-1+ cDC1s originating either from MLPs or CMPs

overall_design: The Affymetrix GeneChip Human Gene 2.0 ST arrays were used to define gene expression profiles in CD141+DNGR-1+ cDC1s

first: Caetano

last: Reis e Sousa


title: Mutant Kras-induced upregulation of CD24 enhances prostate cancer stemness and bone metastasis in prostate cancer.

status: Public on Jul 17 2017

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

institute: National Chung Cheng University

summary: Transcriptional profiling of mouse Prostate cancer cells comparing Pbsn-Cre LSL-KrasG12D P53L/L cells with Pbsn-Cre LSL-BrafV600E P53L/L cells, and to determine the effects of Kras or Braf mutantion on  murine PCa gene expression.

overall_design: Three-condition experiment, Pbsn-Cre LSL-KrasG12D P53L/L cells vs. Pbsn-Cre LSL-BrafV600E P53L/L cells vs. Pbsn-Cre P53L/L cells: 2 wild type replicates, 2 KrasG12D mutant replicates and 2 BrafV600E mutant replicates.

first: C

last: Weng

first: P

last: Ding

first: K

last: Cheng


title: Inhibitors of the histone methyltransferases EZH2/1 induce a potent antiviral state and suppress infection by diverse viral pathogens

city: Bethesda

first: Jesse

last: Arbuckle

state: MD

address: 33 North Drive

department: Laboratory of Viral Diseases

institute: National Institute of Allergy and Infectious Diseases, NIH

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

overall_design: Refer to individual Series


title: ChIP-seq from heart left ventricle (ENCSR988JLN)

status: Public on Jul 16 2017

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

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


title: Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [ChIP-seq TFs]

first: Mickael

last: Orgeur

overall_design: Transcription factor binding profiling of mesenchymal cells extracted from limb buds of E4.5 chick embryos.

first: Stefan

middle: T

last: Börno

first: Bernd

last: Timmermann

first: Jochen

last: Hecht

first: Delphine

last: Duprez

first: Sigmar

last: Stricker


title: WGBS from embryonic facial prominence (ENCSR993XPD)

summary:
Whole genome bisulfite-seq on embryonic 10.5 day mouse embryonic facial prominence

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


title: Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [ChIP-seq Histones]

overall_design: Histone modification occupancy profiling of mesenchymal cells extracted from limb buds of E4.5 chick embryos.


title: Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors


title: ChIP-seq from ascending aorta (ENCSR982QIF)


title: ChIP-seq from thoracic aorta (ENCSR984KWT)


title: Effects of the ArcR gene regulator on global gene expression in Streptococcus gordonii under high arginine or following a shift to no arginine

first: Nicholas

last: Jakubovics


title: ChIP-seq from Peyer's patch (ENCSR982PLJ)


title: ChIP-seq from body of pancreas (ENCSR977CEC)


title: ChIP-seq from uterus (ENCSR979XBX)


title: ChIP-seq from thoracic aorta (ENCSR974OMC)


title: ChIP-seq from GM12878 (ENCSR982FSK)


title: ChIP-seq from vagina (ENCSR962MYX)


title: ChIP-seq from right atrium auricular region (ENCSR967KZJ)


title: ChIP-seq from tibial artery (ENCSR950CDM)


title: Inhibitors of the histone methyltransferases EZH2/1 induce a potent antiviral state and suppress infection by diverse viral pathogens [array]

summary: Epigenetic regulation is based upon a network of complexes that modulate the chromatin character and structure of the genome to impact gene expression, cell fate, and development.  Thus, epigenetic modulators represent novel therapeutic targets to treat a range of diseases including malignancies.  Infectious pathogens such as herpesviruses are also regulated by cellular epigenetic machinery, and epigenetic therapeutics represent a novel approach to control infection, persistence, and the resulting recurrent disease.  The histone methyltransferases EZH2 and EZH1 (EZH2/1) are epigenetic repressors that suppress gene transcription via propagation of repressive H3K27me3 enriched chromatin domains.  However, while EZH2/1 are implicated in repression of herpesviral gene expression, inhibitors of these enzymes suppressed HSV primary infection in vitro and in vivo.  Furthermore, these compounds blocked lytic viral replication following induction of HSV reactivation in latently infected sensory ganglia.  Suppression correlated with the induction of multiple inflammatory, stress, and anti-pathogen pathways as well as enhanced recruitment of immune cells to in vivo infection sites.  Importantly, EZH2/1 inhibitors induced a cellular antiviral state that also suppressed infection with DNA (hCMV, Adenovirus) and RNA (Zika virus) viruses.  Thus, EZH2/1 inhibitors have considerable potential as general antivirals through activation of cellular antiviral and immune responses.

overall_design: The dataset includes gene expression profiling of human foreskin fibroblast (HFF) cells treated with GSK126 (30 µM), GSK343 (35µM) or vehicle for 4 hours with biological triplicates.

first: Paul

last: Gardina

first: Timothy

last: Myers

first: Thomas

middle: M

last: Kristie


title: Inhibitors of the histone methyltransferases EZH2/1 induce a potent antiviral state and suppress infection by diverse viral pathogens [RNA-Seq]

overall_design: The dataset includes gene expression profiling of human foreskin fibroblast (HFF) cells and mouse trigeminal ganglia. HFF cells were treated with GSK126 (30 µM) or vehicle for 1 hour, 2 hours, and 5 hours with biological triplicates.  Trigeminal ganglia from mock or HSV-1 latently infected BALB/c mice were explanted in media containing GSK126 (30 µM) or vehicle for 12 hours with biological triplicates (pooled 4-5 trigeminal ganglia per replicate).


title: Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization.

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: The identification of transcriptional enhancers in the human genome is a prime goal in biology. Enhancers are typically predicted via chromatin marks, yet their function is primarily assessed with plasmid-based reporter assays. Here, we show that two previous observations relating to plasmid-transfection into human cells render such assays unreliable: (1) the function of the bacterial plasmid origin-of-replication (ORI) as a conflicting core-promoter and (2) the activation of a type I interferon (IFN-I) response. These problems cause false-positives and -negatives in luciferase assays and are prohibitive to genome-wide STARR-seq screens, which are dominated by INF-I-related false-positives, suffer from poor signal-to-noise, and miss a majority of enhancers. We overcome both problems by directly employing the ORI as a core-promoter and by inhibiting two kinases central to IFN-I induction. This corrects luciferase assays and enables genome-wide STARR-seq screens in human cells. Comprehensive enhancer activity profiles in HeLa-S3 cells uncover strong enhancers, IFN-I-induced enhancers, and enhancers endogenously silenced at the chromatin level. Our findings apply to all episomal enhancer activity assays in mammalian cells, and are key to the characterization of human enhancers.

overall_design: Assaying transcriptional enhancer activity genome wide in human cells

first: Felix

last: Muerdter

first: Ashley

middle: R

last: Woodfin