title: Identification of variant distribution in ethanol-selected sRNA libraries

summary: In this study we subjected a library of synthetic sRNAs to multiple rounds of ethanol selection and analyzed changes in sRNA variant abundance by high-throughput sequencing.

overall_design: A synthetic sRNA library was generated by randomizing the first nine nucleotides of a RybB scaffold. The library was put under control of the IPTG-inducible PL promoter on a broad host range plasmid backbone and transferred into V. cholerae ΔrpoE. For laboratory selection experiments, the initial ΔrpoE sRNA library and control strains (WT- pCtr, ΔrpoE-pCtr and ΔrpoE-pRybB) were grown to exponential phase and challenged with ethanol. Following 6h of incubation, cells were recovered on agar plates to test for survival. At least 1 million single clones were pooled to generate the enriched sRNA libraries, which were used as input for the next round of selection following the same protocol. High-throughput sequencing of the isolated plasmids after each selection step was used to determine library complexity and distribution of the sRNA variants.

first: Nikolai

last: Peschek

first: Mona

last: Hoyos

first: Roman

last: Herzog

first: Konrad

middle: U

last: Förstner

first: Kai

last: Papenfort


title: Differential expression analysis of wildtype and zip-3(gk3164) mutant with next generation sequencing

status: Public on Jan 30 2019

city: Worcester

first: Cole

last: Haynes

state: Massachusetts

address: 364 Plantation Street, 425

country: USA

institute: U Mass Medical School

type: Expression profiling by high throughput sequencing

summary: ZIP-3 has been shown to repress the mitochondrial-UPR genes and immune response during P. aeruginosa infection. To identify genes repressed by ZIP-3, we compared transcript profiles from wildtype and zip-3(gk3164) worms raised on P. aeruginosa or E. coli.

overall_design: RNA samples were prepared from wild-type(wt) and zip-3(gk3164)(mutant) worms fed either E. coli or P. aeruginosa. Worms were synchronized by bleaching, starved on empty NGM plates for 48h, transferred to E. coli or P. aeruginosa seeded NGM plates for 18h and then harvested. Each experiment was performed in triplicate indicated as 1,2 and 3.

first: Pan

last: Deng


title: Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding

status: Public on Jan 23 2019

city: Darlinghurst

first: Tomasz

last: Szczesnik

state: NSW

address: 405 Liverpool St

country: Australia

institute: Victor Chang Cardiac Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability are limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq.

overall_design: Adenine methylation profiles following expression of Dam-Tcf7l2 or Dam only constructs with wild-type, N126A, or R95A variants of Dam in mouse embryonic stem cells. A negative (uninduced) control is included.

first: Joshua

last: Ho

first: Richard

last: Sherwood


title: Canagliflozin impact on human renal proximal tubular cells (HK2)

status: Public on Feb 27 2019

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: The impact of canagliflozin on gene expression changes was investigated in human renal proximal tubular cells (HK2) after pre-treatment with high glucose.

overall_design: Human renal proximal tubular cells (HK2) were cultured in Keratinocyte-Serum Free Medium containing 10% fetal bovine serum (FBS), 5 ng/ml recombinant epidermal growth factor (rEGF), 0.05 mg/ml bovine pituitary extract (BPE), 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were grown at 37 °C in a humidified atmosphere with 5% CO2. After growth to confluency, cells were serum deprived for 24 hours. Thereafter, cells were either treated with 0.5 µM canagliflozin [n=4] or left untreated [n=4] and subsequently stimulated with high glucose (30 mM).

first: Paul

last: Perco

first: Gert

last: Mayer


title: Small-molecule targeting of brachyury transcription factor addiction in chordoma

status: Public on Jan 20 2019

city: Cambridge

first: Tanaz

last: Sharifnia

state: MA

address: 415 Main Street

department: Chemical Biology and Therapeutics Science Program

institute: Broad Institute

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

overall_design: Refer to individual Series


title: Small-molecule targeting of brachyury transcription factor addiction in chordoma [rnaseq_sgrna]

summary: Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors (TFs). In chordoma, we find that T is associated with a 1.5-Mb region containing “super-enhancers” and is the most highly expressed super-enhancer-associated TF. Strikingly, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. Together, these data demonstrate small-molecule targeting of brachyury TF addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.

overall_design: RNA-sequencing of sg-T- and sg-EGFP-treated UM-Chor1 chordoma cells. Two independent sgRNAs targeting T were used. Two biological replicates were generated for each condition.

first: Stuart

middle: L

last: Schreiber

first: Charles

middle: Y

last: Lin

first: Joanne

middle: D

last: Kotz


city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [GRO-seq_MCF_E2]

status: Public on Feb 10 2019

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: Acutely activated enhancer in response to cell signaling regulate transcription by assembling phase separated ribonucleoprotein complex composed of transcription factors with disordered domains and RNA

overall_design: GROseq experiments was performed to examine the active transcription units and their response to different lenghts of estrogen treatment and 1,6-hexanediol

first: Sreejith

middle: J

last: Nair

first: Yuliang

last: Tang


title: In vivo effects of short-term treatment with Bisphenol A (BPA) on mice pancreatic islets

status: Public on Feb 09 2019

city: Sevilla

first: Abdelkrim

last: Hmadcha

address: Avda Américo Vespucio 24, Parque Científico y Tecnológico Cartuja

department: Regeneration and Cell Therapy

country: Spain

institute: CABIMER

summary:
Bisphenol-A (BPA) is one of the most widespread endocrine disrupting chemicals (EDC) used as the base compound in the manufacture of polycarbonate plastics. Although evidence points to consider exposure to BPA as a risk factor for the development of Diabetes, its actions on whole body metabolism and on pancreatic beta cells are still unclear. The aim of this study was to study the in vivo effects of BPA on mice pancreatic islets, particularly on how it could regulate ion channels expression and function. And thus, bringing mechanistic insight into the suggested association between BPA exposure and health disorders.
We used microarrays to detail the global profile of gene expression to identified different groups of up and down-regulated genes in the work model, with a special focus on genes related to ion channel-mediated actions of BPA in mice pancreatic β-cells.

overall_design: OF1 male mice (10 weeks of age) were used throughout this study. An internal animal care and use committee reviewed and approved the method used (the Ethics Committee from Universidad Miguel Hernández de Elche (Alicante, Spain) (approvals ID: UMH-IB-AN-01–14 and UMH-IB-AN-02-14). BPA was dissolved in tocopherol-stripped corn oil (MP Biomedicals), and a total of 100 μg/kg/day (two injections of 50 μg/kg/day) was administered subcutaneously for four days; the same volume of tocopherol-stripped corn oil (100 μL) was used as vehicle in control animals. Sixteen hours after last injection islets were isolated and prepared for RNA extraction and hybridization on Affymetrix microarrays. We analyzed 3 independent experiments per replicate, and we did 3 replicates per sample.

first: Angel

last: Nadal


title: Tumor-resident memory-like CD8 T cells represent an essential cellular target for cancer immunotherapy

status: Public on Jan 10 2019

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Persistent exposure to high levels of antigen results in the progressive exhaustion of T cells and has been thought to preclude the formation of memory. In contrast to the latter assumption, we show here that tumor-specific CD8 T cells residing in the tumor microenvironment include a Tcf1 expressing sub population that has key characteristics of central memory cells, lack an effector cell signature but display hallmarks of exhausted T cells, including the expression co-inhibitory receptors such as PD1. Similar memory-like cells are identified in melanoma patients. Preclinical mouse models reveal that the expansion of tumor-specific CD8 T cells, the production of terminally differentiated exhausted CD8 T cells and sustained tumor control in response to therapeutic vaccination or immune checkpoint blockade critically depends on the presence of these memory-like CD8 T cells. Tumor immune responses thus harbor tumor resident memory-like CD8 T cell populations, which can be therapeutically targeted to improve immune control of cancer.

overall_design: Naive Tcf7-GFP+ P14 cells (CD45.2) (Naive) were transferred into B6 recipient mice (CD45.1) one day  prior to sub-cutaneous implantation of B16-gp33 tumor cells. When tumors became palpable mice were vaccinated with pg33 peptide plus poly(I:C). Six days later Tcf7-GFP+ P14 cells and Tcf7-GFP- P14 cells amongst  tumor infiltrating lymphocytes (TIL) were flow sorted. Total RNA was extracted, cDNA libraries prepared and sequencing was performed using Illumina HiSeq 2500 technology.

first: Imran

last: Siddiqui

last: Calderon-Copete

first: Sylvain

last: Pradervand

first: Werner

last: Held


title: Safety profiling of genetically engineered Pim-1 kinase overexpression for oncogenicity risk in human c-kit+ cardiac interstitial cells

status: Public on Jan 04 2019

first: Oscar

middle: E

last: Echeagaray

state: CA

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

summary: Bulk RNA-seq to profile of c-kit+ cardiac interstitial cells, comparing the transcriptomes of Pim-1 enhanced cardiac progenitor cells and transfection control

overall_design: Transcriptional profiling of Pim-1 enhanced human derived cardiac interstitial cells by bulk RNA-Seq

first: Mark

middle: A

last: Sussman

first: Kathleen

last: Broughton


title: Small-molecule targeting of brachyury transcription factor addiction in chordoma [ChIP-Seq]

overall_design: H3K27ac ChIP-Seq profiling in chordoma cell lines and patient-derived samples

last: Schreiber

first: Tanaz

last: Sharifnia


title: MicV, VrrA sRNA target identification

status: Public on Jan 22 2019

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

country: Germany

institute: Friedrich-Schiller-Universität Jena

summary: In this study we determined the target spectra of the MicV and VrrA sRNAs via pulse-expression followed by RNA-sequencing.

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

first: Nikolai

last: Peschek

first: Mona

last: Hoyos

first: Roman

last: Herzog

first: Konrad

last: Förstner

first: Kai

last: Papenfort


title: High-resolution map of copy number variations in motor cortex of Control and Sporadic Amyotrphic Lateral Sclerosis patients by using a customized exon-centric comparative genomic hybridization array.

status: Public on Dec 31 2018

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

summary: Amyotrophic lateral sclerosis (ALS) is an incurable and fatal neurodegenerative disease. Increasing the chances of success for future clinical strategies requires more in-depth knowledge of the molecular basis underlying disease heterogeneity. We recently laid the foundation for a molecular taxonomy of ALS by whole transcriptome expression profiling of motor cortex from sporadic ALS (SALS) patients. Here, we analyzed genomic structural aberrations occurring in the same patients, by using a customized exon-centered comparative genomic hybridization array (aCGH) covering a large panel of ALS-related genes. Integrative analysis of copy number profiles with their associated transcriptomic data revealed subtype-specific genomic perturbations and candidate driver genes positively correlated with transcriptional signatures, which might represent novel potential biomarkers and therapeutic targets. This study represents the first comprehensive “omics” analysis of molecular events characterizing SALS pathology, providing a road map to facilitate genome-guided personalized diagnosis and treatments for this devastating disease.

overall_design: Motor cortex samples from 30 patients with clear SALS diagnosis and 10 control individuals were analysed by using an 8x60K custom exon-centric NeuroArray platform v. 2.0 (Agilent Technologies, Santa Clara, CA), tailored to detect single/multi-exon deletions and duplications in a large panel of ALS-related genes and to others additional neurological disorders. Two experimental conditions: DNA test and a reference of the same sex (Euro Reference, Agilent Technologies, Santa Clara, CA) were processed according to the manufacturer’s protocol (Agilent Technologies, Santa Clara, CA). SALS patient DNAs were labeled with Cy5-dUTP and reference DNAs for reference DNAs. Arrays were scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System and aCGH image data were processed using Agilent’s Feature Extraction software. Feature extracted raw data was normalized, analyzed and visualized using Agilent CytoGenomics v. 4.0.3.12 and Genomic Workbench v. 7.0.4.0 software (Agilent Technologies, Santa Clara, CA, USA). GC correction with a window size of 2 kb and Diploid Peak Centralization were used for normalization. The Centralization Normalization Algorithm with a threshold of 6.0 and a bin size of 10 was also used for detecting aberrant regions or regions of constant CNVs. Aberrations were detected by the Aberration Detection Method II algorithm (ADM-2), with a sensitivity threshold of 6.0 and moving average window of 2Mb. Human reference sequence hg19 assembly was used to define the genomic coordinates of detected CNVs.

first: Giovanna

last: Morello

first: Maria

last: Guarnaccia

first: Antonio

middle: G

last: Spampinato


title: Differential expression analysis of wildtype, atfs-1(tm4919) and zip-3(gk3164) mutant with next generation sequencing

first: Cole

last: Haynes

summary: ZIP-3 has been shown to repress the mitochondrial-UPR response. To identify genes repressed by ZIP-3, we compared transcript profiles from wildtype, atfs-1(tm4919) and zip-3(gk3164) worms raised on control RNAi or spg-7 RNAi

overall_design: RNA samples were prepared from wild-type(wt) and zip-3(gk3164)(mutant) worms fed either control RNAi or spg-7 RNAi. Worms were synchronized by bleaching, raised on NGM plates seeded with control RNAi or spg-7 RNAi till L4 stage and then harvested. Each experiment was performed in triplicate indicated as 1,2 and 3.

first: Pan

last: Deng


title: Chemical chaperone screening for Pelizaeus-Merzbacher disease

status: Public on Dec 19 2018

city: Shimotsuke shi

first: Takeshi

last: Kouga

state: Tochigi prefecture

address: Yakushiji 3311-1

country: Japan

institute: Jichi Medical University

summary:
We investigated the changes in the overall gene expression in MO3.13 cells induced by PLP1A243V and piracetam using RNA microarray analyses.
We compared gene expression between PLP1WT and PLP1A243V and the expression profile in MO3.13 stably expressing PLP1A243V with/without piracetam.

overall_design: We extracted 3 kinds of RNA using the RNeasy® Mini kit (QIAGEN N.V., Venlo, Netherlands) in MO3.13 cells stably expressing PLP1A243V 24 h after adding piracetam at 10 µM, PLP1A243V without piracetam, and PLP1WT.


title: Transcriptomic study of the response of the maize pathogen Cochliobolus heterostrophus to a plant phenolic, ferulic acid

status: Public on Jan 18 2019

city: Haifa

first: Benny

last: Horwitz

address: Faculty of Biology

country: Israel

institute: Technion

summary: A comparison of the transcriptomes of wild type Cochliolobolus heterostrophus and a deletion mutant in the redox-sensing transcription factor ChAP1 was made. The aim was to study the role of ChAP1 in the response of this pathogen of maize to exposure to a plant-derived phenolic

overall_design: Wild-type C4 (MAT1-2 Tox1+) and ChAP1 deletion mutant (delta-chap1) strains of C. heterostrophus (see Lev et al. 2005 Eukaryotic Cell https://ec.asm.org/content/4/2/443.long https://ec.asm.org/content/4/2/443.long ) were grown at 22ºC on complete xylose medium (CMX) in 16 h white light, 8 h dark for induction of conidiation  for 7 days. Spores were transferred to liquid CMX and incubated with shaking (200 rpm) at 22ºC for 3 days. The cultures were then treated with 0.5, 1 or 2 mM ferulic acid diluted from a 120 mg/ml solution in dimethyl sulfoxide (DMSO); these samples and the corresponding DMSO controls were incubated for 30 min at 22ºC with shaking (200 rpm), harvested, ground to a fine powder in liquid N2 and total RNA extracted using TriReagent following the manufacturers' protocol. After quality control, sequencing libraries were prepared with the Illumina TruSeq RNA library preparation kit v2 and sequenced on the Illumina HiSeq 2500 platform. The experiment includes 4 independent biological replicates for the WT and 3 independent biological replicates for delta-chap1. Concentration series for ferulic acid (FA).

first: Hiba

last: Simaan

first: Benjamin


title: Gene expression profile of IFNα transgenic mice

status: Public on Dec 10 2018

city: Kato

first: Shunichi

last: Shiozawa

address: 944-25 Fujita

institute: Institute for Rheumatic Diseases

summary: The cause of systemic lupus erythematosus (SLE) is unknown. Interferonα (IFNα) has been suggested as a causative agent of SLE, however, it is not proven, and to what extent and how IFNα contributes to the disease is unknown. We here directly studied the contribution of IFNα to SLE by generating inducible IFNα transgenic mice which showed that conditional up-regulation of IFNα induced a typical manifestation of SLE including serum immune complex (IC), autoantibody against double stranded DNA (anti-dsDNA Ab) and the organ manifestations classical to SLE such as IC-deposited glomerulonephritis, classical splenic onion-skin lesion, and alopecia, epidermal liquefaction, positive lupus-band test of the skin. In the spleen of mice, activated effector CD4 T cells, interferonγ-producing CD8 T cells, B220+CD86+ cells and CD11c+CD86+ cells were increased, and the T cells produced increased amounts of IL-4, IL-6, IL-17 and IFNγ and decreased IL-2. In particular, activated CD3+CD4-CD8- double-negative T (DNT) cells positive for TCRαβ, B220, CD1d-teteramer, PD-1 and Helios, which produced increased amounts of IFNγ, IL-4, IL-17 and TNFα, were significantly expanded. They infiltrated into kidney and induced de novo glomerulonephritis and alopecia when transferred into naïve recipients. Thus, conditional up-regulation of IFNα is sufficient to induce SLE, and the DNT cells as expanded by IFNα are directly responsible for the organ manifestations such as lupus skin disease or nephritis.

overall_design: Gene expression in the splenocytes of IFNα transgenic and control mice was measured.

first: Ken

last: Tsumiyama


title: Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

status: Public on Jan 28 2019

city: London

first: YUHAI

last: CUI

state: ON

address: 1391 Sandford Street

department: London Research and Development Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary: The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis (Arabidopsis thaliana), CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases and core components of PRC2, playing essential roles in plant growth and development. Despite their importance, genome-wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP-tagged CLF/SWN under their respective native promoters and used them for ChIP-seq analyses to profile the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (clf, swn, and clf swn). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the GAGA-like and Telo-box-like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf, but not in swn, were markedly reduced compared with WT; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf, swn, and clf swn, and compared with that in WT. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.

overall_design: Examination of CLF and SWN genome-wide bindings, and the distribution of H3K27me3 in WT, clf, swn, and clf swn seedlings.

first: Jie

last: Shu

first: Yuhai

last: Cui


title: Cyprinus carpio 'koi' Raw sequence reads

status: Public on Jan 15 2019

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

country: China

institute: Nanjing Agricultural University

summary:
Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L.

LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.

overall_design: lncRNAs and mRNAs involved in pigmentation and differentiation in Koi carp were detected by deep sequencing using Illumina HiSeq X-ten (BioProject Accession: PRJNA508277; SRA project: SRP172506).

first: Lanmei

last: Wang

first: Haoran

last: Yin

first: Zaijie

last: Dong

first: Wenbin

last: Zhu

first: Jianjun

last: Fu


title: NSD2 is an actionable driver of prostate cancer metastasis

status: Public on Dec 07 2018

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

state: Catalonia

address: Granvia 199

department: ProCURE

institute: IDIBELL


title: Differetially expressed genes after hTR overexpression in U2OS cells

city: Guangzhou

first: Haiying

last: Liu

address: NO.135, Xingang xi Road, Haizhu District

institute: Sun Yat-sen University

summary: lncRNA is reported to regulate gene transcription in variety of ways. hTR is a lncRNA with 451 nt. It is classical role is serving as template for telomere lengthening. However, it involves in some other biology processes as a lncRNA. To screen for genes regulated by hTR, we performed RNAseq with hTR expressed U2OS cells, using pBabe-U2OS as control.

overall_design: Total RNA was extract from HTR-U2OS and pBabe-U2OS stable cell lines in triplicate. RNAseq was performed using Illumina Hiseq 2000 platform.


title: Binding of an X-specific condensin correlates with a reduction in active histone modifications at gene regulatory elements

status: Public on Jan 08 2019

city: New York City

first: Lena

middle: Annika

last: Street

state: NY

address: 100 Washington Square East

institute: New York University

summary: Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In C. elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using ChIP-seq and mRNA-seq. Across the X, DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

overall_design: Included are ChIP-seq profiles data from C. elegans mixed stage embryos and L3 larva. Data was collected from two to three replicates. ChIP-seq data sets in N2, H3K9me3 null (GW638), X;A fusion (15eh1, YPT41), DCC mutant (CB428), and DCC RNAi knockdown (DPY-27 RNAi) strains were generated using antibodies against three dosage compensation complex proteins (SDC-3, CAPG-1, and DPY-27), histone modifications H3K4me3, H3K27ac, H4K16ac, H4panAc, H3ac, H3K4me1, H3K27me1, H3K27me2, H3K9me3, and H4K20me1, the histone protein H3, IgG, and chromatin associated proteins MDT-15, CBP-1, PQN-85, AMA-1, RNA Pol II, and PHA-4::GFP. PHA-4 was pulled down using anti-GFP in OP37[PHA-4::GFP] strain. We additionally include four replicates of RNA-seq data in L3 larva N2 and X;II and X;V fusion strains.

first: Ana

middle: K

last: Morao

first: Lara

middle: H

last: Winterkorn

first: Chen-Yu

last: Jiao

first: Sarah

last: Albritton

first: Mohammed

last: Sadic

first: Maxwell

last: Kramer

first: Sevinc

last: Ercan


title: Expression data from T24 cells after TRIP13 knockdown

city: Lanzhou

first: YANJUN

last: GAO

state: Gansu

address: 222 Tianshui South Road

department: Urology

institute: the 2nd Hospital of Lanzhou University

summary:
TRIP13 is a crucial regulator of double-stranded break repair and spindle apparatus checkpoint and its abnormal expression has been found in several human cancers, whereas the role of TRIP13 in the malignant development of urothelial bladder cancer has not been fully elucidated.
We used microarrays to find out differrential expressed genes upon TRIP13 konckdown in T24 cells

overall_design: T24 cells tranduced with lentiviruses expressing shTRIP13 or control vector were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Yanjun

last: Gao

first: Qi

last: Guo


title: Characterization of mouse tissues by bulk RNA sequencing

status: Public on Dec 28 2018

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

summary: Total RNA of mice tissues (liver, small intestine, lung and kidney) was extracted using liquid N2 and Trizol.  mRNA extracted from total RNA was subjected to double-stranded cDNA synthesis and Illumina stranded paired end library prep for sequencing.

overall_design: Liver, small intestine, lung and kidney mRNA profiles of 6-10 week old mice were generated by RNA sequencing.

first: Guoji


title: Small-molecule targeting of brachyury transcription factor addiction in chordoma [rnaseq_compound]

city: Cambridge

first: Tanaz

last: Sharifnia

address: 415 Main Street

institute: Broad Institute

summary: Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors (TFs). In chordoma, we find that T is associated with a 1.5-Mb region containing “super-enhancers” and is the most highly expressed super-enhancer-associated TF. Strikingly, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. Together, these data demonstrate small-molecule targeting of brachyury TF addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.

overall_design: RNA-sequencing of THZ1-, actinomycin D-, or DMSO-treated UM-Chor1 chordoma cells. Each compound was tested at two concentrations. Two biological replicates were generated for each condition.

first: Stuart

last: Schreiber

first: Charles

last: Lin

first: Joanne

last: Kotz


title: Distinct structural classes of activating FOXA1 alterations in prostate cancer progression

status: Public on Dec 12 2018

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

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

overall_design: Refer to individual Series


title: Identification of transcriptome and metabolome signatures of fatty liver disease in HepaRG cells exposed to PCB 126 and glyphosate

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

summary: We provide here the alterations in gene expression profiles of HepaRG cells, a validated model for cellular steatosis, exposed to three concentration of the polychlorinated biphenyl (PCB) 126, one of the most potent chemical inducing NAFLD. Additionnally, three concentration of the pesticide active ingredient glyphosate were tested. This ultimately suggested sensitive biomarkers of exposure. A gene ontology analysis showed hallmarks of an activation of the AhR receptor by dioxin-like compounds. Our study provides grounds for the development of molecular signatures of fatty liver diseases to rapidly assess toxic effects of chemicals in the HepaRG cell line.

overall_design: Differentiated HepaRGTM cells (HPR 116) were purchased from Biopredic International. The cells were kept in the general purpose medium until day 8, when the culture becomes well organized and includes well-delineated trabeculae and many canaliculi-like structures. Three concentrations of the PCB were then tested from day 8 to day 14, in order to cover a wide range of biological effects, starting from low environmental exposures (100 pM) to high concentrations of (1 uM), with an intermediate concentration (10 nM). Three concentrations of glyphosate, or one concentration of the Roundup herbicide (Grand Travaux +) were also tested in the same system.

last: Mein


title: Human osteoblasts transfected with miR-320a

status: Public on Nov 15 2018

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

institute: Vall d'Hebron Institute of Oncology

summary: Analysis of gene expression of primary osteoblasts transfected with miR-320a mimic or miR-320a inhibitor or their respective controls.

overall_design: 5 samples were analyzed, each of them transfected with miR-320a mimic or miR-320a inhibitor or their respective controls.

first: Natalia

last: Garcia Giralt


title: Global Quantitative Mapping of Enhancer Activity in Rice Genome by STARR-seq

status: Public on Nov 08 2018

last: He

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

institute: Guangzhou National Laboratory

summary: Enhancers are important regulators of gene expression, but their identification is a challenge in plants. STARR-seq is a method measuring directly the enhancer activity of millions fragments in parallel, which had been successfully used to identify enhancers in Drosophila and human genomes. Here we present a global map of rice enhancers whose activities are quantitatively determined by STARR-seq.We also predicted intergenic enhancers based on DNase I hypersensitivity as described in a previously published work. Predicted enhancers overlap poorly with STARR-seq enhancers, only about 400 sites accounting for 3-4% of total enhancers identified by these two different methods. In summary, our results of STARR-seq reveal that enhancers in a plant genome differ from animal enhancers in several aspects and provide a regulatory element resource for further functional and mechanistic studies in different contexts


title: Symbiotic macrophage-glioma cell interactions in the tumor microenvironment reveal GBM therapeutic vulnerabilities

city: CHICAGO

first: Peiwen

state: IL

address: 303 East Superior Street, Suite 6-512

institute: Northwestern University


title: Physical and molecular landscapes of mouse glioma extracellular vesicles define heterogeneity

city: Boston

first: Aron

last: Gyuris

address: 330 Brookline Avenue

department: Genetics

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) comprise a novel mechanism for cellular communication by transferring protein and nucleic acid cargo between cells.  By utilizing a sequential filtration protocol, we were able to effectively separate microvesicles (MVs), exosomes and membrane-unbound ribonuclear protein complexes (RNPs) released from EGFR- (Acquaviva, 2011) and PDGFR-driven (Jun, 2018) genetically engineered mouse glioblastoma (GMB) cell lines.  Regardless of the oncogenic driver of the tumor, different species of RNA partition into different extracellular compartments, with the mRNA in MVs most closely representing the cellular transcriptome, while miRNAs and tRNA fragments segregate into exosomes and RNPs, respectively.  This EV RNA profile, combined with the cognate proteomics data, also serves as a reference for future GBM biomarker discovery.

overall_design: Examination of small and long RNA libraries from cells, small microvesicles, exosomes and RNPs from an EGFR- and a PDGFR-driven mouse-derived GBM cell line

first: Lorena

last: Pantano

first: Alain

last: Charest


title: Single cell RNA sequencing of Vγ4 and Vγ6 γδT cells from different tissue

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

institute: University medical center Hamburg Eppendorf

summary: IL17-producing γδ T cells (γδ T17) mainly develop in the prenatal phase and persist as long-living self-renewing effector cell in all kind of tissues. They express polyclonal T-cell receptors (TCR), comprising public Vγ4+ and Vγ6+ TCRs with germline-like rearrangements. In particular, Vγ6+ T cells have recently been found in a variety of tissues including enthesis, gingiva or skin. However, their exchange between tissues and the mechanisms of tissue-specific adaptation and residency remain poorly understood. Here, we profiled Vγ6+ T cells isolated from thymus, peripheral lymph nodes (pLN) and skin through single-cell RNA-seq technology and compared those to Vγ4+ T cells. Our data demonstrated that Vγ6+ T cells formed highly homogenous cell populations that could be separated by tissue-specific gene expression signatures.

overall_design: Sort  Vγ4 and Vγ6 γδT cells from peripheral lymph nodes, ear skin and thymus, then do 3'-RNA single cell sequencing (10x genomics).

first: Likai

last: Tan

first: Sarina

last: Ravens


title: H3K27ac ChIP-seq in GBM cell lines SF763 PTEN-KO and U87

last: Chen

summary: H3K27ac is an active enhancer mark, which is associated with higher activation of transcription. To determine the downstream transcriptional targets and pathways of H3K27ac in PTEN-deficient glioblastoma, ChIP-seq was performed in SF763 PTEN-KO and U87 cells.

overall_design: H3K27ac ChIP-seq was performed in SF763 PTEN-KO and U87 cells.

first: Ronald

last: DePinho


title: Small-molecule targeting of brachyury transcription factor addiction in chordoma [ATAC-Seq]

status: Public on Jan 20 2019

first: James

last: Bradner

address: 450 Brookline

institute: Dana-Farber Cancer Institute

overall_design: Paired-end ATAC-Seq profiling in the U-CH2 and MUG-Chor1 chordoma cell lines

last: Schreiber

last: Sharifnia


title: A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation

status: Public on Nov 04 2018

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana Farber Cancer Institute


title: The effect of breed and diet on the liver transcriptome of beef steers divergent in RFI

status: Public on Jan 16 2019

city: Galway

first: Marc

last: Higgins

address: University Road

department: Discipline of Biochemistry

country: Ireland

institute: NUI Galway

summary: The objective of this work was to investigate differential gene expression of Charolais (n=90) and Holstein Freisian (n=77)  steers divergent in RFI. The primary goal was to uncover genes and pathways associated with feed efficiency. Cattle were subjected to three different 70 day dietary phases. Initally animals were offered a high concentrate phase, termed "High Concentrate 1". Following this phase animals were offered sero grazed grass for 70 days followed by another high concentrate phase known as "High Concentrate 2". Prior to each stage beginning a dietary adaption period was allowed. Liver biopsies were taken at the end of each dietary phase for animals deemed as either high or low in RFI. RNA was extracted and liver gene expression was investigated using RNA-Seq.

overall_design: 90 samples were analysed in total. 20 samples were from Charolais animals from the high concentrate phase 1 (n=9 low RFI, n=11 high RFI), and an additional 16 samples were from Holstein-Freisian animals from this stage (n=7 low RFI, n=9 high RFI). From the zero-grazed grass phase, 6 biopsies were analysed from Charolais animals (n=3 low RFI, n=3 high RFI) and a further 18 samples were analysed from Holstein-Freisian animals (n=10 low RFI, n=8 high RFI). Finally, 17 Charolais samples were analysed from high concentrate phase 2 (n=9 low RFI, n=8 high RFI) and 13 Holstein-Freisian samples were analysed by RNA-Seq (n=5 low RFI, n=8 high RFI).

first: Derek

middle: W

last: Morris

first: Clare

last: McKenna

first: Gordon

last: Blackshields

first: Sean

last: Coyle

first: Claire

last: Fitzsimmons

first: David

last: Kenny

first: Mark

last: McGee

first: Sinead

middle: M

last: Waters


title: A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [ChIP-seq]

summary: Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely unknown. Here, we comprehensively map complex assemblies on chromatin and find that ncBAF uniquely localizes to CTCF sites and promoters. We identified ncBAF subunits as major synthetic lethalities specific to human synovial sarcoma and malignant rhabdoid tumor, which share in common cBAF complex perturbation. Chemical degradation of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes retain their hallmark localization to CTCF sites and promoters, and maintain gene expression at retained mSWI/SNF sites to support cell proliferation in a manner distinct from fusion oncoprotein-mediated targeting. Taken together, these findings unmask the unique targeting and function of ncBAF complexes and present new cancer-specific therapeutic targets.

overall_design:
Genomic profiling of mSWI/SNF complex subtypes in naïve EoL-1 and MOLM-13 by ChIP-seq for complex-specific subunits and histone marks, as well as ChIP-seq for BRD9 subunit in nairve Jurkat cellls.  SYO-1 cells were lentivirally infected with vectors containing either shControl or shSSX to assess BRD9 complex localization in synovial sarcoma disease setting.  BRD9 ChIP was performed in TTC1240 after lentiviral infection with empty vector control or SMARCB1 to assess BRD9 localization in malignant rhaboid tumor.

To assess SMARCA4 loss upon dBRD9 treatment in MOLM13, cells were treated with 250nM dBRD9 (at a 1:10,000 dilution) or DMSO control for 6 days and then used for ChIP-seq with a SMARCA4 antibody.  To examine BRD9 localization in Aska, cells were lentivirally infected with pLKO shScramble or shSSX1 and fixed for ChIP 7 days post infection.  In TTC1240, CTCF ChIP was performed on cells lentivirally infected with an empty vector to compare to BRD9 localization before and after SMARCB1 reintroduction in the same cell line.  To assess residual complex localization in TTC1240 upon BRD9 loss, BRD9 and SMARCA4 ChIP-seq was performed in TTC1240 cells treated with either 250nM dBRD9 (1:10,000 dilution) or DMSO control for 7 days.  ChIPs were spiked in for normalization and SMARCA4 ChIP was performed in duplicate from independent samples.

first: Brittany

middle: C

last: Michel

first: Andrew

middle: R

last: D'Avino


title: Epithelial control of colonisation by Streptococcus pneumoniae at the human mucosal surface

status: Public on Jan 12 2019

city: Liverpool

first: Simon

last: Jochems

address: Pembroke Place

institute: Liverpool School of Tropical Medicine

summary: Control of Streptococcus pneumoniae colonisation at human mucosal surfaces is critical to reducing the burden of pneumonia and invasive disease, interrupting onward transmission, and in achieving herd protection. We hypothesised that the pattern of pneumococcal-epithelial engagement dictates the inflammatory response to colonisation, and that this epithelial sensing is linked to bacterial clearance. Here we have used nasal curette biopsies from a serotype 6B Experimental Human Pneumococcal Carriage Model (EHPC) to visualize S. pneumoniae colonisation and relate these interactions to epithelial surface marker expression and transcriptomic profile upregulation. We have used a Detroit 562 cell co-culture model to further understand these processes and develop an integrated epithelial transcriptomic module to interrogate gene expression in the EHPC model. We have shown for the first time that pneumococcal colonisation in humans is characterised by microcolony formation at the epithelial surface, microinvasion, cell junction protein association, epithelial sensing, and both epithelial endocytosis and paracellular transmigration. Comparisons with other clinical strains in vitro has revealed that the degree of pneumococcal epithelial surface adherence and microinvasion determines the host cell surface marker expression (ICAM-1 and CD107), cytokine production (IL-6, IL-8 and ICAM-1) and the transcriptomic response. In the context of retained barrier function, epithelial microinvasion is associated with the upregulation of a wide range of epithelial innate signalling and regulatory pathways, inflammatory mediators, adhesion molecules, cellular metabolism and stress response genes. The prominence of epithelial TLR4R signalling pathways implicates pneumolysin, a key virulence factor, but although pneumolysin gene deletion partially ameliorates the inflammatory transcriptional response in vitro, critical inflammatory pathways persist in association with enhanced epithelial adhesion and microinvasion. Importantly, the pattern of the host-bacterial interaction seen with the 6B strain in vitro is also reflected in the EHPC model, with evidence of microinvasion and a relatively silent epithelial transcriptomic profile that becomes most prominent around the time of bacterial clearance. Together these data suggest that epithelial sensing of the pneumococcus during colonisation in humans is enhanced by microinvasion, resulting in innate epithelial responses that are associated with bacterial clearance.

overall_design: 27 nasal samples coming from 20 healthy adults volunteers around experimental human pneumococcal challenge were analysed (samples were collected 5 days prior or 2 days post experimental challenge). Nasal cells were collected using curettes, after which RNA was extracted and sequenced

middle: P


title: Effects of Diras2-knockdown in murine hippocampal primary cells

status: Public on Dec 01 2018

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary:
Attention-deficit / hyperactivity disorder (ADHD) is a clinically heterogeneous childhood behavioral neurodevelopmental disorder which is highly persistent into adulthood and shows an heritability up to 80%. In previous studies, our group delineated the 9q22 region by both linkage studies and genome-wide association studies as a candidate locus for ADHD. This region harbors the DIRAS2 (MIM: 607863) gene which is coding for a Ras GTPase.
To get more knowledge about the role of Diras2 in the brain, an adeno-associated virus (AAV) was used for a short hairpin RNA (shRNA) induced knock-down of Diras2 gene expression in mouse hippocampal primary cells. To identify possible targets of Diras2 and signalling cascades in which Diras2 might play a role, GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) were used for expression profiling of the RNA samples.

overall_design: We examined the effects of a Diras2 knock-down on gene expression in murine hippocampal cells.

first: Lena

last: Weißflog

first: Heike

last: Weber

first: Andreas

last: Reif


title: Expansion of adult human pancreatic tissue yields organoids harbouring progenitor cells with endocrine differentiation potential

city: Leiden

first: Eelco

last: de Koning

address: Albinusdreef 2

department: Medicine

country: Netherlands

institute: LUMC

summary: Gene expression profiles from ALDH high cells sorted from expanded adult human pancreatic organoids are more similar to fetal pancreatic tissue and ALDH high cells sorted from expanded fetal human pancreatic organoids than to adult human islets or adult islet-depleted exocrine tissue.

overall_design: RNA was isolated from ALDHhi cells sorted from organoids after 7 days expansion derived from human adult pancreatic tissue, ALDHhi cells sorted from organoids after 7 days expansion derived from human fetal pancreatic tissue, primary fetal pancreatic tissue, adult human islets from different donors and adult exocrine (islet-depleted) pancreatic tissue from different donors.

first: Nerys

last: Willams

first: Lennart

last: Kester

first: Alexander

last: van Oudenaarden

first: Cindy

last: Loomans


title: Transcriptome analysis of maize hybrid An’nong 591 and its parental lines under heat stress

status: Public on Nov 24 2018

city: Hefei

first: Yang

last: Zhao

address: changjiang road 130

institute: Anhui Agricultural University

summary: Eighteen samples (three replicates) of the maize hybrid An’nong 591 and its parental lines under control and heat treatment were used for RNA sequencing

overall_design: Examination of the transcriptomic divergence and heterosis-related genes in the seedlings of the three genotypes under heat stress

first: Qing

last: Ma


title: Endovascular progenitors invade melanoma tumors and differentiate towards a variety of vascular beds to promote tumor metastasis

status: Public on Nov 21 2018

city: Woolloongabba

first: Jatin

last: Patel

address: 37 Kent Street

institute: The University of Queensland

summary: Tumors have the capacity to trigger the formation of blood vessels allowing them to spread to other body parts. We examined here the stem cells that form arteries and veins within tumors and propose that their inhibition reduces metastatic spread.

overall_design: Examination of dynamics and differentiation of tissue resident endothelial hierarchy in a melanoma setting

first: Prudence

last: Donovan

first: Kiarash

last: Khosrotehrani


title: Stem cell differentiation trajectories in Hydra resolved at single cell resolution

status: Public on Nov 02 2018

city: Davis

first: Celina

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

summary: The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations but the genetic pathways enabling these dynamic tissue properties are not well understood. We used Drop-seq to sequence 24,985 Hydra cells and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified the transcription factors expressed along these trajectories, thus creating a comprehensive map of all developmental lineages in the adult animal. We unexpectedly found that neuron and gland cell differentiation transits through a common progenitor state, suggesting a shared evolutionary history for these secretory cell types. Finally, we have built the first gene expression map of the Hydra nervous system. By producing a comprehensive molecular description of the adult Hydra polyp, we have generated a resource for addressing fundamental questions regarding the evolution of developmental processes and nervous system function.

overall_design: Drop-seq analysis of homeostatic Hydra vulgaris AEP (24,985 cells, 15 Drop-seq libraries total, 13 libraries for whole animal dissociations, 2 libraries for suspensions enriched for neuronal cells using FACS), ATAC-seq analysis of whole homeostatic Hydra magnipapillata 105 (3 replicated ATAC-seq libraries), Tag-seq analysis of epithelium specific gene expression of homeostatic Hydra vulgaris AEP (3 replicates for body column endoderm, 3 replicates for body column ectoderm).

first: Stefan

last: Siebert

first: Jack

last: Cazet

first: Jeffrey

last: Farrell


title: Distinct structural classes of activating FOXA1 alterations in prostate cancer progression [RNA-Seq]

first: Marcin

last: Cieslik

summary: Expression profiles of 22RV1 prostate cancer cells following FOXA1 genetic engineering and or TLE3 knock-down

overall_design: treatment control design with biological replicates (n=2)

first: Abhijit

last: Parolia

first: Yuping

last: Zhang


title: Microarray of PTEN knockout in SF763 cells

first: Peiwen

last: Chen

summary: We used microarrays to study the global gene expression and identified differentially expressed genes in PTEN knockout SF763 cells, aiming to identify genes and pathways that are regulated by PTEN.

overall_design: PTEN knockout cells were generated by CRISPR genome editing using sgRNAs. The samples used in the microarray analysis were in triplicates.

first: Ronald

last: DePinho


title: HiChIRP reveals RNA-associated chromosome conformation

status: Public on Dec 04 2018

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive

institute: Stanford University

summary: Modular domains of lncRNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here we present HiChIRP, a method leveraging novel bioorthogonal chemistry and customized 3C conditions, that enables interrogation of chromatin architecture focused around a specific RNA of interest down to ~10 copies per cell. HiChIRP of three nuclear RNAs reveal insights into promoter interactions (7SK), telomere biology (TERC), and inflammatory gene regulation (lincRNA-EPS).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HiChIP of CTCF in GM12878 cells. HiChIP of Oct4 in mESCs. HiChIRP of 7SK in mESCs. HiChIRP of TERC in GM12878 cells. HiChIRP of lincRNA-EPS, HiChIP of H3K4me3 and SMC1a, and Hi-C in BMDM wild-type cells. HiChIP of H3K4me3 and SMC1a in lincRNA-EPS KO BMDM cells. ChIRP-seq of lincRNA-EPS in BMDM wild-type cells.

first: Maxwell

last: Mumbach

last: Granja

first: Ryan

last: Flynn

first: Caitlin

last: Roake

first: Ansuman

middle: T

last: Satpathy

first: Adam

last: Rubin

first: Yanyan

last: Qi

first: Zhaozhao

last: Jiang

first: Shadi

last: Shams

first: Bryan

last: Louie

first: Jimmy

last: Guo

first: David

last: Gennert

first: Michael

last: Corces

first: Steven

last: Artandi

first: Paul

last: Khavari

first: Maninjay

last: Atianand

first: Katherine

last: Fitzgerald

first: William

last: Greenleaf


title: The gut microbiome can transmit environmental responses to the next generation

status: Public on Oct 10 2018

city: Umeå

first: Aman

last: Zare

state: Västerbotten

address: University Hospital, buildings 6 K and 6 L

department: Molecular Biology

country: Sweden

institute: Umeå university

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

sample_organism:
Bacteria
Drosophila melanogaster
synthetic construct

overall_design: Refer to individual Series


title: The gut microbiome can transmit environmental responses to the next generation [16s-amplicon]

summary: Environmental perturbations impact gene transcription. A subset of these transcriptional changes can be passed on to the next generation even in the absence of the initial stimulus. This phenomenon is known as transgenerational inheritance of environmental exposures (TIEE). Previous studies have mainly focused on what is transferred through the germ-line, i.e. DNA methylation, histone modifications, non-coding RNAs, etc. Nevertheless, the germ cells are not the only cells that are passed on from one generation to the next. The microbiota is also transmitted together with the host cells. In this study, we investigated the role of the gut microbiome in TIEE using Drosophila melanogaster as a model organism. We have reared flies in cold and control temperatures, 18 and 25 °C respectively, and looked at the transcriptional pattern in their offspring -grown in control condition- using RNA sequencing. To study the effect of the microbiome, we have carefully exchanged the parental feces introduced to the offspring. We observed genes responsive to thermal alteration, which have preserved their transcriptional status transgenerationally. A subset of these genes, mainly genes expressed in gut, were transcriptionally dependent on which microbiome they acquired. These findings show that the microbiota plays a previously unknown role in TIEE. Our study unveiled a new route for transmittance of environmental memories and thus represents an uncharted area to explore for researchers addressing non-genetic transgenerational inheritance.

sample_organism:
Bacteria
synthetic construct

platform_organism:
Bacteria
synthetic construct

overall_design: 16S amplicon sequencing of the fly-food and feces

first: Anna-Mia

last: Johansson

first: Edvin

last: Karlsson

first: Nicolas

last: Delhomme

first: Per

last: Stenberg


title: A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [RNA-seq]

first: Cigall

last: Kadoch

overall_design:
CRL7250 cells were treated in biological duplicate with either DMSO vehicle control , dBRD9 compound, or dBRD9 compound for 24h followed by lentiviral infection with  construct containing V5-SS18-SSX1 to assess role of BRD9 in SS18-SSX1 gene activation.  RNA-seq was performed in biological duplicate in SYO-1 synovial sarcoma cells upon chemical BRD9 degradation by dBRD9 compound or DMSO vehicle control at 3 days and 6 days to assess gene expression changes upon BRD9 perturbation.  SYO-1 cells were lentivirally infected in biological duplicate with pGIPZ shControl, pGIPZ shBRD9, or pGIP shSMARCE1 to assess if BRD9 and SMARE1 knockdown are transcriptionally similar.  RNA-seq was collected in biological duplicate from TTC1240 cells treated with either DMSO or dBRD9 as for SYO-1.
To assess gene expression changes upon BRD9 loss, TTC1240 and MOLM-13 cells were treated with 250nM dBRD9 (1:10,000 dilution) or DMSO control for 7 days (TTC1240) or 6 days (MOLM-13) in duplicate.

first: Brittany

last: Michel

first: Andrew

last: D'Avino


title: SWOG 0120, A Prospective Observational Biologic Study of Asymptomatic Patients With Monoclonal Gammopathy and Plasma Proliferative Disorders

status: Public on Nov 07 2018

city: Little Rock

first: Brian

last: Walker

state: AR

address: 4301 W Markham St.

institute: University of Arkansas for Medical Sciences

summary: The purpose of this study was to take samples of bone marrow and blood to learn more about monoclonal gammopathy or myeloma without symptoms. Specifically, the researchers want to understand more about genetic changes in the tumor and about the response of immune systems to a tumor.

overall_design: All cases of clinical myeloma (CMM) are preceded by an asymptomatic monoclonal gammopathy (AMG), classified as either monoclonal gammopathy of undetermined significance (MGUS) or asymptomatic multiple myeloma (AMM). We analyzed data from AMG patients (n 5 331) enrolled in a prospective, observational clinical trial (S0120). Baseline data from clinical variables, gene expression profiles (GEP) of purified tumor cells, and findings of magnetic resonance imaging (MRI) were correlated with the risk of progression to CMM requiring therapy. GEP of purified tumor cells revealed that all molecular subtypes of CMM are also represented in the AMG phase. An increased risk score (>-0.26) (based on a 70-gene signature, GEP70) was an independent predictor of the risk of progression to CMM. Combination of elevated serum free light chain, M-spike, and GEP70 risk score identified a subset with high risk (67% at 2 years) of progression to CMM requiring therapy. Importantly, absence of these factors in AMM patients predicted low risk similar to MGUS. Detection of multiple (>1) focal lesions by MRI also conferred an increased risk of progression. These data demonstrate that signatures associated with high-risk CMM impact disease risk and support inclusion of genomic analysis in the clinical management of AMGs.


title: lncRNA and mRNA expression signatures in OVCAR3 cells: control vs. miR-200a transfected

city: Shanghai

last: Liu

address: 2699 west gaoke road

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

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

summary: To further development of the effects of miR-200a in ovarian cancer OVCAR3 cells，we have employed lncRNA and mRNA microarray as a discovery platform to identify lncRNA and mRNA expression in miR-200a overexpressing ovarian cancer cells. OVCAR3 cells were transfected with lentiviral vector with eGFP, encoding miR-200a and negative control vector (LV- miR-200a and LV-CON,) by using polybrene. The dysregulation of miR-200a was confirmed by using RT-PCR. RNA was extracted and detected by a lncRNA and mRNA microarray in LV-miR-200a and LV-CON OVCAR3 cells. The different expression of lncRNA and mRNA in LV-miR-200a and LV-CON OVCAR3 cells was analyzed to explore the mechanism that miR-200a affect ovarain cancer cells.

overall_design: miR-200a overexpression induced lncRNA and mRNA expression in OVCAR3 cells was measured in LV-miR-200a and LV-CON groups.  3 control replicates at each group.


title: Distinct structural classes of activating FOXA1 alterations in prostate cancer progression [ChIP-Seq]

first: Marcin

last: Cieslik

address: 500 S State St

institute: University of Michigan

summary: Chromatin binding profiles for FOXA1, AR, and TLE3 in prostate cancer cell lines with different FOXA1 genotypes. Full-length and truncated forms of FOXA1 are distinguished by C-terminal and N-terminal antibodies.

overall_design: Mutant relative to wild-type comparisons including CRISPR knockouts, exogeneous overexpression, and endogeneous mutations.

first: Abhijit

last: Parolia

first: Yuping

last: Zhang


title: Effect of Prematurity on Genome Wide Methylation in the Placenta

status: Public on Sep 26 2018

city: Providence

first: Jessica

last: Schuster

state: RI

address: 200 Chestnut St

department: Pediatrics

institute: Women and Infants Hospital

type: Methylation profiling by high throughput sequencing

summary: Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns.  Despite decades of research, its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The “fetal origins” hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility.   Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages.  We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs). Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p<0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p<0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth. These studies form the basis for future studies on the epigenetics of preterm birth, "fetal programming” and the impact of environment exposures on this important clinical challenge.

overall_design: Methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) on 9 placentas with gestational age from 25 weeks to term using Illumina HiSeq2500

first: James

middle: F

last: Padbury


title: Interleukin-1β induces mitochondrial DAMP production to activate STING-dependent innate immune programs

status: Public on Sep 21 2018

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Here we report that exogenous IL-1β induces TBK1-mediated interferon regulatory factor 3 (IRF3) activation and autophagic flux in human myeloid and epithelial cells. IL-1β-induced innate immune activation is dependent upon the DNA sensing pathway adaptor, stimulator of interferon genes (STING), through the recognition of mitochondrial DNA by cyclic GMP-AMP synthase (cGAS). Thus, IL-1β potentiates pathogen-induced interferon production and signal transducer and activator of transcription (STAT) signaling to amplify innate immune responses.

overall_design: A time series single cell RNA-seq analysis of interleukin-1β-treated human alveolar epithelial cells.

first: Lauren

middle: D

last: Aarreberg

first: Katharina

last: Esser-Nobis

first: Connor

middle: B

last: Driscoll

first: Justin

last: Roby

first: Andrey

last: Shuvarikov

first: Richard

last: Green

last: Gale Jr


title: Profiling of 18 - 45 nt small RNAs in the cauda epididymal sperm of mice and rats.

status: Public on Oct 31 2018

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

summary: Total RNAs were extracted from the purified cauda epididymal spermatozoa of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult), and the 18 - 45 nt fraction small RNAs were subjected to library construction and deep sequencing, using Illumina GAIIx.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Deep sequencing profiling of 18 - 45 nt small RNAs in the cauda epididymal sperm of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g) by Illumina GAIIx.

first: Yonglian


title: Profiling of 18 - 45 nt small RNAs in the caput epididymal sperm of mice and rats

summary: Total RNAs were extracted from the purified caput epididymal spermatozoa of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult), and the 18 - 45 nt fraction small RNAs were subjected to library construction and deep sequencing, using Illumina HiSeq 2000.

overall_design: Deep sequencing profiling of 18 - 45 nt small RNAs in the caput epididymal sperm of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult) by Illumina HiSeq 2000.


title: Evaluation of APOL1 ASO in a novel model of APOL1-associated renal disease

status: Public on Oct 16 2018

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

summary: African Americans develop end-stage renal disease at a higher rate compared to European Americans due to two polymorphisms (G1 and G2 risk variants) in the apolipoprotein L1 (APOL1) gene that are common in people of African ancestry. Not all homozygous risk allele carriers, however, develop renal disease suggesting that modifying factors (“second hits”) are required. Although the compelling genetic evidence provides an exciting opportunity for personalized medicine in chronic kidney disease (CKD), drug discovery efforts have been greatly hindered by the fact that APOL1 expression is limited to humans and select nonhuman primates. We describe a novel physiologically-relevant genomic mouse model of APOL1-associated renal disease that expresses human APOL1 from the endogenous human promoter, resulting in expression in similar tissues and at similar relative levels as humans. While naïve genomic APOL1 transgenic mice did not exhibit a renal disease phenotype, a single administration of IFNγ was sufficient to robustly induce proteinuria only in APOL1 G1 transgenic mice, despite inducing kidney APOL1 expression in both G0 and G1 mice, serving as a clinically-relevant “second hit.” We also report on the discovery of the first APOL1 inhibitor, IONIS-APOL1Rx, a Generation 2.5 antisense oligonucleotide (ASO) targeting APOL1 mRNA. Treatment of APOL1 G1 mice with IONIS-APOL1Rx prior to IFNγ challenge robustly and dose-dependently inhibited kidney and liver APOL1 expression and protected against IFNγ-induced proteinuria, indicating that the disease-relevant cell types are sensitive to ASO treatment. Collectively, these data suggest that IONIS-APOL1Rx may be an effective therapeutic for APOL1 nephropathies and warrants further development.

overall_design: APOL1 G0 and G1 transgenic mice were dosed with PBS (vehicle), 50 mg/kg control ASO (non-targeting ASO of the same chemistry as targeting ASO) or 50 mg/kg APOL1 ASO once/week for 4 weeks. One day after the last ASO dose, cohorts were divided and half were challenged with PBS and half were challenged with IFNgamma. Kidney and Liver tissues were harvested 48 hours after challenge for analysis. N=3-4 per group.

first: Mariam

last: Aghajan

first: Chris

last: Hart


title: Effects of light-at-night on the rat liver - a role for the autonomic nervous system (Experiment 1)

city: Venlo

first: Anne-Loes

last: Opperhuizen

address: Deken van Oppensingel 23

institute: Maastricht University

summary:
Exposure to light at night (LAN) has been associated with serious pathologies, including obesity, diabetes and cancer. Recently we showed that 2 hours of LAN impaired glucose tolerance in rats. Several studies have suggested that the autonomic nervous system (ANS) plays an important role in communicating these acute effects of LAN to the periphery. Here, we investigated the acute effects of LAN on the liver transcriptome of male Wistar rats. Expression levels of individual genes were not markedly affected by LAN, nevertheless pathway analysis revealed clustered changes in a number of endocrine pathways. Subsequently, we used selective hepatic denervations (sympathetic (Sx), parasympathetic (Px), total (Tx, i.e., Sx plus Px), sham) to investigate the involvement of the ANS in the effects observed. Surgical removal of the sympathetic or parasympathetic hepatic branches of the ANS resulted in many, but small changes in the liver transcriptome, including a pathway involved with circadian clock regulation, but it clearly separated the four denervation groups. On the other hand, analysis of the liver metabolome was not able to separate the denervation groups, and only 6 out of 78 metabolites were significantly up- or downregulated after denervations. Finally, removal of the sympathetic and parasympathetic hepatic nerves combined with LAN exposure clearly modulated the effects of LAN on the liver transcriptome, but left most endocrine pathways unaffected.
Conclusion: One-hour light-at-night acutely affects the liver transcriptome. Part of this effect is mediated via the nervous innervation, as a hepatectomy modulated and reduced the effect of LAN on liver transcripts.

overall_design: Male Wistar rat liver samples were used for microarray analysis. The experiment consists of three experimental animal groups of which two were exposed to 1 hour of light at night (LAN) and one of those groups also received a liver denervation. The following groups were included: Sham-DARK (control group, n=8), Sham-LAN (n=8, to test effects of LAN) and Tx-LAN (n=8, to test whether a total denervation modulates effects of LAN).

first: Ewout

last: Foppen

first: Martijs

last: Jonker

first: Paul

last: Wackers

first: Martijn

last: van Faassen

first: Michel

last: van Weeghel

first: Linda

last: van Kerkhof

first: Eric

last: Fliers

first: Andries

last: Kalsbeek


title: CFP1 safeguards male meiotic progression by regulating meiotic gene expression

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

summary: Meiosis occurs specifically in germ cells to produce sperm and oocytes that are competent for sexual reproduction. Multiple factors are required for successful meiotic entry, progression, and termination. Trimethylation of histone H3 on lysine 4 (H3K4me3), a mark of active transcription, has been implicated in spermatogenesis by forming double strand breaks (DSBs). The role of H3K4me in transcriptional regulation during meiosis however, remains poorly understood. Here, we reveal that mouse CXXC finger protein 1 (Cfp1), a component of H3K4me methyltransferases Setd1a/b, is dynamically expressed in differentiating male germ cells and safeguards meiosis by controlling gene expression. Depletion of Cfp1 in male germ cells resulted in infertility with reduced H3K4me3, spermatogenic arrest, and repression of essential germ cell development and meiosis genes. Importantly, ChIP-Seq analysis revealed that Cfp1 is mainly enriched at transcriptional start sites to promote gene expression and H3K4me2/3 levels at pachytene stage. The most highly enriched genes were associated with meiosis and homologous recombination during differentiation of spermatocytes to round spermatids. Additionally, missense mutations of human CFP1 were prevalent in patients with nonobstructive azoospermia. Therefore, our study establishes a mechanistic link between CFP1-mediated transcriptional control and meiotic progression, and provides unprecedented genetic basis for understanding human sterility.

overall_design: We performed ChIP-Seq (Cfp1 and H3K4me3) analysis in P21 mouse spermatocytes.

first: C

first: D

last: Seol

first: H

last: Yoo

first: K

last: Hong

first: Y

last: Choi


title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by TL1A

status: Public on Aug 24 2018

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

summary:
TNF-like ligand 1A (TL1A) is a member of TNF receptor superfamily and involved in the pathogenesis of autoimmune diseases  including rheumatoid arthritis (RA) by inducing apoptosis via intracellular death domain or promoting inflammation through the activation of NFκB by binding to its specific receptor death receptor 3 (DR3). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble TL1A in addition to Fas-ligand (FasL) and LIGHT and inhibits the signaling of TL1A via DR3. Therefore, TL1A-DcR3/DR3 signaling may be involved in the pathogenesis of RA by modulating apoptosis and proliferation of RA-FLS.
We hypothesized that TL1A regulates the gene expression in RA-FLS. We used to search for genes in which expression in RA-FLS is regulated by TL1A.

overall_design: RA-FLS were obtained from 4 RA patients (sample1-4). Each sample was incubated with either 1.0 μg/ml recombinant human TL1A protein or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2. Gene expression in RA-FLS stimulated by TL1A was compared with that of their respective non-stimulated controls.

first: Toshihisa

last: Maeda

first: Yasushi

last: Miura

first: Shinya

last: Hayashi

first: Masahiro

last: Kurosaka

first: Ryosuke

last: Kuroda


title: The gut microbiome can transmit environmental responses to the next generation [RNA-Seq]

first: Aman

last: Zare

overall_design: Total RNA profiling of fruitfiles rearead in cold and control temperature.

first: Anna-Mia

last: Johansson

first: Edvin

last: Karlsson

first: Nicolas

last: Delhomme

first: Per

last: Stenberg


title: Single-cell virus sequence of influenza infections that trigger innate immunity

status: Public on Oct 05 2018

city: Seattle

first: Jesse

last: Bloom

state: WA

address: 1100 Fairview Ave N, room B3-123

institute: Fred Hutch Cancer Research Center

type: Genome variation profiling by high throughput sequencing

summary: The outcome of viral infection is extremely heterogeneous at the cellular level, and infected cells only sometimes activate innate immunity. Here we assess how the genetic variation inherent in viral populations contributes to this heterogeneity. We do this by developing a new approach to determine both the cellular transcriptome and full-length sequences of all viral genes in single influenza-infected cells. Infections that activate an innate-immune response in single cells are associated with viral defects that include amino-acid mutations, internal deletions, and failure to express key genes. However, immune activation remains stochastic in cells infected by virions with these defects, and sometimes occurs even in cells infected by virions that express unmutated copies of all genes. Our work shows that the genetic variation present in influenza virus populations substantially contributes to but does not fully explain the heterogeneity in infection outcome and immune activation in single infected cells.

sample_organism:
Homo sapiens
Canis lupus familiaris
Influenza A virus (A/WSN/1933(H1N1))

overall_design:
Combined single-cell transcriptomics and viral genome sequencing of influenza infected cells.
A549 cells with an IFN reporter were infected with the A/WSN/1933 strain of influenza virus, and enriched for IFN+ cells. Then single-cell transcriptomics was performed on a 10X Chromium (v2 reagents) and viral mRNA was enriched for full-length PacBio sequencing.


title: Tetraploidy in Rodent Cardiac Stem Cells Confers Enhanced Biological Properties

city: San Diego

first: Oscar

middle: E

last: Echeagaray

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of diploid and tetraploid cardiac progenitor cells

overall_design: Transcriptional profiling of diploid and tetraploid CPCs by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

middle: A

last: Sussman

first: Kathleen

last: Broughton


title: Effects of diets differing in energy and protein content on the adipose tissue transcriptome of Norwegian Red Heifers

status: Public on Sep 20 2018

city: Aas

first: Hilde

middle: Kristine Lyby

last: Wærp

address: Arboretveien 6

department: Animal and Aquacultural Sciences

country: Norway

institute: Norwegian University of Life Sciences

summary: Effects of heifer feeding regimes on growth characteristics, metabolism, endocrinology, health and subsequent milk yield  has been described in several studies. This indicates that  nutritional impacts have both short- and long-term effects on the animal’s metabolic regulation. Adipose tissue has an important role in whole-body metabolic regulation, as it is the main site for both lipid synhtesis, storage and mobilization as well as an endocrinologically active organ. However, little is known about bovine adipose metabolism at gene level, and what is done is mostly found in mature cows by means of microarrays.  The goal of this study was to apply next-generation RNA sequencing on the adipose tissue of Norwegian Red heifers fed differently, in order to gain knowledge about nutritionally induced regulatory mechanisms in growing dairy cattle. The objectives were to:  1) Describe the differential gene expression in the adipose tissue of heifers fed diets differing in energy and protein content; 2) Describe the long-term changes in adipose gene expression occuring within treatment groups between the experimental feeding period and 6 months after the transition from experimental diets to a similar diet offered to all animals; 3) Identify any post-treatment effects of the experimental feeding as expressed by differential gene expression between treatment groups still present 6 months after the termination of experimental feeding; and 4) To identify candidate genes for further studies on the breeding and feeding for improved feed efficiency and production in the Norwegian Red.

overall_design: The heifers were allocated to 4 experimental treatment groups at 3 months of age; Low-protein/high-energy, high-protein/high-energy, low-protein/low-energy and high-protein/low-energy. The heifers belonged to two different genetic groups, one bred for high milk yield and one bred for low occurence of clinical mastitis. The treatment groups were balanced in this regard. 24 samples were collected at 12 months of age, during the experimental feeding period. There were 6 replicates per treatment group. Transition to a joint pregnancy diet for all animals was performed immediately after confirmed pregnancy (day 28-42 of gestation). New samples were collected from the same animals at month 7 of gestation (20-24 months of age), to give a total of 48 sequenced RNA samples.

last: Lyby Wærp

first: Sinead

last: Waters

first: Matthew

last: McCabe

first: Paul

last: Cormican

first: Ragnar

last: Salte


title: Expression data from V194D Matn3 mutant Xbp1 WT and KO P5 mouse costochondral cell preparation

status: Public on Sep 22 2018

city: Newcastle Upon Tyne

first: Katarzyna

last: Pirog

address: International Centre for Life

institute: Newcastle University

summary:
Multiple epiphyseal dysplasia (MED) results from mutations in cartilage structural proteins COMP, MATN3 and type IX collage. V194D Matn3 is a mouse model of MED in which a signifficant contribution of ER stress has been detected.
In order to test whether ER stress contribution was a beneficial or detrimental component of the disease, V194D Matn3 mice were crossed with a cartilage specific knock-out of Xbp1, and transcriptomic analysis was performed using the Affymetrix 420A Mouse Array.

overall_design: Chondrocytes were extracted from postnatal day 5 ribs of Xbp1 WT and KO mice on V194D Matn3 or WT Matn3 background. RNA was extracted from isolated chondrocytes using Trizol reagentand pooled from 3 separate extractions. A GeneChip 3’ expression assay (Mouse430_2 Affymetrix) was used to analyse gene expression. Quality control checks for control hybridizations were performed using Microarray Suite 5.

first: Jamie

last: Soul


title: ChIP-seq of Sgo1p on mitotic chromosomes of Saccharomyces cerevisiae

status: Public on Sep 01 2018

city: East Lansing

first: Min-Hao

last: Kuo

state: MI

address: Room401, 603 Wilson Road

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

summary: We report the genome-wide localization of Sgo1p in mitosis of Saccharomyces cerevisiae using ChIP-seq. The high resolution mapping clearly shows a tripartite domain of Sgo1p in each mitotic chromosome. This domain requires the wildtype tension sensing motif (TSM) of histone H3.

overall_design: Examination of Sgo1p localization in wildtype TSM, tsm-(H3G44S) and overexpressed-Sgo1p strains, in triplicate.

first: Deng

last: Xiexiong

first: Kuo

last: Min-Hao


title: Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

status: Public on Aug 01 2018

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

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

overall_design: Refer to individual Series

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

last: Fu

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt

first: Yan

last: Jaszczyszyn

first: Mirit

last: Aladjem

first: Peter

last: Aplan

first: Olivier

last: Hyrien


title: ZIKV infection increases HUVECs endothelial barrier permeability and activates inflammatory cytokines

status: Public on Aug 31 2018

city: Reno

first: Subhash

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

institute: University of Nevada, Reno

summary: The objective of this assay was to determine the effects of ZIKV on HUVEC cells

overall_design: Purified HUVECs were infected with two strains of ZIKV (PRVABC59 and IBH30656) and mRNA was subjected for differential gene expression

first: Stephen

last: St. Jeor


title: Comprehensive analysis of lncRNAs and circRNAs reflects the functional specialization in oxidative and glycolytic skeletal muscles

status: Public on Aug 30 2018

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: The biochemical and functional differences between oxidative and glycolytic muscles affect human muscle health and animal meat quality, but the epigenetic regulation with respect to lncRNAs and circRNAs remains largely unknown. Here, we employed porcine oxidative and glycolytic skeletal muscles, at growth curve inflection point, to survey variant global lncRNAs and circRNAs expression using RNA-seq. In total, we obtained 540 million raw reads approximately 81.02 Gb of high quality data. After a strict filtering process, 4,046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including oxidation-reduction process, glycolytic process, fatty acid metabolic, PPAR signaling pathway, which are closely related to the different phenotypes between oxidative and glycolytic muscles. Additional, we also identified 810 circRNAs, 137 of them were differentially expressed (p < 0.05). The host genes of circRNAs were related to motor activity, transition between fast and slow fiber and ATP metabolic process by function enrichment analysis. Interestingly, we found circRNA290-miR27b-Foxj3 and circRNA9210-miR-23a-MEF2C taken as two competing endogenous network, which was closely linked to muscle fiber-type switching. circRNA41-miR-217-SIRT1 network was connected with mitochondria biogenesis in muscle. Furthermore, we found 44.69%, 39.19% and 54.01% of differentially expressed mRNAs, lncRNAs and circRNAs were siginificantly enriched pig QTL regions (traits of meat quality and growing development), respectively. Togeter, this study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological function, which improve understanding of muscle metabolism and development from epigenetic perspectives.

overall_design: lncRNA profiles of porcine oxidative and glycolytic skeletal muscles were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 4000.

first: Mailin

last: Gan

first: Zhengdong

last: Tan

first: Xiao

last: Cheng

first: Dongmei

last: Jiang

first: Guoqing

last: Tang

first: Yanzhi

first: Mingzhou

last: Li

first: Xuewei

first: Shunhua

last: Zhang

first: Li

last: Zhu


title: Twist1-Haploinsufficiency Selectively Enhances the Osteoskeletal Capacity of Mesoderm-derived Parietal Bone through Downregulation of Fgf23

status: Public on Sep 15 2018

city: Stanford

first: Natalina

last: Quarto

address: 257 Campus Drive

department: Surgery - Plastic and Reconstructive Surgery

institute: Stanford University School of Medicine

summary:
Purpose: This study investigates the postnatal impact of Twist1 haploinsufficiency on the osteoskeletal ability and regeneration on two calvarial bones arising from tissues of different embryonic origin: the neural crest-derived frontal and the mesoderm-derived parietal bones.
Results: Twist1 haplonsufficiency selectively enhanced osteogenic and tissue regeneration ability of mesoderm-derived parietal bones. Twist1 haplonsufficiency triggers its selective activity on mesoderm-derived parietal bone through downregulation of the bone-derived hormone Fgf23.
Conclusions: Twist1 haploinsufficiency preferentially triggers osteogenic induction of parietal bones which may be beneficial to optimize treatments for skeletal regeneration, reconstruction and repair of mesoderm-derived bone, as well as to alleviate skeletal abnormalities caused by Twist1 haploinsufficiency.

overall_design: Total RNA profiles of 21-day old wild type (WT) and Twist1+/- mice were generated by sequencing using Illumina NextSeq.

first: Siny

last: Shailendra

first: Nathaniel

last: Meyer

first: Siddharth

last: Menon

first: Andrea

last: Renda

first: Michael

last: Longaker


title: Repli-seq profile from resting (G0) and cycling (S) phase untreated B cells

first: Andre

last: Nussenzweig

summary: In this study, we map sites of replication initiation and breakage in primary cells at high resolution under conditions of replication stress.  We show that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(dA:dT) tracts flanking the initiation site. Paradoxically, large (>20 bp) homopolymeric (dA/dT) tracts are also preferential sites of polar replication fork stalling and collapse. We propose that the evolutionary expansion of poly(dA:dT) tracts in eukaryotic genomes serves to promote replication initiation, but at the cost of increasing chromosome fragility.

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

last: Fu

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt

first: Yan

last: Jaszczyszyn

first: Mirit

last: Aladjem

first: Peter

last: Aplan

first: Olivier

last: Hyrien


title: Effects of light-at-night on the rat liver - a role for the autonomic nervous system (Experiment 2)

first: Anne-Loes

last: Opperhuizen

overall_design: Male Wistar rat liver samples were used for microarray analysis. Two experiments are included in this project, the data of the experiments are submitted seperately. The current experiment consists of three experimental animal groups that received an hepatic denervation of the autonomic nervous system (sympathetic (Sx, n=5), parasympathetic (Px, n=5) or total denervation (Tx, n=5)) and two control groups (Sham denervation (n=5), Intact (n=4)).

first: Ewout

last: Foppen

first: Martijs

last: Jonker

first: Paul

last: Wackers

first: Martijn

last: van Faassen

first: Michel

last: van Weeghel

first: Linda

last: van Kerkhof

first: Eric

last: Fliers

first: Andries

last: Kalsbeek


first: Andre

last: Nussenzweig

overall_design: Nascent RNA profile in B, and T cells untreated and upon HU treatment.

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela


title: Effects of light-at-night on the rat liver - a role for the autonomic nervous system

first: Anne-Loes

last: Opperhuizen


title: Effect of PDZ domain binding Kinase inhibition using TOPK-32 (called PBKi) on C4-2 cell transcriptome

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Analysis of C4-2 prostate cancer cell line after 6 hrs of treatment with TOPK-32. PBK is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of PBK in prostate carcinogenesis.

overall_design: This experiment was designed to understand the regulation of transcriptome by PDZ domain binding kinase, which is an important kinase with role in cell cycle. The cells were treated with a catalytic inhibitor TOPK32 which inhibits the kinase activity of PBK protein.

first: Mohammad

last: Asim

first: Charlie

last: Massie

first: Suraj

last: Menon


title: Effect of PBK knockdown on C4-2 cell transcriptome

summary: Analysis of C4-2 Prostate cancer cell line after 72 hours of knockdown. PBK is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of PBK in prostate carcinogenesis.

overall_design: This experiment was designed to understand the regulation of transcriptiome by PDZ domain binding kinase (PBK), which is an important kinase with role in cell cycle. In order to achieve this, the endogenous protein was knocked down using siRNA pool that targets the PBK mRNA.


title: mTORC1/2 inhibition re-sensitizes platinum-resistant ovarian cancer by disrupting selective translation of DNA damage and survival mRNAs

status: Public on Jul 31 2018

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

type:
Expression profiling by array
Other

summary: Using platinum-resistant OVCAR-3 cells treated with the selective mTORC1/2 inhibitor INK128/MLN128, we conducted genome-wide transcription and translation studies and analyzed the effect on cell proliferation, AKT-mTOR signaling and cell survival, to determine whether carboplatin resistance involves selective mRNA translational reprogramming, and whether it is sensitive to mTORC1/2 inhibitio.n

overall_design: Polysome profiling using OVCAR-3 cells treated with INK128, carboplatin, or carboplatin + Ink128 compared to control DMSO treated cells

last: Ernlund

first: Gizelka

last: David-West


title: Identification of kidney transplant patients at risk for cutaneous squamous cell carcinoma by differentially methylated regions in T cells (II)

status: Public on Jul 13 2018

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

institute: Amsterdam UMC (AMC)

type: Methylation profiling by genome tiling array

summary:
We aim to discover differentially methylated regions (DMRs) in peripheral T cells involved in de novo cSCC development after kidney transplantation. This was a retrospective study on biobank patient material.
We matched kidney transplant patients with (future) cSCC to those without cSCC and studied genome-wide DNA methylation (450k arrays) of T cells after transplantation but prior to the clinical onset of the first cSCC.

overall_design: Pure T cell samples of 38 patients were analyzed. No replicates are included, all samples are unique. Kidney transplant patients with a (future) cSCC were matched to control kidney transplant patients without cSCC.