title: NUGC3 cells treated with siVGLL1

status: Public on Apr 20 2019

city: Daejeon

first: Bo-Kyung

last: Kim

address: Kwahag-ro

institute: KRIBB

summary: VGLL1 is involved in the regulation of proliferation and metastasis in gastric cancer cells and in vivo mouse models. To understand the downstream regulation of VGLL1, we conducted a microarray analysis of VGLL1 siRNA-treated NUGC3 cells.

overall_design: NUGC3 cells were treated with 20nM siSC or siVGLL1 for 48h.

first: B

middle: K


title: Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids [15°C]

status: Public on May 04 2019

city: Düsseldorf

first: Heidrun

middle: Sigrid

last: Windisch

state: NRW

address: Universitätsstrasse 1

department: Cell Biology and Zoology

country: Germany

institute: Heinrich-Heine-University

type: Expression profiling by high throughput sequencing

summary: The availability of polyunsaturated fatty acids (PUFAs) in food items influences the fitness of organisms at higher trophic levels. Omega 3 and omega 6 fatty acids are essential compounds that cannot be synthesised de novo in these animals. Especially the omega 3 PUFA eicosapentaenoic acid (EPA) is an important molecule, as it is a limiting nutritional component for growth and reproduction in numerous marine and freshwater zooplankton species. With our transcriptomic study in Daphnia magna we address the transcriptomic network behind the metabolism and conversion that is connected to physiological EPA-limitation under temperature stress (20°C vs. 15°C).

overall_design: We conducted a feeding experiment in Daphnia magna with strictly controlled diets to address EPA-dependent expression profiles. Two different EPA-free basis food sources were used in the experiment: the green alga (GA) Acutodesmus obliquus and the Cyanobacterium (CY) Synechococcus elongatus. The PUFA EPA was added via liposomes to half of the experimental groups fed with GA or CY to provide a comparable design for monitoring effects of EPA availability. In addition, we also monitored Daphnia magna fed with Cryptomonas ssp. (CRY), serving as a natural positive control (contains naturally EPA). We analysed animals that were exposed to the defined food conditions from hatch until they reached maturity. In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 mature specimens to ensure appropriate amounts for RNA extraction and comparability. Using the Illumina HiSeq 4000 platform in paired-end mode we gathered ~ 52.9 million reads per single replicate for transcriptomic analyses.

middle: S

first: Patrick

last: Fink


title: RNA-seq of the roots of Arabidopsis thaliana plants growing in  soil treated under different fertilization regimes.

status: Public on Apr 06 2019

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

country: USA

institute: The University of North Carolina at Chapel Hill

summary: This study evaluates the transcriptome of 3 Arabidopsis thaliana genotypes (Col-0, phf1 and phr1/phl1)  growing in soil treated under a gradient of fertilization regimes.

overall_design: Each of the three Arabidopsis genotypes was grown in soil from all 18 plots (6 plots per P treatment). In addition, a 4th P regimen designated ‘Low+P’ was created by adding additional P to a set of pots with low P. The amount of P added to these pots is based on the difference in total P between Low and High P plots. The average difference between Low and High P over all the plots is 42 mg P per kg soil [41]. Per pot, this is 12.6 mg P (accounting for 300 g soil per pot). Thus, a 10 ml solution consisting of 4.2 mg P in the form of 20% K2HPO4 and 80% KH2PO4 was added to the pots in 3 applications (Week 2, 4 and 6) before watering (in order to distribute the P through the soil).

first: Omri

last: Finkel

first: Gabriel

last: Castrillo

first: Jeff

last: Dangl


title: The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response

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

overall_design: Refer to individual Series


title: Time series RNA-seq analyses of Drosophila S2R+ cells after insulin stimulation

status: Public on Apr 04 2019

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary:
Purpose: identifying genes  responding to insulin stimulation in S2R+ cells  through whole transcriptome RNA-seq analyses
Methods: Total RNA was extracted from S2R+ cells using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries were constructed with  Illumina TruSeq  mRNA Library Prep Kit  , libraries were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center).
Results: Using an time series data analysis workflow incorporating polynormials , we identified 1254 temproally differentially expressed genes responding to insulin stimulation in the S2R+ cells.

overall_design: the pre-starved S2R+ cells ( with serum free medium) were stimulated with insulin; triplicate samples were collected at basline and every 20minutes time interval up to three hours; transcriptome profiling

first: Xiaochun

last: Ni

first: Martha

middle: L

last: Bulyk

first: Jonathan

last: Zirin

first: Norbert

last: Perrimon


title: Transcriptional responses of expressing Drosophila melanogaster IRP1A alleles in the prothoracic gland

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 116th Street and 85th Avenue

department: Biological Sciences

country: Canada

institute: University of Alberta

summary: We report the genome-wide profiling of hand-dissected ring glands that expressed one of the six flag-tagged transgene: IRP1AWT and IRP1BWT, which are both wild-type; IRP1AC450S and IRP1BC447S, both of which can only assume the apo-form; as well as IRP1A3R3Q and IRP1B3R3Q, both of which are presumed to be non-RNA-binding

overall_design: Genome-wide profiling of 40 hours after L2/L3 molting ring gland in Drosophila melanogaster larvae were generated with two replicate per condition

first: Huynh

last: Nhan

first: King-Jones

last: Kirst


title: RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a 185-members bacterial synthetic community under full and low phosphate conditions

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings growing in the presence of a 185-member bacterial SynCom under different phosphate availability

overall_design: Arabidopsis seeds (wild-type Col-0) were germinated on Johnson medium containing 0.5 % sucrose with 1 mM Pi (in the form of KH2PO4) for 7 days in the vertical position. Plants were then transferred to 50 µM Pi (low) or 1000 µM (High)


title: Ascorbic acid–induced TET activation mitigates adverse hydroxymethylcystosine loss in renal cell carcinoma

status: Public on Apr 03 2019

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: Although clear cell renal cell carcinoma (ccRCC) has been shown to result in widespread aberrant cytosine methylation and loss of 5-hydroxymethylcytosine (5hmC), the prognostic impact and therapeutic targeting of tis epigenetic aberrancy has not been fully explored. Analysis of 576 primary ccRCC samples demonstrated that loss of 5hmC was significantly associated with aggressive clinicopathologic features and was an independent adverse prognostic factor. Loss of 5hmC alsopredicted reduced progression-free survival after resection of nonmetastatic disease. The loss of 5hmC in ccRCC was not due to mutational or transcriptional inactivation of ten eleven translocation (TET) (4. AUTHOR: TET also appears as Tet.  If these mean the same thing, choose one style to use throughout.) enzymes, but to their functional inactivation by l -2-hydroxyglutarate (L2HG), which was overexpressed due to the deletion and underexpression of L2HG dehydrogenase(L2HGDH). Ascorbic acid (AA) reduced methylation and restored genome-wide 5hmC levels via TET activation. Fluorescence quenching of the recombinant TET-2 protein was unaffected by L2HG in the presence of AA. Pharmacologic AA treatment led to reduced growth of ccRCC in vitro and reduced tumor growth in vivo, with increased intratumoral 5hmC. These data demonstrate that reduced 5hmC is associated with reduced survival in ccRCC and provide a preclinical rationale for exploring the therapeutic potential of high-dose AA in ccRCC.

overall_design: We studied cytosine methylation patterns in 2 control and 4 AA-treated RCC cells.

first: Kith

last: Pradhan

first: Niraj

last: Shenoy


title: High throughput sequencing analyzes small RNA profile alteration in the exosomes from lung cancer patients and healthy controls

status: Public on Mar 14 2019

city: Beijing

first: Hua

last: Fang

address: Xicheng district Fu Xing Men Wai Da Jie No.20

department: Department of Oncology

country: China

institute: Fu Xing Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to compare the small RNA expression profiles in the peripheral exosomes and try to find biomarkers for early diagnosis of lung adenocarcinoma
Methods: Exosome was extracted from peripherial blood samples from 5 patients with lung adenocarcinoma and 5 healthy controls. RNA was extracted and microRNA profile was analyzed by high througput sequencing.
Results: The expression of 5 microRNAs was found significantly altered in patients with lung adenocarcinoma

overall_design: Examination of peripheral blood exosome microRNAs from 5 patients with lung adenocarcinoma and 5 healthy controls


title: The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

status: Public on Mar 11 2019

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

country: United Kingdom

institute: Imperial College

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Escherichia coli
Thermoplasma acidophilum
synthetic construct


title: Transcription factors IRF8 and PU.1 are required for follicular B cell development and BCL6-driven germinal center responses

status: Public on Mar 30 2019

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: The IRF and Ets families of transcription factors regulate the expression of a range of genes involved in immune cell development and function. However, the understanding of molecular mechanisms of each family member has been limited due to their redundancy and broad effects on multiple lineages of cells.  Here, we report that double deletion of floxed Irf8 and Spi1 (encoding PU.1) by Mb1-Cre (designated DKO mice) in the B cell lineage resulted in severe defects in the development of follicular and germinal center (GC) B cells. Class switch recombination and antibody affinity maturation were also compromised in DKO mice. RNA-seq and ChIP-seq analyses revealed distinct IRF8 and PU.1 target genes in follicular and activated B cells. DKO B cells had diminished expression of target genes vital for maintaining follicular B cell identity and GC development. Moreover, our findings reveal that expression of BCL6, which is critical for development of germinal center B cells, is dependent on IRF8 and PU.1 in vivo, providing a mechanism for the critical role for IRF8 and PU.1 in the development of GC B cells.

overall_design: ChIP-Seq analyses using naïve FO B cells,with rabbit IgG, anti-IRF8, anti-PU.1, anti-H3K27Ac. RNA-Seq analyses using total RNA from FACS-purified FO B cell of WT and DKO mice.

first: Hongsheng

last: Wang

first: Shweta

last: Jain

first: Jian-Xin

last: Lin

first: Jangsuk

last: Oh

first: Chenfeng

last: Qi

first: Yuanyuan

last: Gao

first: Jiafang

last: Sun

first: Tomomi

last: Sakai

first: Zohreh

last: Naghashfar

first: Sadia

last: Abbasi

first: Alexander

last: Kovalchuk

first: Silvia

last: Bolland

first: Stephen

last: Nutt

first: Warren

middle: J

last: Leonard

first: Herbert

middle: C

last: Morse III


title: The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

first: Tobias

last: Warnecke

summary: We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

overall_design: Examination of Mnase digestion products along the course of T.acidophilum growth phase

first: Antoine

last: Hocher


title: H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles [ChIP-Seq - muscle]

status: Public on Mar 08 2019

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: The histone variant H2A.Z is enriched in nucleosomes surrounding the transcription start site of active promoters, suggesting that it might be implicated in transcription. It is also required during mitosis. However, evidences obtained so far mainly rely on correlative evidences obtained in actively dividing cells. We have defined a paradigm in which cell cycle cannot interfere with H2A.Z transcriptional studies by developing an in vivo systems to invalidate H2A.Z in terminally differentiated post-mitotic muscle cells to dissociate its role during transcription from its role during mitosis. ChIP-seq, RNA-seq and ATAC-seq experiments performed on H2A.Z KO post-mitotic muscle cells show that this histone variant is neither required to maintain nor to activate transcription. Altogether, this study provides in vivo evidence that in the absence of mitosis H2A.Z is dispensable for transcription and that the enrichment of H2A.Z on active promoters is rather a marker than an actor of transcriptional activity.

overall_design: We analyze by ChIP-seq assay the genome-wide distribution of H2A.Z in muscle cells.

first: Edwige

last: Belotti

first: Nicolas

last: Lacoste

first: Thomas

last: Simonet

first: Kiran

last: Padmanabhan

first: Lorrie

last: Ramos

first: Defne

last: Dalkara

first: Isabella

last: Scionti

first: Ali

last: Hamiche

first: Stefan

last: Dimitrov

first: Laurent

last: Schaeffer


title: H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles [RNA-Seq - muscle]

overall_design: To address the effect of H2A.Z on both basal and activated transcription, we have used both skeletal muscle isolated from innervated and denervated control WT and H2A.Z null 7 weeks-old animals. Denervation was carried out by ablation (cutting) of the sciatic nerve of one hind mouse leg. The other hind leg (innervated) was used as a control. RNA-seq was carried out from 3 biological replicates isolated from both innervated and denervated skeletal muscles (tibialis).


title: The role of archaeal histones in gene expression - a synthetic biology perspective

sample_organism:
Escherichia coli
Methanothermus fervidus


title: The role of archaeal histones in gene expression - a synthetic biology perspective [Methanothermus fervidus]

summary: Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription.  Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription.

overall_design: Correlation between genome-wide occupancy of the archaeal histones HMfA and HMfB in E.coli and transcriptional changed triggered by their expression, coupled with comparison between the histones' binding patterns in Methanothermus fervidus and E. coli.

first: Maria

last: Rojec


title: The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)


title: Analysis of MLLT3 genomic distribution and related chromatin features in uncultured fetal liver hematopoietic stem-progenitor cells [ChIPseq_MLLT3_OE]

status: Public on Mar 06 2019

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

summary: MLLT3 binds to TSS of genes active in FL-HSPC

overall_design: Sorted HSPC from 4 weeks cultured cells were sorted and crosslinked. MLLT3 V5 K4me3 K36me3 K79me2 were immunoprecipitated from sonicated chromatin (100,000-200,000 cells per IP) DNA was amplified with Nugen Ovation V2 kit and sequenced in single end 50bp in multiplexed run on an Illumina HiSeq4000 instrument.

first: Andrew

middle: T

last: Nguyen

first: Timothy

last: Bolan

first: Yanling

last: Wang

first: Fides

middle: D

last: Lay

first: Mattias

last: Magnusson

first: Siavash

last: Kurdistani

first: Hanna

last: Mikkola


title: Analysis of MLLT3 genomic distribution and related chromatin features in uncultured fetal liver hematopoietic stem-progenitor cells [ChIPseq_FL_HSPC]

overall_design: MLLT3 K4me3 K9ac K79me2 Pol2 were immunoprecipitated from sonicated chromatin (50,000-200,000 cells per IP) DNA was amplified with Nugen Ovation V2 kit and sequenced in single end 50bp in multiplexed run on an Illumina HiSeq4000 instrument.


title: Dietary intake regulates the circulating pro-inflammatory monocyte pool

status: Public on Feb 22 2019

city: New York

last: Jordan

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Caloric restriction is considered to be anti-inflammatory. In this study we examined the effect of fasting on peripheral leukocyte populations. We found that short-term fasting affects metabolic and pro-inflammatory activity of monocytes and decreases numbers of circulating monocytes. For this study, we sorted hepatocytes from fed and fasted mice, monocytes from bone marrow from fed and fasted mice, and monocytes from bone marrow from wildtype and Ccr2-deficient mice.

overall_design: 39 samples; 2-4 replicates per condition

first: Navpreet

last: Tung

first: Samuel

last: Rose

first: Christie

last: Chang

first: Miriam

last: Merad


title: RNA sequencing of isogenic BRCA2 haploinsufficient vs. wild-type T-ALL cells

status: Public on Feb 20 2019

first: Alejandro

last: Gutierrez

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: We found a high frequency of heterozygous Fanconi-BRCA pathway mutations in pediatric T-ALL.  BRCA2 was the most commonly mutated gene.  We transduced Cas9-expressing Jurkat cells, which lacked an identifiable BRCA2 mutation, with an integration-defective lentiviral guide RNA expression construct targeting exon 11 of BRCA2 (NM_000059).  Single-cell cloning and sequencing analysis revealed two distinct clones harboring monoallelic BRCA2 frameshift mutations, termed clones W4 and W5.  Each of these clones was subjected to RNA sequencing analysis.

overall_design: RNA sequencing was performed on 2 independent BRCA2 haploinsufficient Jurkat clones and 2 controls (parental and Cas9-transduced) Jurkat clones, using paired end 75 bp reads on an Illumina NextSeq 500 instrument.

first: James

last: Degar


title: Single-nucleotide resolution profiling of N6-methyladenosine in SETD2 knockdown HepG2 cells [m6A miCLIP-seq]

status: Public on Feb 21 2019

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 knockdown and control HepG2 cells by miCLIP-seq, and found the depletion of H3K36me3 by SETD2 silencing globally reduced m6A in the human transcriptome.

overall_design: miCLIP-seq in HepG2 cells with stable expressed SETD2 or non-specific control shRNAs.

first: Huilin

last: Huang

first: Hengyou

last: Weng

first: Keren

last: Zhou

first: Tong

last: Wu

first: Chuan

last: He

first: Jianhua

last: Yang


title: Analysis of chromatin accessibility in uncultured fetal liver hematopoietic stem-progenitor cells and upon MLLT3 overexpression [ATACseq]

first: Vincenzo

last: Calvanese

summary: MLLT3 binds to open gene TSS

overall_design: Nuclei from 50,000 cells were tagmented and fragments were amplified and sequenced in a paired end run on HiSeq2500

first: Andrew

last: Nguyen

first: Timothy

last: Bolan

first: Yanling

last: Wang

first: Fides

last: Lay

last: Magnusson


title: Novel mutations segregating with Complete Androgen Insensitivity Syndrome and their molecular characteristics.

status: Public on Feb 18 2019

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: We analysed three interesting, rare cases of CAIS (Complete Androgen Insensitivity Syndrome) and report three hitherto undisclosed causes of the disease. Comparative RNA-Seq analysis of CAIS and control samples (3 testicular oligobiopsies from men with normal spermatogenesis) revealed 4,293 significantly deregulated genes.

overall_design: The comparative analysis of gene expression profiles by RNA-Seq between individuals with CAIS (n=3) and control (men with normal spermatogenesis) (n=3)

first: Malcher

last: Agnieszka

first: Kurpisz

last: Maciej


title: Gene expression analysis of SJG6 CONTROL and NICD

status: Public on Mar 05 2019

first: Vasiliki

last: Salameti

address: Great Maze pond, Guy's Hospital, 28th Floor

department: CSCRM

institute: King's College London

summary: Mutational landscape of Oral Squamous Cell Carcinoma (OSCC) is predominated by frequent inactivating mutations in EGF- like ligand binding domain of NOTCH1. However role of NOTCH1 signalling in tumorigenesis is highly context and cell type dependent. In this study, we investigated phenotypic effect of NOTCH1 mutations in primary line derived from OSCC biopsy. Based on gain-of-function assays in NOTCH1 mutant line we demonstrated regulation of cell behaviour and morphology, by NOTCH1 intracellular domain (NICD) leading to changes in cell proliferation, migration, clonal growth and differentiation. Importantly, overexpression of NICD results in upregulation of ETV7/TEL2 which negatively regulates SERPINE1 expression and confers malignant cells with less aggressive phenotype. Further knockdown of SERPINE1 expression simulated the phenotypes observed upon rescue of NICD. In accord with our cell-based model we observed strong correlation between NOTCH1, ETV7 and SERPINE1 expression  in OSCC primary tumours indicating similar deregulated mechanisms during oral carcinogenesis. Overall this study suggests a tumour suppressive role of NOTCH1 in OSCC and highlights possible mechanisms leading to changes in cell behaviour and morphology in absence of NICD potentially by regulating TEL2 and SERPINE1 expression.

overall_design:
A lentiviral system was used to restore active domain of NOTCH1 (NICD) in the SJG6 line carrying a truncating mutation (here-on referred to as SJG6 + NICD). Gene Expression Profiling of SJG6 CONTROL and SJG6 NICD was performed to delineate candidate gene/s clusters deregulated in response to NICD expression.
Affymetrix one-color experiment,Organism: Human ,Affymetrix Human Gene 1.0 ST Array , Labeling kit: Affymetrix GeneChip Kit

first: Fiona

last: Watt

first: Vassia


title: Genome-wide study of the role of the histone demethylase dLsd1 in oogenesis

status: Public on Feb 08 2019

city: Toulouse Cedex 9

first: Luisa

last: Di Stefano

state: France

address: LBCMCP - CNRS UMR5088 -  IFR 109  Bât 4R3-B1 118 route de Narbonne

institute: Université Paul Sabatier - Toulouse III

summary: The histone demethylase LSD1 is a key chromatin regulator that plays a crucial role in development. It has been shown to act both as a co-repressor and a co-activator of genes expression and to affect the expression of many genes important for development. In Drosophila, dLsd1 is essential for oogenesis; however, our current knowledge of dLsd1 function is insufficient to explain its precise role in the ovary. To better define the role of dLsd1 in oogenesis, we performed genome-wide analysis of dLsd1 binding in the ovary by Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq).

overall_design:
ChIP-seq profiles of dLsd1 binding in young wild type (w1118) ovaries were generated by deep sequencing in triplicate.

The ChIP-seq antibody was generated in the Dyson team in Boston [PMID 17462898]


title: Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps [ATAC-seq]

status: Public on Feb 14 2019

city: Santa Ana

first: Camden

last: Jansen

state: California

address: 10631 Rockhurst Ave

institute: UCI

summary: We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.

overall_design: We use the C1 Fluidigm system to profile gene expression and chromatin accessibility in single-cells during pre-B cell differentiation.

first: Ricardo

middle: N

last: Ramirez

first: Ali

last: Mortazavi


title: Expression pattern in dSG knockout mutant mice and effect of treatment with ifetroban

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

institute: Vanderbilt University

summary: We sequenced RNA from left ventricle of dSG knockout and wild type mice treated with vehicle or ifetroban

overall_design: RNASeq of left ventricle tissue from dSG knockout vs wild type mice, each  treated with vehicle or ifetroban


title: Gene expression data from murine bone-marrow osteo and adipo progenitor cells

status: Public on Feb 28 2019

city: Odense

first: Moustapha

last: Kassem

address: JB Winsløwsvej 25.1

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark

summary: To identify the molecular mechanism determining the lineage commitment of bone-marrow progenitors, we compared basal gene expression profiles of progenitors committed to adipogenic or osteogenic lineages. We characterize several differentially expressed metabolic and signalling pathways.

overall_design: Two clonal cell lines were cultured in triplicates under standard culture conditions. Pooled samples were prepared for microarray analysis.

first: Hanna

last: Taipaleenmäki

first: Bassem

middle: M

last: Abdallah

first: Michaela

last: Tencerova

first: Anders

last: Haakonsson


title: Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model

status: Public on Jan 07 2019

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

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

overall_design: Refer to individual Series


title: Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model [RRBS]

summary: We have recently developed a nonhuman primate (NHP) model to address the effects of hyperandrogenemia (modestly elevated testosterone; T), a high-fat, obesogenic Western-style diet (WSD), or combined T+WSD. To address the molecular mechanisms underlying adipocyte dysfunction, visceral adipose tissue biopsies were analyzed for whole-genome gene expression and DNA methylation, using RNA-seq and reduced-representation bisulfite sequencing (RRBS), respectively.  We show that the combination of T + WSD induces a significantly stronger transcriptional response than T or WSD alone, including regulation of genes whose expression is altered in adipose tissue of PCOS women. Gene expression patterns indicate alterations in cAMP, LXR/RXR, HIPPO, Wnt signaling and eicosanoid and retinol biosynthesis pathways.  Analysis of DNA methylation shows that genes from the cAMP signaling pathway are also differentially methylated in T +WSD, which also globally resulted in a greater number of differentially methylated regions (DMRs) than T or WSD alone. Collectively, our results show that hyperandrogenemia and WSD exhibit synergistic effects on the visceral adipose tissue transcriptome and methylome, resulting in activation of biological processes that may contribute to the adipose tissue dysfunction characteristic of PCOS.

overall_design: White Adipose Tissue biopsies from four experimental groups of rhesus macaques (control, testosterone, western style diet, and testosterone + western style diet) of 6 replicates per group, subjected to whole transcriptome analysis and reduced representation bisulfite sequencing.

first: Lucia

last: Carbone

middle: A

first: Oleg

last: Varlamov


title: sequencing data from control and PTEN-deficient mouse brain microvascular transcriptomes

first: Jun

last: Wang

address: 20 Dongdajie

institute: Beijing Institute of Lifeomics

summary: Expression profiling of control and PTEN deficient cerebrovascular endothelial cells by high throughput sequencing.

overall_design: Identification of genes and signaling pathways regulated by PTEN in adult brain endothelial cells.

first: Yaxiong

last: Cui

first: Zhenyang

last: Yu

first: Wen-Jing

first: Wenliang

last: Ji

first: Qing

last: Zhou

first: Yan

last: Chen

first: Hui

last: Jiang

first: Huanming

last: Yang

first: Weixiang

last: Guo

first: Xiao


title: Single-cell multi-omic integration compares and contrasts features of brain cell identity

city: Cambridge

first: Evan

last: Macosko

state: Ma

address: 75 Ames St, Broad Institute

institute: Broad Institute

summary: To flexibly model single-cell datasets, we developed LIGER, an algorithm and software package that delineates shared and dataset-specific features of cell identity.  We applied it to four diverse and challenging analyses of human and mouse brain cells, the first two of which include newly generated single-cell transcriptome datasets for mouse and human regions. First, we determined region-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis (BNST). Second, we analyzed expression in the human substantia nigra (SN), integrating cell types across donors, and relating cell types to those in the mouse (using mouse SN data from Saunders et al., 2018 (GEO: GSE116470)). The main cell types identified include neurons, astrocytes, microglia, oligodendrocytes, polydendrocytes, and endothelial cells. Third, we jointly leveraged in situ and single-cell expression data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we integrated mouse cortical single-cell RNA-seq and DNA methylation profiles, revealing mechanisms of cell-type-specific gene regulation. Integrative analyses using LIGER promise to accelerate investigations of cell-type definition, gene regulation, and disease states.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single nuclei were extracted and isolated from 1mm biopsy punches from the BNST of 15 mouse brains (8 male and 7 female replicates), and sequenced using the 10X Chromium system (V3). In total, 204,737 BNST nuclei were recovered. Single nuclei were extracted and isolated from manually dissected samples of the SN of seven de-identified postmortem human donors, and sequenced using the 10X chromium system (V2). In total, 44,274 SN nuclei were recovered.

first: Joshua

last: Welch

first: Velina

last: Kozareva

first: Ashley

last: Ferreira

first: Charles

last: Vanderburg

first: Carly

last: Martin


title: Deciphering cis-regulatory logic with 100 million synthetic promoters (MNase)

status: Public on Jan 01 2019

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

summary: In order to test our model of gene regulation, we measured nucleosome occupancy of our random promoter library using Mnase-seq.

overall_design: The pTpA library was grown in glucose (YPD), with four different replicates.

first: Ronen

last: Sadeh


title: Gene expression data comparing Wilms tumor primary samples to patient-derived xenografts

city: Memphis

first: Tong

last: Lin

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

summary: The lack of model systems limits the preclinical testing of novel therapies to address Wilms tumor patient groups with poor outcomes. Therefore, we established 45 heterotopic Wilms tumor patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). These WTPDX include six showing diffuse anaplasia, nine from patients who went on to experience disease relapse, and thirteen from patients with bilateral disease. WTPDX retained the genetic alterations and the global transcriptomic and methylation profile of corresponding primary WT. In addition, favorable histology WTPDX were chemosensitive, while unfavorable histology WTPDX were resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool for the testing of novel targeted therapies in the era of precision medicine.

overall_design: Total RNA was extracted from 16 selected Wilms tumor patient-derived xenografts, 13 available corresponding primary tumor specimens, and three normal kidney specimens using the Qiagen RNeasy Midi kit (Qiagen, Hilden, Germany). Commercially available pooled total RNA from four human fetal kidneys was also included (Takara, Kusatsu, Japan).

first: Andrew

last: Jackson Murphy


title: Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model [RNA-Seq]

first: Brett

last: Davis

first: Lucia

last: Carbone

first: Oleg

last: Varlamov


title: Placenta-specific DMRs maintain methylation across gestation.

status: Public on Feb 05 2019

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

type: Methylation profiling by genome tiling array

summary: One possible mechanism leading to the apparent polymorphic placenta-specific DMRs would be the failure to maintain allelic methylation during gestation. For a temporal comparison, we performed methylation profiling on first trimester chorionic villus sampling (CVS) and compared it with corresponding samples at term. This revealed that DNA methylation level at placenta-specific DMRs is highly stable between the two points. In addition, to ensure that the methylation profiles were uniform across the placental plate, we determined the placenta-specific DMR profiles from multiple biopsies from the same term placentas. Biopsies collected from the opposite sides of the cord insertion site also showed high correlations, suggesting that methylation does not vary greatly between sampling sites. Finally, we compared placenta samples from dizygotic twins and triplets. As in the other cases, this revealed that the correlations between samples of the same gestations (sharing the same in utero environment and maternal exposures) were also higher than between unrelated samples.

overall_design: Bisulphite converted DNA from 12 human placenta samples (two pairs of first trimester CVS and samples at term, two pairs of opposite sides biopsies from the same term placentas, one pair of dyzigotic twin term placentas and one trio of triplet placenta samples) were hybridised to the Illumina Infinium HumanMethylationEPIC and HumanMethylation450 BeadChips.

first: Jose

middle: R

first: David

last: Monk


title: Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps [scRNA-Seq]

first: Camden

last: Jansen

first: Ricardo

last: Ramirez

first: Ali

last: Mortazavi


title: Sphingosine kinase 2 signaling modulates altered expression profile of host genome in a murine model of Pseudomonas aeruginosa pneumonia.

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

summary:
We present the set of pseudomonas responsive genes activated in the WT mice in comparison with Sphk2-/- thereby revealing the genes that could contribute to the protection seen in Sphk2-/- mice.
Methods: Lung mRNA profiles of 8 week old male wild-type (WT) and Sphingosine kinase 2 knock out (Sphk2−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two way ANOVA (ANOVA). qRT–PCR validation was performed using SYBR Green assays
Genetic deletion of Sphk2-/-resisted alteration of host pulmonary genome by PA infection of the lungs promoting its own virulence thereby conferring significant protection against PA pneumonia.

overall_design:
Age- and weight-matched male WT, Sphk1-/-, and Sphk2-/- mice were administrated a single intratracheal infusion of sterile PBS or PA103 in P (1x106 CFU/mouse). After 24 h of treatment,  lung tissue was collected.
Lung tissue was perfused with PBS prior to harvesting from the mice, and processed immediately after harvesting. Whole lung tissue was used to isolate total RNA using microRNeasy® kit (Qiagen, Maryland, Cat no. 74004).

last: Ebnezer

first: Panfeng

last: Fu

first: Anantha

last: Harijith

first: Viswanathan

last: Natarajan


title: Expression profiling of genes induced by atovaquone treatment

status: Public on Dec 21 2018

city: Boston

first: Michael

last: Xiang

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The drug atovaquone inhibits the mTOR pathway, as identified by western blotting to phospho-S6 and phospho-4E-BP1. However, this effect only occurs at longer time points (2-5 hours) and is blocked by cycloheximide or actinomycin D, demonstrating that de novo gene expression is required. To identify the factor upregulated by this drug, we performed gene expression profiling in two separate cell lines that respond to atovaquone.

overall_design: U266 cells were treated with vehicle (DMSO) or atovaquone (15 micromolar) for 2 hours. K562 cells were treated with vehicle or atovaquone (20 micromolar) for 5 hours. RNA was harvested by Trizol, further purified by RNeasy spin column, and then submitted to the Dana-Farber Cancer Institute Molecular Diagnostics Laboratory.

last: Frank


title: Downregulation of Cholinergic Receptor Alpha 5 (CHRNA5)  in MCF7 breast cancer cells

status: Public on Dec 16 2018

city: Ankara

first: Ozlen

last: Konu

address: Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

summary: Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5), an important susceptibility locus for nicotine addiction and lung cancer, is not well studied in breast cancer. In our study, CHRNA5 was transiently depleted in MCF7 cells and transcriptomic changes were compared to siRNA controls. We for the first time showed by microarray analysis that silencing of CHRNA5 in MCF7 breast cancer cells, downregulated genes involved in the cell cycle and proliferation while resulting in reduced cell viability, DNA synthesis and G1 growth arrest. In addition, simultaneous treatment of CHRNA5 siRNA and topoisomerase inhibitors showed an important role of CHRNA5 in increased drug sensitivity. Phalloidin stained CHRNA5 siRNA treated cells on the other hand exhibited a distinct cellular morphotype with increased cellular extensions and a transcriptome characterized by mixed expression of epithelial-mesenchymal genes. Through bioinformatics analysis of the public transcriptome data we demonstrated a strong positive association of expression signature of CHRNA5 RNAi with that of a differentiated cell as well as hormone starvation. Hence, our study implicates CHRNA5 as an antiproliferative differentiation marker in breast cancer.

overall_design: MCF7 cells were seeded in 6-well plates. After 24 h, cells were treated either with 10nM of siRNA against several CHRNA5 spliced variants (FlexiTube, SI03051111, Qiagen) or the respective negative controls (AllStars Negative Control siRNA, 1027280, Qiagen) using HiPerFect transfection reagent (301704, Qiagen). Treatments were performed for 72h (3 days) after which RNA was extracted. Experiments were performed using two biological replicas.  Affymetrix HGU133 Plus 2 platform was used for expression profiling of siRNA treated and corresponding siRNA control exposed MCF7 cells, according to the manufacturer’s protocols.

first: Ermira

last: Jahja

first: Huma

last: Shehwana

first: Sahika

last: Koker


title: RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures

status: Public on Dec 11 2018

city: Wageningen

first: Julien

last: Rougeot

state: Gerlderland

address: Droevendaalsesteeg 1  Building 107

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research

summary: We used different zebrafish transgenic lines to sort macrophages, neutrophils and immature lymphoid cells from 5-6 day old zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature.

overall_design: For infection experiments, zebrafish embryos were manually dechorionated at 24 hours post fertilization (hpf) and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) was added after 1 day to prevent melanisation. After the incubation period, embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis, amplification and library preparation were performed as previously described. (Rougeot et al., 2014, Methods Mol Biol 1197:41-66).

first: Ania

last: Zakrzewska

first: Vincenzo

last: Torraca

first: Zakia

last: Kanwal

first: Hans

first: Herman

middle: P

last: Spaink

first: Annemarie

last: Meijer


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of armadillo repeat containing 12 (ARMC12)

status: Public on Nov 30 2018

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of a public microarray dataset, we identified armadillo repeat containing 12 (ARMC12) as a novel ARM member associated with the progression of NB. To investigate the mechanisms underlying the oncogenic functions of ARMC12, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of ARMC12. The results showed that stable over-expression of ARMC12 led to altered expression of 6125 human mRNAs, including 2901 up-regulated genes and 3224 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, invasion, and metastasis by bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to ARMC12 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Total RNA of cells stably transfected with empty vector or ARMC12 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: Deciphering cis-regulatory logic with 100 million synthetic promoters

first: Carl

last: de Boer

summary: In order to generate data suitable to decipher cis-regulatory logic, we generated ~100 million synthetic promoters (in yeast) comprised of random DNA and measured their expression by FACS (sorting into 18 bins).

overall_design: One such library (pTpA) was tested in glucose (YPD), galactose (YPGal), and glycerol (YPGly), the other (Abf1TATA) only in glucose. A separately constructed pTpA library of limited complexity was assayed separately, yielding higher quality expression measurements. A final library containing diverse promoter scaffolds was tested in glucose. The sequences flanking the random 80 bp oligo were as follows: the pTpA distal region was (pT) GCTAGCAGGAATGATGCAAAAGGTTCCCGATTCGAACTGCATTTTTTTCACATC and proximal region (pA) was GGTTACGGCTGTTTCTTAATTAAAAAAAGATAGAAAACATTAGGAGTGTAACACAAGACTTTCGGATCCTGAGCAGGCAAGATAAACGA (up to the theoretical TSS). For Abf1TATA, the distal region was GCTAGCTGATTATGGTAACTCTATCGGACTTGAGGGATCACATTTCACGCAGTATAGTTC and proximal was GGTTTATTGTTTATAAAAATTAGTTTAAACTGTTGTATATTTTTTCATCTAACGGAACAATAGTAGGTTACGCTAGTTTGGATCCTGAGCAGGCAAGATAAACGA. In both cases, 80 Ns were inserted in between proximal and distal regions. The scaffold library contained a variety of proximal and distal DNA fragments, and was grown in YPD. The Native80 and designed-sequence libraries were grown in YPD and used a strain of S288C with Ura3 deleted. All others used strain Y8205 (Boone Lab).


title: PLC-PRF-5 cells treated with sorafenib, sorafenib probe or DMSO

status: Public on Dec 12 2018

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

summary: We used an expression profiling chip to detect the expression profile of PLC cells after they were treated with sorafenib and sorafenib probe

overall_design: PLC-PRF-5 cells were treated with sorafenib (10 μM), sorafenib probe (10μM) or DMSO for 24 h. TRIzol Reagent (Invitrogen) was then used to lyse cells and extract the total RNA.

first: Weilong

last: Zhong


title: The aldosterone-induced transcriptome of isolated mouse collecting duct cells

status: Public on Nov 28 2018

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

summary: Analysis of collecting duct response to low NaCl or high NaCl diet at the gene expression level. Results provide insight into transcriptional changes in principal and intercalated cells that occur in response to changes in dietary NaCl.

overall_design: Total RNA obtained from collecting duct cells isolated from mice fed low NaCl or high NaCl diet for 5 days.

first: Elizebeth

last: Swanson

first: Jonathan

middle: W

last: Nelson

first: Kayla

last: Erspamer

first: Chao-Ling

last: Yang

first: Sophia

last: Jeng

first: Shannon

last: McWeeney


title: Bacterial sepsis triggers an antiviral response that causes translation shutdown

status: Public on Nov 16 2018

city: Indianapolis

first: Michael

middle: Thomas

last: Eadon

state: IN

address: 950 W. Walnut St R2 202

institute: Indiana University

summary: In response to viral pathogens, the host upregulates antiviral genes that suppress translation of viral mRNAs. However, induction of such antiviral responses may not be exclusive to viruses as the pathways lie at the intersection of broad inflammatory networks that can also be induced by bacterial pathogens. Using a model of Gram-negative sepsis, we show that propagation of kidney damage initiated by a bacterial origin ultimately involves antiviral responses that result in host translation shutdown. We determined that activation of the Eif2ak2-Eif2α axis is the key mediator of translation initiation block in late phase sepsis. Reversal of this axis mitigated kidney injury. Furthermore, temporal profiling of the kidney translatome revealed that multiple genes involved in formation of the initiation complex were translationally altered during bacterial sepsis. Collectively, our findings implicate that translation shutdown is indifferent to the specific initiating pathogen and is an important determinant of tissue injury in sepsis.

overall_design: Bulk 20 um thickness specimens from cross-sectional human kidney biopsies embedded in OCT underwent RNA sequencing. All subjects had ATN, AIN, or a mix of both conditions.

first: Eadon

last: Michael

first: Hato

last: Takashi


title: Gene expression profiling during adhesion formation induced by cecum cauterization

status: Public on Dec 07 2018

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: Abdominal adhesions form in response to peritoneal trauma that can occur during surgery. Postoperative adhesions, which develop in approximately 50-85% of patients who have undergone abdominal surgery, often result in severe complications, including intestinal obstruction, female infertility, chronic pain, and contraindication of surgery for future abdominal illnesses such as cancer. Here, we investigated the cell source of collagen production in postoperative adhesions and explored molecular mechanisms of adhesion using microarray.

overall_design: Transcriptional profiling of C57BL/6 mouse cecum tissues isolated at 3 different time points during adhesion formation, namely at 3 h, 12 h or 72 h after cauterization and the sham operation, was assessed using microarray analysis

first: Naoki

last: Uyama

first: Soichi

last: Kojima

first: Jiro

last: Fujimoto


title: Tomato gene expression profile in response to B. amyloliquefaciens CFCF

city: heraklion

first: Anastasia

last: Dimopoulou

state: Crete

address: Nikolaou Plastira 100

department: IMBB

country: Greece

institute: FORTH

summary: To elucidate the molecular and metabolic changes in tomato plants that occur by the interaction of tomato roots and MBI600 elicitors, fifteen-day-old tomato seedlings were transferred to liquid MS (2 seedlings/2mL of medium in wells of 24-well-plates) and after 3 hours the medium was supplied with MBI600 CFCF to 1/5 v/v volume or with flg22 peptide (Eurogentec) to a final concentration of 1μΜ. Seedlings were collected in different time points after treatment (6 and 24h). Three independent experiments were performed. Each experiment included 2 biological replicates per treatment and each replicate was a pool of two seedlings. Sixteen genes were selected and their transcript levels were tested by Real-Time qPCR. A pathway analysis was performed and the complex signaling network that is implicated in MBI600-host interactions was mapped. The coordinated expression of genes that participate in biosynthetic pathways or are responsive to auxin, JA/ET, SA and redox signalling of biotic and abiotic stress responses, suggests that PGPR elicitors and metabolites activate (non-specifically) plant defense.

overall_design: MBI600 elicitors induced gene expression in tomato seedlings was measured at 6 and 24 hours after exposure to water or flg22 or MBI600 CFCF. Two independent experiments were performed at each time (6 or 24 hours) using different plants for each experiment.

first: A

first: I

last: Theologidis

first: Nicholas

last: Skandalis


title: Factor cooperation for chromosome discrimination in Drosophila

status: Public on Dec 05 2018

city: Planegg-Martinsried

first: Christian

last: Albig

address: Großhaderner Strasse 9

department: Biomedical Center

institute: Ludwig-Maximilians-University Munich

summary: Transcription regulators select their genomic binding sites from a large pool of similar, non‑functional sequences. Although general principles that allow such discrimination are known, the complexity of DNA elements often precludes a prediction of functional sites. The process of dosage compensation in Drosophila allows exploring the rules underlying binding site selectivity. The male-specific-lethal (MSL) Dosage Compensation Complex selectively binds to some 300 X-chromosomal ‘High Affinity Sites’ (HAS) containing GA‑rich ‘MSL recognition elements’ (MREs), but disregards thousands of other MRE sequences in the genome. The DNA‑binding subunit MSL2 alone identifies a subset of MREs, but fails to recognize most MREs within HAS. The ‘Chromatin-linked adaptor for MSL proteins’ (CLAMP) also interacts with many MREs genome‑wide and promotes DCC binding to HAS. Using genome‑wide DNA‑immunoprecipitation we describe extensive cooperativity between both factors, depending on the nature of the binding sites. These are explained by physical interaction between MSL2 and CLAMP. In vivo, both factors cooperate to compete with nucleosome formation at HAS. The male‑specific MSL2 thus synergises with a ubiquitous GA‑repeat binding protein for refined X/autosome discrimination.

overall_design: ChIP-seq: ChIP-Seq of MSL2 and CLAMP in S2 cells treated with control, trl or clamp RNAi (3 biological replicates each); DIP-seq: DNA immunoprecipitation (DIP) of recombinant MSL2 and CLAMP after incubation with sheared genomic DNA from S2 cells (3 biological replicates each); ATAC-seq: ATAC-seq from S2 cells and Kc cells untreated (4 biological replicates each) or treated with control, msl2 or clamp RNAi (3 biological replicates each).

first: Silke

last: Krause

first: Catherine

last: Regnard

first: Peter

middle: B

last: Becker


title: Systematic evaluation of conditional gene essentiality changes across 4 yeast strains

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: The extent by which different genetic backgrounds affect conditional gene essentiality is understudied. Here, 4 whole-genome knockout libraries were screened to systematically record changes in conditional gene essentiality. Gene expression changes between the reference strain and the other three were measured to gain more knowledge on the molecular determinants of these changes.

overall_design: A total number of 8 samples were analysed, each one in triplicate. The 8 total samples included the four strains grown in two different conditions; regular media and in exposed to 20mM of Caffeine for 4 hours. All samples were harvested when cultures reached O.D. of 0.4.

first: Bede

last: Busby

first: Marco

last: Galardini

first: Ferris

last: Jung

first: Nayara

last: Doimo de Azevedo

first: Athanasios

last: Typas


title: Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps

city: Santa Ana

first: Camden

last: Jansen

address: 10631 Rockhurst Ave

institute: UCI

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

overall_design: Refer to individual Series


title: Arg1 expression defines immunosuppressive subsets of immune infiltrating cells in cancer

first: Seth

last: Garren

state: MA

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Tumor-associated macrophages (TAM) have attracted attention as they can modulate key cancer-related activities, yet TAM represent a heterogenous group of cells that remain incompletely characterized. In growing tumors, TAM are often referred to as M2-like macrophages, which are cells that display immunosuppressive and tumorigenic functions and express the enzyme arginase 1 (Arg1). Here we combined single cell intravital imaging with scRNA seq to uncover the topography and molecular profiles of Arg1+ macrophages in mice. We further assessed how immunotherapeutic interventions impact these cells directly in vivo. We show that: i) Arg1+ macrophages are more abundant in tumors compared to other organs; ii) there exist two morphologically distinct subsets of Arg1 TAM defined by previously unknown markers (Gbp2b, Bst1, Sgk1, Pmepa1, Ms4a7); iii) anti-Programmed Cell Death-1 (aPD-1) therapy decreases the number of Arg1+ TAM while increasing Arg1– TAM; iv) accordingly, pharmacological inhibition of arginase 1 does not synergize with aPD-1 therapy. Overall, this research defines subsets of immunosuppressive myeloid cells with powerful complementary single cell analytical approaches that pave the way for a more intricate understanding of TAM behavior.

overall_design: We report the application of 10x Genomics single-cell RNAseq of live CD45+ cells sorted from MC38 tumors injected in C57BL/6J mice.  Tumors were injected intradermally and grown for 7 days before treatment with either control injection or antiPD-1 antibody for 3 days.


title: Neuromesodermal Progenitors are a Conserved Source of Spinal Cord with Divergent Growth Dynamics

status: Public on Nov 01 2018

city: Utrecht

first: Maria

last: Florescu

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: With a genetic clone tracing method (ScarTrace), we labelled early embryonic progenitors and find a strong clonal similarity between spinal cord and mesoderm tissues.

overall_design: We provide ScarTrace data for different organs from 6 zebrafish.

first: Andrea

last: Attardi

first: Timothy

last: Fulton

first: Leila

last: Muresan

first: Martin

middle: O

last: Lenz

first: Courtney

last: Lancaster

first: Jan

last: Huisken

first: Alexander

last: van Oudenaarden

first: Benjamin

last: Steventon


title: DNA methylation in AgRP neurons regulates voluntary exercise behaviour in mice

status: Public on Nov 10 2018

city: Houston

first: Harry

last: MacKay

state: TX

address: 1100 Bates Ave

institute: Baylor College of Medicine

summary: Knock out of Dnmt3a in AgRP neurons leads to a sedentary, adiposity-prone adult phenotype associated with widespread changes in DNA methylation and gene expression.

overall_design: Genome-wide bisulfite-seq and RNA-Seq of FACS-sorted neural (NeuN+) nuclei from the arcuate nucleus of the hypothalamus.

first: C

last: Scott

first: Jack

last: Duryea

middle: S

last: Baker

first: Eleonora

last: Larisky

first: Amanda

middle: E

last: Elson

first: Theodore

last: Garland Jr

first: Marta

last: Fiorotto

first: Rui

last: Chen

first: Yumei

last: Li

first: Cristian

last: Coarfa

first: Richard

last: Simerly

first: Robert

last: Wateland


title: Clonal evolution of pre-malignant B-cells in the absence of AID

status: Public on Nov 03 2018

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

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

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

summary: We used microarrays to investigate gene expression changes in Aid-/- + Pax5+/- tumor cells.

overall_design: Bone marrow leukemic cells of 5 Aid+/- + Pax5+/- and 3 Aid-/- + Pax5+/- mice compared with bone marrow proB and preB cells of 4 WT mice.

first: Guillermo

last: Rodríguez-Hernández

first: Friederike

last: Opitz

first: Pilar

last: Delgado

first: Angel

middle: F

last: Alvarez-Prado

first: Inés

last: González-Herrero

first: Javier

last: Raboso-Gallego

first: Ana

last: Casado-García

first: Alberto

last: Orfao

first: Oscar

last: Blanco

first: Diego

last: Alonso-López

last: De Las Rivas

first: Sara

last: de Tena-Dávila

first: Markus

last: Muschen

first: Francisco

middle: J

last: Criado

first: María

last: Cenador

first: Carolina

last: Vicente-Dueñas

first: Julia

last: Hauer

first: Almudena

last: Ramiro

last: Sanchez-Garcia

first: Arndt

last: Borkhardt


title: Drosophila egg chambers: control vs. ectopic JAK/STAT and EGFR signaling

status: Public on Oct 30 2018

city: Princeton

last: Wittes

state: New Jersey

address: Lewis Thomas Lab, Washington Road

department: Department of Molecular Biology

institute: Princeton University

summary: During Drosophila melanogaster oogenesis, the JAK/STAT and EGFR pathways are both required to specify a population of somatic epithelial cells called the posterior follicle cells (PFCs). The PFCs are important because they generate a signal at mid-oogenesis that is required to establish the embryonic axes. To identify novel PFC-expressed transcripts, egg chambers containing ectopic PFCs were generated and microarrays were then used to identify upregulated transcripts. To generate ectopic PFCs, GAL80TS / CyO ; UAS-Upd, UAS-λtorpedo/TM6B flies were crossed to GR1-GAL4 flies to obtain the genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-λtorpedo. Sibling females of genotype GAL80TS/+ ; GR1-GAL4/TM6B were dissected as controls.

overall_design: A reference design was used to control for dye bias in a two-color experiment. Reference (WT) RNA was isolated from the ovaries of OreR flies. Experimental RNA was isolated from the ovaries of 5-8 day old flies of genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-λtorpedo and control RNA from ovaries of 5-8 day old flies of genotype GAL80TS/+ ; GR1-GAL4/TM6B. Three biological replicates each were performed for the experimental and control conditions. A total of 6 arrays were used. Experimental and control RNA was labeled with Cy5 and universal common reference RNA with Cy3.


title: Expression data from human umbilical cord-derived mesenchymal stem cells

status: Public on Sep 23 2018

city: Shanghai

first: Lin

last: Liangyu

state: Shanghai

address: 320 Yueyang Road

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

summary:
Mesenchymal stem cells (MSCs) have been shown to exert therapeutic effects on various autoimmune diseases. However, such therapeutic effect is not always achieved. Among many reasons, MSC culture methodologies may account for the these differences. It is known that oxygen concentration could profoundly affect the properties of MSCs. Therefore, we compared human umbilical cord derived MSCs cultured under hypoxic and normoxic conditions.
We used microarrays to profile the gene expression of human umbilical cord derived MSCs under 10% oxygen and normoxia conditions.

overall_design: MSCs were cultured under different oxgen tension were applied to microarray analysis

first: Liangyu

last: Lin

first: Liming

last: Du


title: Next-generation sequencing analyses of the differently expressed genes of wild type, PtomitAPX-antisense and PtomitAPX-overexpression transgenic suspension cells

status: Public on Oct 23 2018

city: Beijing

first: Bin

last: Yin

address: Tsinghua East Road

institute: Beijing Forestry University

summary:
PtomitAPX, which is a newly discovered ascorbate peroxidase (APX) specifically localized in the mitochondria of Populus tomentosa. Our antisense and overexpression studies are based on PtomitAPX.
[Abstract]  Plant mitochondria are major organelles of reactive oxygen species (ROS) production, are also targeted by ROS, which reduces mitochondrial efficiency and increases ROS production in a self-destructive cycle. Ascorbate peroxidase have pivotal roles in ROS-scavenging because even very low concentrations are sufficient for H2O2 decomposition We identified two ascorbate peroxidases, PtomitAPX and PtosAPX, are targeted to mitochondria in Populus tomentosa Carr. PtosAPX which is the homologous gene of arabidopsis thaliana sAPX, is also dual targeted to both chloroplast and mitochondria but is closer to chloroplastic isoform by ELISA and qPCR analysis. And PtomitAPX which is specifically targeted to mitochondria, is primary APX in mitochondria. The expression of PtomitAPX was significantly different from that of PtosAPX. PtomitAPX plays an important role in controlling the ROS balance and maintaining mitochondrial structure and function, thus regulating cell PCD and plant development in P  opulus tomentosa Carr. The structure and function of mitochondria, particularly the efficiency of oxidative phosphorylation (OXPHOS), were impaired, cell PCD were increased and plant growth was retarded and partially restored by exogenous ASA in antisense PtomitAPX transgenic Populus,. The PtomitAPX expression level showed a strong relationship with ROS balance, mitochondrial structure, and plant growth. Our findings provide valuable insight into the unexplored mechanism of independent ROS balance by the ascorbate-glutathione cycle in mitochondria. Moreover, the data enhance understanding of the central role of mitochondria during plant growth, particularly in non-photosynthetic tissues of woody trees.
Methods: Total RNA was isolated from wild type (WT), antisense (anti-3) and overexpression (OX) cells using TRIzol reagent according to the manufacturer’s protocol (Invitrogen). The samples were sequenced using an Illumina Genome Analyzer (HiSeq™ 2000; Illumina, San Diego, CA). The raw reads were data-filtered to obtain high-quality clean reads. The clean reads were mapped to the P. trichocarpa reference genome and reference genes using SOAPaligner/SOAP2.
No more than two mismatches were allowed in the alignment. Gene expression levels were calculated as reads per kilobase per million reads (RPKM). Differential expression analysis among the WT, anti-3 and OX was performed using the DEGseq R package based on normalized read counts. A corrected P value of < 0.001 and |log2Ratio| > 1.5 were set as the threshold for significantly differential expression.
Results: Compared with the WT, 3571 genes with significantly different expression levels (fold change > 1.5 or < −1.5, and corrected P < 0.001) were detected in anti-3 and 95.58% (3413) of them reverted or partial reverted to WT in anti-3 treated with 1 mM AsA. RNA-seq analysis of WT, overexpression, and overexpression cells treated with 10 mM H2O2, were also employed. Compared with the WT, 5542 genes with significantly different expression levels(fold change > 1.5 or < −1.5, and corrected P < 0.001) were detected in OX and 66.47% (3684) of them were reverted or partial reverted to WT in OX treated with 10 mM H2O2.

overall_design: Populus tomentosa suspension cells mRNA profiles of WT, anti-3 and OX were generated by deep sequencing via Illumina HiSeqTM 2000.

first: Hai

last: Lu


title: HIV-1 permanently disrupts homeostatic ILCs and expands inflammatory TCF7-dependent memory NK cells

status: Public on Nov 09 2018

city: Worcester

first: Alan

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School


title: Genome wide RNA-seq of iBMDMs upon VSV infection

status: Public on Oct 05 2018

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

summary: VSV infection affects various gene expression

overall_design: Wild-type iBMDMs (immortalized bone-marrow-derived macrophages cells) were infected with VSV (Vesicular Stomatitis Virus) for 6 hours. Genome wide RNA-Seq screen was did to detect gene expression.

first: Lili

first: Fuping

last: You


title: Dazl regulates germ cell survival through a network of polA-proximal mRNA interactions [GC1-spg cells (parental line) iCLIP]

status: Public on Sep 18 2018

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

summary: The RNA binding protein Dazl is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in DAZL null mice are unknown.  Here, we mapped transcriptome-wide Dazl-RNA interactions in vivo, revealing Dazl binding to thousands of mRNAs via polyA-proximal 3’UTR interactions.  In parallel, fluorescence activated cell sorting and RNA-Seq identified mRNAs sensitive to Dazl deletion in male germ cells.  Despite binding a broad set of mRNAs, integrative analyses indicate that Dazl post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes critical for germ cell proliferation and survival.  Additionally, we provide evidence that polyA sequences have key roles in specifying Dazl-RNA interactions across the transcriptome.  Altogether, our results reveal a mechanism for Dazl-RNA binding, and illustrate that Dazl functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival.

overall_design: iCLIP libraries from monoclonal cell line with doxycyline inducible Dazl expression (GC-1-spg parental line)

first: Leah

middle: L

last: Zagore


title: Dazl regulates germ cell survival through a network of polA-proximal mRNA interactions [GC1-spg cells (parental line) Ribosome Profiling and RNA-seq]

summary: The RNA binding protein Dazl is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in DAZL null mice are unknown.  Here, we mapped transcriptome-wide Dazl-RNA interactions in vivo, revealing Dazl binding to thousands of mRNAs via polyA-proximal 3?UTR interactions.  In parallel, fluorescence activated cell sorting and RNA-Seq identified mRNAs sensitive to Dazl deletion in male germ cells.  Despite binding a broad set of mRNAs, integrative analyses indicate that Dazl post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes critical for germ cell proliferation and survival.  Additionally, we provide evidence that polyA sequences have key roles in specifying Dazl-RNA interactions across the transcriptome.  Altogether, our results reveal a mechanism for Dazl-RNA binding, and illustrate that Dazl functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival.

overall_design: Ribosome Profiling and RNA-seq libraries from monoclonal cell line with doxycyline inducible Dazl expression (GC-1-spg parental line)

middle: D


title: Gene expression profiles of CEBPβ-overexpressed alveolar macrophages after A20-Ad treatment

status: Public on Oct 01 2018

first: shanshan

last: liu

address: No.1 Xian Nong Tan St. Xi Cheng District

institute: Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Although recent progressions have provided significant mechanistic insights into the pathogenesis of pulmonary fibrosis (PF), few of anti-PF therapeutics show certain promise for this devastating disease. Chronic or repeated lung injury results in chronic inflammation, which functions as a major driven force to promote PF development. Here we report that chronic lung injury inactivates ubiquitin-modifying enzyme A20 to cause a progressive accumulation of transcription factor C/EBPb in macrophages, which produce a number of pro-fibrotic factors to promote PF development. Elevated GSK-3b expression, in response to chronic lung injury, interacts with and phosphorylates A20 to suppress C/EBPb degradation in macrophages. Enforced expression of A20 or pharmacological acceleration of C/EBPb degradation by a peptide restores the A20 activity and provides potent therapeutic efficacy against experimental PF. Our studies reveal a regulatory mechanism of the GSK-3b-A20-C/EBPb axis in alveolar macrophages, by targeting which can treat PF and fibroproliferative lung diseases.

overall_design: mRNA profiles of CEBPβ-overexpressed alveolar macrophages after A20-Ad treatment were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: Shan-shan

last: Liu

first: Xiao-xi

last: Lv


title: Deregulation  associated with cardiac conduction defects in Myotonic Dystrophy Type 1 using TU-Tagging

status: Public on Jul 18 2018

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

summary: Total RNA was extracted from about 10, 1-week or 5-weeks old, entire or dissected (head, legs, wings and ovaries removed) adult flies, using TRIzol reagent (Invitrogen) following manufacturer’s instructions. The following genotypes dedicated for TU-tagging cell - specific transcript isolation were used: Hand>LacZ;HA-UPRT, Hand>MblRNAi;HA-UPRT, Hand>Bru3;HA-UPRT and Hand>960CTG;HA-UPRT

overall_design: Examination of gene expression in different genotypes with TU-tagging method

first: Emilie

last: Plantie

first: Lucie

last: Picchio


title: Expression data from control or Hnf6/Oc2 compound mutant mouse embryonic spinal cords

status: Public on Jul 31 2018

city: Brussels

first: Frederic

last: Clotman

address: avenue Hippocrate, 55 boxB1.55.11

department: Institute of Neuroscience

country: Belgium

institute: UCLouvain

summary:
In the embryonic spinal cord, cardinal populations of interneurons (INs) diversify into specialized subsets and migrate to defined locations within the spinal parenchyma.However, the factors that control IN diversification and migration remain almost totally unknown. We demonstrate with  that Onecut proteins regulate the diversification and the migration of V2 INs in the spinal parenchyma.
To identify genes downstream of Onecut transcription factors that may contribute to V2 interneuron differentiation and distribution, we performed a microarray comparison of control and of OC-deficient spinal cord transcriptome at e11.5, namely at the stage when significant numbers of V2 cells have been generated and are initiating migration

overall_design: 5 controls and 5 Hnf6/Oc2 compound mutant mouse embryos

first: Audrey

last: Harris

first: Maria

last: Hidalgo-Figueroa

first: Gauhar

last: Masgutova

first: Frédéric


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Human ATAC-Seq]

status: Public on Oct 12 2018

city: New York

first: Xiao

last: Xu

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

summary: Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions.

overall_design: RNA purified from nuclei or cytoplasm from mouse, rat, or human cerebellum. ATAC-seq was also performed using cerebellar nuclei from the three species.

first: X

first: E

middle: I

last: Stoyanova

first: A

last: Lemiesz

first: J

last: Xing

first: D

middle: C

last: Mash

first: N

last: Heintz


title: RNAseq of (Dimethylfumarate)DMF-induced changes in murine Tc17 CD8+ cells

status: Public on Jul 11 2018

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

institute: Institute of Medical Microbiology

summary: IL-17-producing CD8+ (Tc17)T cells are implicated in the pathogenesis of multiple sclerosis (MS), thereby representing a promising target for therapy. We found that dimethyl fumarate (DMF), a first-line medication for MS upregulated reactive oxygen species (ROS) by glutathione depletion in murine Tc17 cells, which limited IL-17 and diverted Tc17 cells towards cytotoxic T lymphocyte (CTL) signature. DMF enhanced PI3K-AKT-FOXO1-T-bet- as well as STAT5-signaling leading to restricted permissive histone state at the Il17 locus. T-bet-deficiency, inhibiting PI3K-AKT, STAT5 or histone deacetylases prevented DMF-ROS-mediated IL-17 suppression. In MS patients with stable response, DMF suppressed IL-17 production by CD8+ T-cells and triggered diversion from Tc17 towards CTL signature along with enriched ROS-, PI3K-AKT-FOXO1-signaling, demonstrating comparable regulation across species. Accordingly, in the mouse model for MS, DMF limited Tc17-encephalitogenicity. Our findings disclose DMF-ROS-AKT-driven pathway, which selectively modulates Tc17 fate to ameliorate MS, thus opening avenue to develop markers and targets for specific therapy.

overall_design: Examination of DMF-induced expression changes in 3 conditions, 3 samples each: murine TC17 cells without treatment as control group, murine Tc17 cells treated with DMF and murine Tc17 cells treated with DMF and Glutathione(GSH)

first: Christina

last: Lückel

first: Matthias

last: Klein

first: Federico

last: Marini

first: Tobias

last: Bopp


title: lncRNA expression in colon cancer cells and paired normal epithelial cells from five colon cancer patients

status: Public on Jul 29 2018

city: Callaghan

first: Lei

last: Jin

state: NSW

address: University Drive

country: Australia

institute: The University of Newcastle

summary: To investigate lncRNA expression in colon cancer cells in comparison with paired normal colon epithelial cells by use of lncRNA microarray.

overall_design: lncRNA expression profiles in laser capture micro-dissected (LCM) colon cancer cells of surgically resected colon cancer tissues and paired normal colon epithelial cells were detected by lncRNA microarray

first: Hamed

last: Yari


title: RNAseq of (Dimethylfumarate)DMF-induced changes in human CD8+ memory cells

overall_design: CD8+ memory cells from human blood


title: Genome-wide identification of protein binding sites in mammalian cells.

status: Public on Jul 10 2018

first: Liu

last: Fenglin

address: Courtyard 1, Beichen West Road

institute: Chinese Academy of Sciences

summary: We report the application of genome-wide protein binding sites capture (GWPBS-Cap) technology for high-throughput profiling of protein binding sites in mammalian cells. By obtaining over 37 billion bases of sequence from NaCl washed chromatin DNA in each group, we got an unprecedented view into genome-wide binding patterns of many DNA binding proteins of Hela cells. We find that active promoters contain more PBSs with lower NaCl tolerance and our technology provides a genome-wide landscape of DNA-protein interactions.

overall_design: Identification of 6 different groups of DNA-protein binding patterns in 1 cell types.

first: Fenglin

last: Liu

first: Yuxiang

last: Zhang


title: Gene expression analysis of mouse brain regions after chronic social defeat stress (CSDS)

status: Public on Jul 04 2018

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

summary: Chronic psychosocial stress is a risk factor for psychiatric disorders, and genetic factors interact in conferring susceptibility. The chronic social defeat stress (CSDS) mouse model allows identifying factors underlying resilience and susceptibility to chronic psychosocial stress. We used RNA-sequencing to identify genes and pathways affected by CSDS in three brain regions: medial prefrontal cortex (mPFC), ventral hippocampus (vHPC), and bed nucleus of the stria terminalis (BNST), of male mice from strains C57BL/6Crl and DBA/2Crl.

overall_design: Ribo-depleted RNA was sequenced with Illumina High-Seq 2000 and Next-seq 500 from mPFC (C57BL/6Crl: control n = 6, resilient n = 6, susceptible n = 6; DBA/2Crl: control n = 6, susceptible n = 8), BNST (C57BL/6Crl: control n = 5, resilient n = 5, susceptible n = 5; DBA/2Crl: control n = 5, resilient n = 3, susceptible n = 5), and vHPC (C57BL/6Crl: control n = 6, resilient n = 8, susceptible n = 3; DBA/2Crl: control n = 6, susceptible n = 5) 6-8 days after the last CSDS.


title: Integrative Genomic Analysis Reveals Novel Regulatory Mechanisms of eyeless During Drosophila Eye Development

status: Public on Sep 26 2018

first: Kelvin

last: Yeung

address: One Baylor Plaza, Room S242

department: Pathology

summary: eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila. However, the molecular mechanisms through which Ey regulates target genes and pathways have not been characterized at the genomic level. Using ChIP-Seq, we generated an endogenous Ey binding profile in Drosophila developing eyes. These data sets will serve as a valuable resource for future studies on Ey and eye development.

overall_design: ChIP-Seq of endogenous eyeless, H3K4me1, H3K18Ac, H3K27Ac and PolII in developing Drosophila late third instar eye discs.

first: Graeme

last: Mardon

first: Chen

last: Rui


title: Expression profiling of endometrial cancer of different grades

status: Public on Jun 15 2018

city: Sosnowiec

first: Urszula

last: Mazurek

address: Jedności 8

country: Poland

institute: Medical University of Silesia

summary: The present study has focused on the identification of the differences between expression patterns of genes in endometrial cancer.

overall_design:
For microarray analysis  27 samples were used: 3 control samples, 7 - G1 samples, 11 - G2 samples and 6 - G3 samples.

contributor: Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland


title: Evaluation of induced cellular cytokine profile in response to Rifampin-mono resistant Mycobacterium tuberculosis strain

status: Public on Jun 11 2018

city: Tehran

first: Farzam

last: Vaziri

address: 12th Farvardin Ave, Jomhhoori St

country: Iran

institute: Pasteur Institute of Iran

summary: Comparing of induced cellular cytokine profile in response to Rifampin-mono resistant and H37Rv Mycobacterium tuberculosis strains

overall_design: qPCR gene expression profiling. THP-1 cell line was infected separately  by two M.tb strains . Equal amount total RNA from each infected cell was pooled prior to gene expression analysis.

first: Parvaneh

last: Ravan

first: Shima

last: Hadifar

first: Ava

last: Behrouzi

first: Abolfazl

last: Fateh

first: Seyed

last: Siadat


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines III

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines ( pancreatic cancer, renal cell carcinoma, oral squamous cell carcinoma, prostate cancer and bladder cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (PC3, SK-MES-1, SW1990, MDA-MB-231 and PANC1) were treated with miRNAs ( miR-144-3p, miR-144-5p, miR-204-5p, miR-130-5p and miR-130-3p), siRNAs (si-PIR).

first: Takayuki

last: Arai


title: Cardiac mesoderm induction by Tbx6 without exogenous factors

status: Public on Oct 19 2018

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Cardiac mesoderm, a precursor for all cardiovascular lineages, is a promising cell source for basic research and clinical applications. BMP/Nodal/Wnt signaling induces cardiac mesoderm in embryonic stem cells (ESCs); however the molecular mechanism is unclear and the differentiation protocols are labor-intensive. Identification of a master regulator that induces cardiac mesoderm is needed. Here we found that Tbx6 directly reprogrammed mouse fibroblasts into cardiac mesoderm-like cells, which differentiated into cardiomyocytes and smooth muscle cells with addition of lineage-specific transcription factors. In mouse ESCs, BMP/Activin (Nodal) induced Tbx6 in cardiac mesoderm, while inhibition of Tbx6 blocked differentiation into cardiac mesoderm and cardiomyocytes. Conversely, transient expression of Tbx6 induced cardiac mesoderm in ESCs without exogenous factors, and generated all cardiovascular lineages. Mechanistically, Tbx6 directly upregulated Mesp1, inhibited Sox2, and activated BMP/Nodal/Wnt signaling to induce cardiac mesoderm. Thus, Tbx6 acts as a key regulator for cardiac mesoderm induction, and our findings provide new insights into the mechanism of cardiovascular differentiation.

overall_design: In this study, we compared the global gene expression patterns of iTbx6 T-GFP ESCs with or without Dox administration. RNA was extracted from embryoid body at day2 and day4 after differentiation.

first: Taketaro

last: Sadahiro

first: Masaki

last: Ieda


title: Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to plants and animals

status: Public on Jul 17 2018

city: Qingdao

first: xiao

last: fan

address: Nanjing Road 106

institute: Yellow Sea Fisheries Research Institute

summary: Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. Thus, DNA methylation seems to play an important role in kelp, which has not been reported before.

overall_design: We generated bisulfite treated genomic DNA sequencing from male, female haploid gametophytes and diploid sporophytes of S. japonica.

first: Xiao

last: Fan

first: Naihao

last: Ye


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [Spermatogonia PolyA-Seq]

status: Public on May 22 2018

first: Donny

last: Licatalosi

country: USA

summary: Dazl (deleted in azoospermia like) is a member of the DAZ family of germ cell-restricted RNA binding proteins required for gametogenesis from worm to human.  The direct RNA targets and functions of these essential proteins are poorly understood.  Here, we generated high-resolution, transcriptome-wide maps of Dazl-RNA interactions in mouse testes.  These maps provide important insights into the mechanism of Dazl recruitment to mRNA and reveal Dazl binding to thousands of mRNAs predominantly through sequence-specific interactions near the polyA tail.  Using transgenic mice and fluorescence activated cell sorting (FACS), we isolated DAZL knockout germ cells and used RNA-Seq to identify mRNAs sensitive to DAZL-ablation.  Intersecting the RNA-Seq and Dazl-RNA interaction datasets revealed that Dazl enhances expression of a subset of directly-bound transcripts, namely mRNAs for a network of essential cell cycle regulatory genes.  Collectively, our integrative analysis delineates a Dazl-dependent post-transcriptional gene regulatory program essential for mammalian germ cell maintenance.

overall_design: PolyA Seq libraries generated from isolated spermatogonial cells

first: Leah

last: Zagore


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [Adult RNA-Seq]

overall_design: RNA-seq libraries generated from 8 week CD1 mouse testes


title: Microarray data from hUCBMSC to investigate the role of resveratrol in the restoration of monocrotophos induced cellular damages.

status: Public on Oct 16 2018

city: Lucknow

first: Ruchi

last: Yadav

state: Uttar Pradesh

address: Malhour, Gomti Nagar Extension

department: Amity Institute of Biotechnology

country: India

institute: Amity University Uttar Pradesh, Lucknow Campus, Lucknow

summary:
Analysis of human umbilical cord blood mesenchymal stem cell (hUCBMSC) derived neuronal cells  exposed with (10 μM) concentration of resveratrol (RV),(50 ng/ml) concentrations of nerve growth factor(NGF) and (10 μM+50 ng/mL) concentrations of RV+NGF , respectively for 30 minutes . hUCBMSC were co-exposed with monocrotophos (MCP) and RV, MCP and NGF, MCP and RV+NGF before cell differentiation and after cell differentiation. Results provide insight into the role of RV in the restoration of MCP-induced cellular damages, thus proving to have a therapeutic potential against organophosphate pesticide-induced neurodegeneration.
We used microarrays to detail the global programme of gene expression underlying the neurotoxicity of MCP and neuroprotection of RV on of human cord blood derived mesenchymal stem cells (hCBMSCs). Differential gene expression studies identified the role of RV and NGF in survival, proliferation and neuronal differentiation of hCBMSCs. Microarray analysis also identified distinct classes of up-regulated genes during this process.

overall_design: Total 10 samples were prepared from human umbilical cord blood mesenchymal stem cells (hUCBMSC) for RNA extraction and hybridization on Affymetrix microarrays. hUCBMSC without any exposure is taken as control samples (control). hUCBMSC were exposed with resveratrol (RV), nerve growth factor (NGF), and resveratrol + nerve growth factor (RV+NGF). To study the neurotoxicity of MCP and neuroprotection of RV before cell differentiation(pre exposed samples), hUCBMSC were co-exposed with monocrotophos (MCP) and RV (MCP pre exposed RV), MCP and NGF (MCP pre exposed NGF), MCP and RV+NGF (MCP pre exposed RV+NGF) .We also studied the effect of RV and NGF on hUCBMSC after cell differentiation (post exposed samples), hUCBMSC were co-exposed with monocrotophos (MCP) and RV (MCP post exposed RV), MCP and NGF (MCP post exposed NGF), MCP and RV+NGF (MCP post exposed RV+NGF).

first: Sadaf

last: Jahan

first: Prachi

last: Srivastava

first: Aditya

last: Pant


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [P6 iCLIP]

overall_design: Dazl iCLIP libraries generated from postnatal day 6 mouse testes (3 biological replicates)


title: RNA-sequencing of GmWRKY54 over-expression and null plants

status: Public on May 31 2018

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: WRKY transcriptional factors play important roles in response to various abiotic stresses. In this study, we demonstrate that inserting a copy of soybean WRKY54 driven by a constitutive promoter of CMP (cestrum yellow leaf curling virus) or a drought induced promoter of RD29a, improves drought tolerance in transgenic soybean plants. GmWRKY54 is a transcriptional activator and regulates expressions of large numbers of stress-related genes. Using a GO enrichment toolkit, we found that GmWRKY54 up-regulated GO terms related to transcriptional regulator and gene expression and down-regulated GO terms related to photosynthesis and membrane. Using a co-expression network analysis, we find that dozens of genes are negatively co-expressing with photosynthetic genes. These genes are related to ABA signaling pathway, Ca2+ signaling pathway and transcriptional factors. Transgenic plants confer drought tolerance through improving stomatal closure, reducing transpiration rate and reducing membrane damage during water deficit. GmWRKY54 activates expression of these ABA or Ca2+ signaling-related genes, which finally regulates stomatal aperture. GmWRKY54 binds to the promoter regions of genes encoding an ABA receptor (PYL8-1), two calcium dependent protein kinase (CPK3-1 and CPK3-2), a CBL (Calcineurin B-like protein) interacting protein kinase (CIPK11-2), a SnRK family protein kinase and a ferritin, suggesting that they are the direct targets of GmWRKY54. Our study reveals that GmWRKY54 significantly improves drought tolerance in soybean and regulates expression of large numbers of drought-related genes, suggesting that GmWRKy54 maybe a master regulator of drought response.

overall_design: Three transgenic soybean samples, A004A, A005B and B010C and the control plants (null) were chosen for RNA-seq. Both well-water samples and dehydrated samples were analyzed.

first: Da-Wei

last: Liang

first: Hao-Wei

last: Chen

first: Xiao-Hua

last: Bian

first: Ming

last: Shen

first: Wan-Ke

last: Zhang

first: Biao

last: Ma

first: Qing

last: Lin

first: Wan-Hong

last: Cao

first: Jin-Song

first: Shou-Yi


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [Adult PolyA-Seq]

first: Donny

address: 2109 Adelbert Rd

overall_design: PolyA Seq libraries generated from 8 week CD1 mouse testes


title: UMI-count modeling and differential expression analysis for single-cell RNA sequencing

status: Public on Apr 30 2018

city: Memphis

first: Xiang

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41. We also inlcude a bulk RNA-seq study of unsorted and sorted cells using CD44 as a marker

overall_design: Single cell RNA-seq of Rh41 using the 10x Genomics. For bulk RNA-seq, there are three batches, each corresponds to three samples: sorted CD44 high, sorted CD44 low and unsorted. C2, C6, C7: CD44high subspopulation (Batch 1/2/3); C3, C4, C5: CD44low subpopulation (Batch 1/2/3); C1, C8, C9: CD44 unsorted (Batch 1/2/3)

first: Wenan

first: John

last: Easton


title: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [Adult HITS-CLIP]

institute: Case Western Reserve University

overall_design: Dazl HITS CLIP libraries generated from 8 week CD1 mouse testes (3 biological replicates)

first: Leah