title: Concomitant Loss of Smad4 and Activation of Wnt Signaling Triggers Enterocyte De-differentiation and Adenoma Formation

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: In the current work, we add to the understanding of differentiated-cell-derived tumorigenesis by demonstrating that simultaneous loss of SMAD4 and activation of the WNT pathway triggers stem cell properties and adenoma formation in the differentiated epithelium. Under normal conditions, SMAD4 loss does not immediately affect the normal tissue homeostasis in the intestine. However, after approximately 6 months, adenomas will develop and feature elevated WNT signaling, suggesting that SMAD4 loss predisposes to WNT-driven tumors. Interestingly, ectopic elevation of WNT in the context of a SMAD4 mutant background triggers stem cell activity and adenoma formation in the differentiated epithelium. Thus Smad4 functions to suppress villus cells from re-entering the cell cycle and functioning as stem cells upon exposure to high levels of WNT. Thus, we report a new mechanism through which differentiated cells can contribute to tumor formation.

overall_design: RNAs were extracted from crypt jejunal epithelia of the indicated genotypes (Smad4f/f;Villin-CreER(T2)  and Smad4f/f; Ex3f/+;Villin-CreER(T2)) in triplicates, one day following 4 consecutive days of tamoxifen injection. Uninjected mice served as control. After flushing the freshly harvested jejunum with cold PBS, the epithelia was dissociated from underlying mesenchyme by incubating with 3 mM EDTA/PBS at 4°C as described previously (Perekatt, 2014), and filtered through 70 micron filter to isolate the crypts. The crypts were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.

first: Ansu

middle: O

last: Perekatt

first: Pooja

last: Shah

first: Shannon

last: Cheung

first: Namit

last: Kumar

last: Wu

first: Jin

last: Xing

first: Qiang

last: Fang

last: Gao

first: Shilpy

last: Joshi

first: Eileen

last: White


title: Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [ChIP-seq]

status: Public on Jul 23 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T cell development and selection is orchestrated in the thymus by a specialized niche of diverse stromal populations. By transcriptional single cell sorting, we de novo characterize the entire stromal compartment of the thymus. We identified dozens of cell states within the thymic stroma, with thymic epithelial cells (TEC) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC-IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient of Pou2f3, a tuft cells master regulator, resulted in complete and specific depletion of mTEC-IV, without affecting other TEC populations. Overall, our study comprehensively defines all stroma cells in the thymus and identifies a new TEC lineage associated with chemosensory properties that may potentially link the adaptive immune system to environmental and neurological signals.

overall_design: Transcriptional profiling of single cells from the stroma of mouse thymus, generated from deep sequencing of tens of thousands of cells, reveled 4 subpopulations of medullary epithelial cells. ChIP-seq assay profile the enhancer landscape of these subpopulation.

first: Jakub

last: Abramson

first: Chamutal

last: Bornstein

first: Shir

last: Nevo

first: Amir

last: Giladi

first: Noam

last: Kadouri


title: Cigarette smoke and pancreatic cancer: Evidence for increased pancreatic cancer stem cell population

status: Public on Jul 21 2018

city: Omaha

first: Moorthy Palanimuthu

last: Ponnusamy

state: Nebraska

address: 42nd and Emile

department: Biochemistry and Molecular Biology

country: USA

institute: University of Nebraska Medical Center

type: Expression profiling by high throughput sequencing

summary: Cigarette smoking is one of the major risk factors for Pancreatic Cancer. Our goal in this study is to investigate mechanistic link between smoking and pancreatic cancer stem cell (CSC) enrichment. We report that cigarette smoking augments pancreatic CSCs and this process occurs by the activation of Paf1/PD2, a major stem ness marker. We also report that the cigarette smoke activates Paf1/PD2 through nACHRα7-ERK1/2-FOSL1 signaling axis.

overall_design: We treated HPNE and Capan1 cells withc followed by whole transcriptome analysis using RNA sequencing.

first: Ponnusamy

middle: P

last: Moorthy

first: Rama

middle: K

last: Nimmakayala


title: EpCAM Based Capture Detects and Recovers Circulating Tumor Cells From  Subtypes of Breast Cancer Except Claudin-low

status: Public on Jul 22 2018

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

summary:
Circulating tumor cells (CTCs) potential utility as a liquid biopsy is of great interest in breast cancer.  The goal of this study is to use RNA-seq to show that we can capture CTCs  using EpCAM based gating for most of the breast cancer subtypes and detection of breast cancer specific genese are independent of sequencing plateformt.
Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the hg 18.  Data analysis  revealed a significant detction of  breast cancer specific genes in CTCs and such signature genes  overlap between two sets of data yet provided complementary insights in transcriptome profiling.

overall_design: CTCs can be sucessfuly isolated using EpCAm technique and represent an overall signature gene profile of breast cancer tumors.

first: Alexander

last: Ring

first: Neal

last: Mineyev

first: Weizhu

last: Zhu

first: Emily

last: Park

first: Chip

last: Lomas

first: Min

last: Yu

first: Dany

last: Barrak

first: Victoria

last: Forte

first: Debasish

last: Tripathy

first: Julie

middle: E

last: Lang


title: High throughput sequencing of human fibroblast WS1 cells after 5 Gy X-ray irradiation

status: Public on Jul 20 2018

city: Suzhou

first: shuyu

last: zhang

state: Jiangsu

address: 199 Ren'ai Road

country: China

institute: Soochow University

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

overall_design: Refer to individual Series


title: L1CAM dependent transcriptional programs in brain metastatic cells

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

summary: L1CAM dependent gene expression programs in vitro and ex vivo were analyzed by translating ribosome affinity purification and sequencing (TRAP-Seq).

overall_design: EGFP-Rpl10a+, shControl or shL1CAM expressing H2030-BrM cancer cells were seeded to organotypic brain slice, cultured for 48h, and processed through the TRAP protocol. Cells under regular tissue culture (0h) were collected as pre-vascular cooption controls.

first: Manuel

last: Valiente-Cortes

first: Emrah

last: Ekrem Er

first: Joan

last: Massague


title: A variant NuRD complex containing PWWP2A/B excludes MBD2/3 and directs HDAC activity to regulate histone acetylation and RNA Pol II dynamics at active genes

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford


title: lncRNA and mRNA-sequencing of WS1 cells after 5Gy of X-Ray irradiation

summary:
Purpose: The goal of this study was to compare the lncRNA and mRNA expression profile of human fibroblast WS1 cells between 0 Gy and 5 Gy X-ray irradiation.
Methods: lncRNA and mRNA-sequencing of WS1 cells were generated  using  Illuminal Hiseq4000, RNA-seq reads were mapped to human genome hg19 by hisat2 software. Cuffdiff software was used to analysis the differentially expressed levels of LncRNA and mRNA FPKM.
Results: We  identified different expressed levels of  88780 lnRNA and 20311 mRNA transcripts in WS1 cells between 0 Gy and  5 Gy X-ay irradiation.
Conclusion: Our study first  revealed the detail of  lncRNA and mRNA expression profiles of WS1 cells after 5Gy of X-Ray irradiation

first: Shuyu

last: Zhang


title: RIP-sequencing reveals that X-ray irradiation infection ELAVL1 binding RNA sites

summary: We report the application of RIP-sequencing technology for high-throughput profiling of ELAVL1 protein on the effect of lncRNA an mRNA in WS1 cells after 5 Gy X-ray irradiation

overall_design: Examing protein(ELAVL1)-RNA(lncRNA and mRNA) interaction sites in WS1 cell after X-ray irradiation


title: A variant NuRD complex containing PWWP2A/B excludes MBD2/3 and directs HDAC activity to regulate histone acetylation and RNA Pol II dynamics

summary: Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3-containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes.

overall_design: ChIP-seq analysis of chromatin epigenetics changes between wildtype and PWWP2A/B double knockout mouse embryonic stem cells. Conventional ChIP methods were applied for PWWP2A/B and derived truncated proteins. Calibrated ChIP-seq were applied for investigating the NuRD-variant complex recruitment (HDAC1 and MTA2), acetylation alterations (H3K27ac and H3K9ac), and RNA Polymerase II dynamics.

first: T

first: G

first: N

last: Brockdorff


title: Transcriptional convergence of oligodendrocyte lineage progenitors during development

city: Chippendale

first: Darya

middle: Pavlovna

last: Vanichkina

state: New South Wales

address: 32 Queen Street

country: Australia

institute: University of Sydney

summary: Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryo- genesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different oligodendrocyte (OL) states at adult stages. Here, we present bulk and single-cell transcriptomics resources providing insights on how transitions between these states occur. We found that post-natal OPCs from brain and spinal cord present similar transcriptional signatures. Moreover, post-natal OPC progeny of E13.5 Pdgfra+ cells present electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves, indicating that Pdgfra+ pre- OPCs rewire their transcriptional network during development. Single-cell RNA-seq and lineage tracing indicates that a subset of E13.5 Pdgfra+ cells originates cells of the pericyte lineage. Thus, our results indicate that embryonic Pdgfra+ cells in the CNS give rise to distinct post-natal cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions.

overall_design: Total RNA-seq of E13.5 and P7 PDGFRA+ cells from PDGFRA/GFP mice from brain and spinal cord (n = 3 replicates).


title: Genome-wide map of histone H3 lysine 36 tri-methylation in wild type mouse myocytes and myocytes bearing a muscle-specific H19/Igf2 enhancer deletion

city: Bethesda

first: Megan

middle: Leigh

last: Sampley

state: MD

address: 6 Center Drive

department: Program on Genomics of Differentiation

institute: NICHD

summary: We report a genome-wide study of the role of a muscle-specific Igf2/H19 transcriptional enhancer in global histone modifications in primary mouse myocytes. We generated 1.7 billion bases of sequence from DNA purified by the chromatin immunoprecipitation of H3K36me3 in wild type myocytes and myocytes bearing a deletion of the enhancer.  Because H3K36me3 is reported to mark transcribed gene regions, we generated these data to develop a list of genes that are directly or indirectly regulated by this muscle enhancer. This study provides additional insight into how this muscle-specific enhancer potentially regulates a transcriptional network in mouse skeletal myocytes.

overall_design: Examination of 1 histone modification in a wild type myocyte line and a mutant myocyte line

middle: L

first: Apratim

last: Mitra

first: Karl

last: Pfeifer


title: Compound PIP-RBPJ-1 treated human neural stem cells

status: Public on Jul 19 2018

city: Kyoto

first: Yulei

address: kyoto,tanakamonnzenncyo8-1, hyakumanbenn haitu 318

country: Japan

institute: Kyoto U

summary: The study of the compond PIP-RBPJ-1‘ function on neural stem cell. Synthetic DNA-binding inhibitors capable of gaining precise control over neurogenesis factors could obviate the current clinical barriers associated with small molecule use in regenerative medicine. Here, we show the design and bio-efficacy of a synthetic ligand PIP-RBPJ-1 to cause promoter-specific suppression of neurogenesis-associated HES1, and its downstream genes. Furthermore, PIP-RBPJ-1 alone could alter the neural system-associated notch signaling factors and remarkably induce neurogenesis with an efficiency that is comparable to a conventional approach. Here is one day treatment of the PIP-RBPJ-1 on neural stem cells.

overall_design: We studied the coumpound on the human neural stem cell for one days. For microarray, we have two samples, the treatment sample and the negtive control DMSO, both of which have two replicates.

first: Ganesh

middle: N

last: Pandian

first: Zutao

last: Yu

first: Tingting

first: Yue

last: Li

first: Jayant

last: Darokar

first: Kaori

last: Hashiya

first: Toshikazu

last: Bando

first: Hiroshi

last: Sugiyama


title: Transcriptome sequencing of Wild-type and psmb11-/- thymic epithelial cells

city: Montreal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

summary:
Purpose: as regulator of protein degradation, proteasomesregulate pratically all cellular functions. We assume that psmb11 specific expression by cortical thymic epithelial cells (cTECs) could have far reaching effect on cTECs biology and their involvment in thymocytes' education.
Method: We analyzed the poly(A)+ transcriptome of TEC populations by RNA-sequencing (RNA-Seq) in order to gain novel insights into psbm11 functions
Results: We demonstrate here that psmb11-deficiency affects the transcription of 450 genes in cortical thymic epithelial cells
Conclusion: Our study reveals that one of psmb11 cellular roles could rely on transcriptional regulation and more important, inhibition of mTEC-lineage engagement in cTEC differenciation.

overall_design: The mRNA profiles of cTEC, mTEClo and mTEChi from 11 thymi of 6-8 weeks-old wilt type (WT) and psmb11-/- mice were generated by RNA-sequencing using Illumina HiSeq2000

first: S

last: Brochu

first: M

last: Laisné

first: C


title: G-Protein-Coupled Receptor 68 Negatively Regulates IL-22 Production in Human Th17 Cells

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary:
Purpose: To identify novel genes regulated by the aryl hydrocarbon receptor that influence human Th17 cell function.
Methods:  Naïve CD4 T cells from peripheral blood of six healthy human volunteers were cultured under four experimental conditions for three days: anti-CD3 and anti-CD28 antibodies (Media control), Media with Th17 conditions (IL-6, TGF-b, IL-1b, IL-23), Th17+FICZ and Th17+CH223191. Total RNA was extracted from each sample on day 3 and sequenced in a paired-end 2x50bp strategy on an Illumina HiSeq1500.  A total of six donors were analyzed.
Results:  AhR activation with FICZ suppressed IL-17 production from human CD4 T cells and increased IL-22.  AhR inhibition with CH223191 potently suppressed IL-22 and modestly increased IL-17 production.  On day 3, the number of significantly regulated genes for each treatment were 975 (Th17), 88 (Th17+FICZ) and 142 (Th17+CH223191).  11 common genes were significantly regulated by all three treatments.  One of these, GPR68, was investigated further in functional studies since its expression correlated with IL-22 production.  Activation of GPR68 with a positive allosteric modulator suppressed IL-22 concentrations in human Th17 cell cultures.
Conclusions:  Our study demonstrates that GPR68 activation can negatively regulate IL-22 production from human CD4 T cells in the presence of an AhR agonist.  RNA-seq is a powerful method to identify novel gene targets that regulate cytokines involved in chronic inflammatory diseases.

overall_design: Naïve CD4 T cells were purified from peripheral blood mononuclear cells isolated from six patient samples. Four experimental conditions were created for each sample: media only (control); Th17 differentiated; Th17+FICZ; and Th17+CH223191. Total RNA was extracted from each sample on day 3 and sequenced in a paired-end 2x50bp strategy on an Illumina HiSeq1500.  Differential gene expression analysis identified genes that were expressed at significantly different levels than the control (Media).  Ingenuity pathway analysis revealed the most common cellular functions for genes regulated by each treatment.

first: Jeremy

last: McAleer

first: Bryanna

last: Roar

first: Jun

last: Fan

first: Donald

middle: A

last: Primerano


title: Transcriptional Basis of Neuronal Diversity in the Mammalian Brain

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Neuronal diversity is a defining feature of the mammalian brain deemed necessary for realizing the complex function of the nervous system. In order to begin to understand the transcriptional basis of this diversity, we collected more than 170 neuronal and non-neuronal cell type-specific transcriptomes defined operationally by transgenic mouse lines and anatomical regions. The dataset indicates that the genes specifically expressed in neuronal cell types are biased toward long genes. We revealed that these long genes have higher capacities to be differentially expressed between cell types and thus assume an important role in diversification of the neuronal transcriptomes. Since mobile element insertions are the main cause of the gene elongations, we propose that exaptation of the inserted mobile elements significantly contributed to the neuronal diversity.

overall_design: Examination of whole cell transcriptomes in 174 cell types.

first: Lihua

last: Wang

first: Yasuyuki

last: Shima

first: David

last: Hunt

first: Andrew

last: Lemire

first: Erina

last: Hara

first: Mac

last: Hooks

first: Dimitri

last: Tränkner

first: Jayaram

last: Chandrashekar

first: Adam

last: Hantman

first: Sacha

last: Nelson


title: Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: The pancreas of vertebrates is separately derived from both the dorsal and ventral endodermal domains. However, the difference between these two programs has been unclear. Here, using a pancreatic determination gene, Pdx1, driven GFP transgenic mouse strain, we identified Pdx1-GFP highly expressing cells (Pdx1high) and Pdx1-GFP lowly expressing cells (Pdx1low) in both embryonic dorsal Pdx1-expressing region (DPR) and ventral Pdx1-expressing region (VPR). We analyzed the transcriptomes of single Pdx1low and Pdx1high cells from the DPR and VPR. In the VPR, Pdx1low cells have an intermediate progenitor identity and can generate hepatoblasts, extrahepatobiliary cells, and Pdx1high pancreatic progenitor cells. In the DPR, Pdx1high cells are directly specified as pancreatic progenitors, whereas Pdx1low cells are precocious endocrine cells. Therefore, our study defines distinct road maps for dorsal and ventral pancreatic progenitor specification. The findings provide guidance for optimization of current β-cell induction protocols by following the in vivo dorsal pancreatic specification program.

overall_design: The overall goal of this study was understanding the programs of ventral and dorsal pancreatic progenitor development. Specifically, to get an overall gene expression profiles during ventral and dorsal pancreas development, we performed bulk cell RNA-seq in E10.5 ventral and dorsal pancreatic progenitor cells purified from Pdx1-GFP transgene embryos; E14.5 ventral and dorsal endocrine progenitor cells from Ngn3-GFP transgene embryos; and E17.5 ventral and dorsal beta cells from Insulin-RFP transgene embryos. To determine the progress and cell type components during the specification of pancreatic progenitor in ventral and dorsal domains, we performed single-cell transcriptomic analysis in sorted Pdx1-GFP+ cells from ventral and dorsal pancreatic buds.

first: Lin-Chen

last: Li

first: Wei-Lin

last: Qiu


title: Relative accessability of HSV1 genomic DNA compared with its host cell (ATAC-seq)

city: Berkeley

middle: Trombley

last: McSwiggen

address: 470 Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

summary: To compare the relative accessability of HSV1 DNA compared with its host DNA, we performed ATAC-seq analysis.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1 strain KOS

overall_design: Cells were left uninfected; infected for 2, 4, or 6 hours; or infected for 6 hours in the presence of phosphonoacetic acid to prevent genome replication. ATAC-seq was performed as per standard published protocols.

middle: T

first: Robert

last: Tjian

first: Xavier

last: Darzacq


title: Transcriptome analysis of high glucose loaded mouse embryo at 2-cell stage treated with ZGW

city: adelaide

first: qi

last: liang

address: north terrace

institute: university of adelaide

summary:
Purpose: Zuo-Gui-Wan (ZGW) is a classic formula in Traditional Chinese Medicine (TCM). Previous studies have shown that it is not only beneficial for Impaired Glucose Tolerance (IGT) of adults but also the offspring. This study is in order to understand the molecular mechanisms of the efficacy of ZGW on IGT.

Methods: We used high glucose loaded 2-cell stage mouse embryos as a model, and took advantage of single-cell RNA sequencing technology to analyze the transcriptome of the model with or without ZGW.

Results and Conclusions: Results showed that high glucose can down-regulate genes in the ribosome pathway while ZGW can reverse this inhibition and as a result promote the development of embryos loaded with high glucose. We found that high glucose can affect sugar metabolism and influence mitochondrial function, but that ZGW can promote sugar metabolism via the tricarboxylic acid cycle mainly through up-regulating the genes in the respiratory chain and oxidative phosphorylation. The regulation of mitochondrial energy metabolism is the main effect of ZGW on high glucose loaded embryos.

Significance: This research not only revealed the global gene regulation changes of high glucose affecting 2-cell stage embryos, but also provided insight on the potential molecular mechanisms of ZGW on the IGT model.

overall_design: Three groups: control group(1), model group(4) and drug group(7), each group has three biological replicates.

first: Qi

last: Liang

first: Qiang

last: Song


title: Embryonic brain of wild-type mice vs. luxoid mice

status: Public on Jul 18 2018

city: TaipeiCity

first: Yi-Chao

last: Lee

address: YuancyuSt

country: Taiwan

institute: Taipei Medical University

summary: Comparison of forebrain and midbrain from embryonic day 10.5 C57BL/6 wild-type mice and luxoid mice.

overall_design: E10.5 wild-type brain vs. luxoid brain. Biological replicates: 2 wild-type mice replicates, 2 luxoid mice replicates.

first: Hsin-Chuan

last: Lin

first: Yung-Hao

last: Ching

first: Chi-Chen

last: Huang

first: Ping-Chieh

last: Pao

first: Yi-Hua

first: Wen-Chang

last: Chang

first: Tzu-Jen

last: Kao


title: Striatal transcriptome of a mouse model of ADHD reveals a pattern of synaptic remodeling

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Despite the prevalence and high heritability of Attention-Deficit/Hyperactivity Disorder (ADHD), genetic etiology remains elusive. Clinical evidence points in part to reduced function of the striatum, but which specific genes are differentially expressed and how they sculpt striatal physiology to predispose ADHD are not well understood. As an exploratory tool, a polygenic mouse model of ADHD was recently developed through selective breeding for high home cage activity. Relative to the Control line, the High-Active line displays hyperactivity and motor impulsivity which are ameliorated with amphetamine. This study compared gene expression in the striatum between Control and High-Active mice to develop a coherent hypothesis for how genes might affect striatal physiology and predispose ADHD-like symptoms. To this end, striatal transcriptomes of High-Active and Control mice were analyzed after mice were treated with saline or amphetamines. The pseudogene Gm6180 for n-cofilin (Cfl1) displayed 20-fold higher expression in High-Active mice corresponding with reduced Cfl1 expression suggesting synaptic actin dysregulation. Latrophilin 3 (Lphn3), which is associated with ADHD in human populations and is involved in synapse structure, and its ligand fibronectin leucine rich transmembrane protein 3 (Flrt3), were downregulated in High-Active mice. Multiple genes were altered in High-Active mice in a manner predicted to downregulate the canonical Wnt pathway. A smaller and different set of genes including glyoxalase (Glo1) were differentially regulated in High-Active as compared to Control in response to amphetamine. Together, results suggest genes involved in excitatory synapse regulation and maintenance are downregulated in ADHD-like mice.  Consistent with the molecular prediction, stereological analysis of the striatum from a separate set of mice processed for imunohistochemical detection of synaptophysin revealed approximately a 46% reduction in synaptophysin immunoreactivity in High-Active relative to Control. Results provide a new set of molecular targets related to synapse maintenance for the next generation of ADHD medicines.

overall_design: There are a total of 20 samples: 5 striatum samples from control strain males treated with saline, 5 straitum samples from high-active strain males treated with saline, 5 striatum samples from control strain males treated with amphetamine, and 5 striatum samples from high-active strain males treated with amphetamine.

first: Anastasia

middle: M

last: Sorokina

middle: C

first: Tassia

last: Goncalves

first: Joseph

middle: V

last: Gogola

first: Petra

last: Majdak

first: Sandra

last: Rodriguez-Zas

first: Justin

middle: S

last: Rhodes


title: RecBCD Coordinates Repair of Two Ends at a DNA Double-Strand Break, Preventing Aberrant Chromosome Amplification [ChIP-seq]

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

institute: University of Edinburgh

summary: In the bacterium Escherichia coli, RecBCD coordinates repair of two ends at a DNA double-strand break, preventing aberrant chromosome amplification

overall_design:
RecA binding to the chromosome of four E. coli strains was analysed by RecA-ChIP.  Two biological repeats were carried out for each of the four strains. Two strains experienced an induced DNA double strand break (DL4184 and DL5699) and two did not (DL4201 and DL6204).  Two strains are wild-type for the recD gene (DL4184 and DL4201) and two strains have the recD gene deleted (DL5699 and DL6204).

This series contains two re-analyzed samples from GSE77181 (GSM2045608 and GSM2045609).

first: Martin

last: White

first: Manuel

last: Lopez-Vernaza

first: A

last: Mahedi Hasan

first: David

last: Leach


title: MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [mutant MEF2C]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that transgenic Mef2cS222A/S222A mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. MEF2C phosphorylation was required for leukemia stem cell maintenance, induced by MARK kinases in cells, and blocked by selective MARK inhibitor MRT199665, which caused apoptosis of MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C. These findings identify signaling-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.

overall_design: RNA-sequencing of human leukemia cell line with induction of wildtype or mutant MEF2C.

first: Fiona

last: Brown

first: Alex

last: Kentsis


title: Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 in mice

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary: Dietary restriction (DR) is the most studied non-genetic intervention capable of extending lifespan across multiple taxa. Modulation of specific genes, primarily within the insulin/insulin-like growth factor signalling (IIS) and the mechanistic target of rapamycin (mTOR) signalling pathways can also act to extend lifespan and health span in model organisms. For example, both male and female mice lacking insulin receptor substrate 1 (IRS1) are long-lived and are protected against several age-associated pathologies. However, it remains unclear as to how these particular interventions act mechanistically to produce their beneficial effects, and indeed whether different interventions act through shared or distinct processes. In the following study we investigated multi-tissue transcriptional responses in 15-month-old wild type and IRS1 null mice fed an ad libitum diet (WTAL and KOAL respectively) or fed a 30% DR diet (WTDR or KODR respectively). Using an RNAseq approach we noted little transcriptional overlap between liver, skeletal muscle, brain and white adipose tissue within either WTDR or KOAL mice, but that a high correlation coefficient of differentially expressed genes existed within the same tissue across WTDR and KOAL mice. Additionally, many metabolic features were similarly shared between WTDR and KOAL mice. Overall, we report that significant overlap exists in the tissue-specific transcriptional response between long-lived DR mice and IRS1 null mice, further supporting the notion of mechanistic overlap between these long-lived mouse models. However, there was evidence of disconnect between transcriptional signatures and in certain phenotypic measures between KOAL and KODR, in that additive effects on body mass and body composition were observed but that DR induced a unique set of genes and pathways in these already long-lived mice.

overall_design: Gene expression analysis of four tissue types (brain, skeletal muscle, liver or white adipose tissue) from two genotypes of mice (wild type or insulin receptor substrate 1 gene knockout) in two dietary conditions (ad libitum or 30% dietary restriction). WTAL (n=2), WTDR (n=3), KOAL (n=3) and KODR (n=3).

first: Colin

last: Selman

first: Melissa

last: Page

first: Eugene

middle: F

last: Schuster

first: Pawel

last: Herzyk

first: Dominic

middle: J

last: Withers


title: Study of ribosome dynamics after osmotic stress in Lsm1 and Pat1 deletions

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: In this study, we aim to understand how the fates of stress-activated mRNAs are determined under stress conditions by isolating individual osmostress-activated mRNA species, quantitating the proteins associated in vivo with each of them, and analyzing how deletion of these proteins impact on the expression of stress-activated genes. By comparison with the proteome associated with individual not stress-related mRNA species, we show specific proteins to be preferentially binding to osmostress-activated mRNAs, notably members of the cytoplasmic Pat1 / Lsm1 – 7 complex. We evaluated the impact of this complex on the stress response by analyzing expression of osmostress-activated genes, production of osmo-protein and, mapping ribosome transit at single nucleotide resolution using 5’-phosphate sequencing of mRNAs in lsm1 and pat1 mutants. We conclude that our biochemical co-purification approach has successfully identified RNA-binding proteins with a particular role in regulating post-transcriptional expression of stress-activated mRNAs.

overall_design: We performed 3 biologically independent 5PSeq experiments before stress (t0) and 30 minutes after osmotic stress (t 30).

first: Elena

last: Garre

first: Per

last: Sunnerhagen


title: RecBCD Coordinates Repair of Two Ends at a DNA Double-Strand Break, Preventing Aberrant Chromosome Amplification

first: Benura

last: Azeroglu

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

overall_design: Refer to individual Series


title: RecBCD Coordinates Repair of Two Ends at a DNA Double-Strand Break, Preventing Aberrant Chromosome Amplification [MFA]

summary: The effect of an induced site-specific DNA double-strand break on DNA abundance across the chromosome of E. coli cells expressing or not RecD protein, was investigated by marker frequency analysis.

overall_design: gDNA was isolated from two independent cultures ('biological repeats') of four, exponentially growing E. coli strains.  Two strains experienced the induced DNA double-strand break (DL2006 and DL3391), two did not (DL2573 and DL3743).  Two strains were wild-type for the recD gene (DL2006 and DL2573), two had the recD gene deleted (DL3391 and DL3743). gDNA was also isolated from two independent stationary phase cultures of strain DL2573.  The libraries of the 10 gDNA preps were multiplexed and run 4 seperate times ('sequencing runs')

first: Martin

last: White


title: Essential roles of mitochondria biogenesis regulator Nrf1 in retina development and homeostasis

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

summary: Purpose: RNA-seq analysis for E13.5 wildtype vs. Nrf1-flox/flox:Six3-Cre retinas

overall_design: Retinal mRNA profiles of E13.5 wild type (WT) and Nrf1-/- mouse retinas were generated by deep sequencing in duplicates using Illumina Hiseq 3000.

first: Takae

last: Kiyama


title: Nuclear dynamics of the Set1C subunit Spp1 prepares meiotic recombination sites for break formation

status: Public on Jul 17 2018

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: This study investigates the nuclear localizations and dynamics of COMPASS proteins using ChIP-seq and competition ChIP.

overall_design: 46 samples from ChIP-seq (Spp1 WT, Spp1 mutants, Bre2 with multiple time points, controls: input and NoTag) and 18 samples from competition ChIP-seq (Spp1-GFP and Spp1-MYC in multiple time points and replicates).

first: Szekvolgyi

last: Lorant


title: Basal hair follicle stem cell mRNA expression levels of mice at 3, 19 and 24 months of age

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

country: Spain

institute: Centre for genomic regulation (CRG)

summary: Analysis of gene signatures on HFSCs (CD49f High/Cd34+) during normal chronological aging.

overall_design: Adult hair follicle stem cells were isolated through FACS sorting from total skin (back and belly) using antibodies towards CD49 and CD34 surface proteins and mRNA was extracted using total mRNA purification commercial columns.

first: Bill

last: Keyes

first: Mari-Carmen

last: Ortells


title: Fine-tuning Mybl2 levels are required for proper MET process during somatic reprogramming [RNA-seq]

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

institute: University of Birmingham

summary: Genome wide data investigating the role of Mybl2 in reprogramming

overall_design: 2 biological replicates of RNA-seq in control and Mybl2 overexpression conditions

first: Paloma

last: Garcia


title: Genome-wide comparative analysis in Solanaceae plants reveals evolution of novel miRNAs targeting defense genes in Capsicum spp.

city: Seoul

first: Chanseok

last: Shin

address: 1, Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

country: South Korea

institute: Seoul National University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: MicroRNAs (miRNAs) play roles in various biological processes including growth, development, and defense in plants. Recent studies revealed that some plant miRNAs could produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs) and they regulate cascade of gene expression.  Results: We performed genome-wide comparative analysis of miRNAs and their targets in Solanaceae plants in an evolutionary perspective. miRNAs were mapped onto 12 chromosomes and microsynteny analysis, based on miRNAs and their flanking genes, revealed about 86% of conserved miRNAs in pepper maintained synteny with those of tomato or potato. Degradome analysis revealed that many of genes related to transcription or defense response are regulated by miRNAs in Solanaceae plants. We found several miRNAs in pepper targeting a number of genes encoding nucleotide-binding and leucine rich repeat (NLR) or receptor-like protein (RLP), known as major players in defense responses. In addition, resistance-related miRNAs trigger phasiRNA production indicating amplification of regulation of the disease-resistant gene families. Among them, specifically evolved miRNAs in pepper, can-miR-n033a and can-miR-n026, targets many NLRs and RLPs in an expanded subgroup in pepper, respectively.  Conclusions: Taken together, miRNAs might be generated and evolved to regulate diverse genes involved in plant immunity in Solanaceae. This study provides an insight into possible co-evolution between resistance-related miRNAs and defense genes in pepper.

sample_organism:
Capsicum annuum
Solanum lycopersicum
Solanum tuberosum

overall_design: Total RNAs were extracted from whole tissue of pepper, tomato and potato.

first: Taewook

last: Kim

first: Eunyoung

last: Seo

first: June-Hyun

last: Park

first: Seon-In

last: Yeom

first: Doil

last: Choi


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [RRBS]

status: Public on Jul 15 2018

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

institute: Weizmann Institute of Science

type: Methylation profiling by high throughput sequencing

summary: Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.

overall_design: Mbd3f/- MEFs that carry DOX-inducible OKSM cassette were used,  and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/- established iPSC line (after 3 passages or more), and WT v6.5 mouse ESCs were used as positive controls. DNA methylation was measured in each time point using reduced representation bisulfite sequencing (RRBS).

first: Asa

last: f Zviran

first: Elad

last: Chomsky

first: Yoach

last: Rais

first: Nofar

last: Mor

first: Jacob

last: Hanna


title: Agilent zebrafish V3 array 4´44K microarray-Ochratoxin A treated with 6-48 hpf zebrafish embryos

status: Public on Jul 16 2018

city: Taipei

first: Ting-Shuan

last: Wu

address: 5F ,No 1, Sec 1, Jen-Ai Rd

institute: ntu

summary: Ochratoxin A (OTA) is a fungal secondary metabolite widely found in cereal and a wide variety of foods; it also exhibits carcinogenic effects, nephrotoxicity, and teratogenicity. In this study, the zebrafish was applied to investigate the effects of ochratoxin A on gene expressions in zebrafish embryos.

overall_design: Ochratoxin A  mediated mRNA expression in zebrafish embryos which were exposed from 6 hpf to 48 hpf with doses of 0 and 0.5 micromolar.

first: Biing-Hui

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6-48 hpf zebrafish embryos

summary: To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos.

overall_design: Ochratoxin A  mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf to 48 hpf with doses of 0 and 0.5 micromolar.


title: Gene expression profiling in different organs of chickpea

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, global transcriptome profiling was performed for different organs of ICC 4958 (leaves, roots, flowers and young pod) and leaves of wild chickpea, PI 489777. More than 50 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed.

sample_organism:
Cicer arietinum
Cicer reticulatum

platform_organism:
Cicer arietinum
Cicer reticulatum

overall_design: Total RNA was extracted from all samples and cDNA libraries were prepared. Sequencing was performed on Illumina HiSeq platform to generate 51 bp single-end (leaf, flower and young pod), 46 bp single-end (root) or 100 bp paired-end (leaf of wild chickpea) reads. Pre-processing was performed using NGS QC Toolkit to remove adapters and low-quality reads. Filtered high-quality reads were mapped on the chickpea genome using TopHat2 pipeline (v2.0.0). To analyze gene expression, reference-guided assembly was generated using Cufflinks (v2.0) and differential expression of genes was determined by Cuffdiff.

first: Vikash

middle: K

last: Singh

first: Rohini

last: Garg


title: The impact of CXCL5 overexpression on the primary tumor microenvironment of B16F1 melanomas

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: CXCL5, a strong neutrophil-chemoattractant, has been reportet to be expressed in different cancer entities with diverse outcomes in disease progression. Contradictory outcome in disease progression in different tumor entities might be explained by a tumor type specific expression pattern of chemokines, chemokine receptors and growth factors that act in concert with CXCL5. This study evaluates the impact of CXCL5 expression on the tumor mircoenvironment in a syngeneic mouse melanoma model.

overall_design: 105 B16F1 and B16F1-CXCL5 murine melanoma were injected intradermally into the flank skin of C57BL/6 J mice. Primary tumors were grown up to 250-350mm³, excised, snap frozen and then processed for RNA sequencing.

first: A

last: Forsthuber

first: O

first: K

last: Lipp

first: R

last: Loewe


title: HDAC3-mediated regulation of the circadian gene Per1 contributes to age-related impairments in hippocampal memory and synaptic plasticity

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

summary: We performed an RNA Sequencing experiment on dorsal hippocampal tissue from six groups of animals: Aging (18-20-month-old) HDAC3flox/flox homecage (H3F-HC); Aging (18-20-month-old) HDAC3flox/flox 60min post training (H3F-BV); Aging (18-20-month-old) wildtype homecage (OWT-HC); Aging (18-20-month-old) wildtype 60min post training (OWT-BV); Young (2-4-month-old) wildtype homecage (YWT-HC); Young (2-4-month-old) wildtype 60min post training (YWT-BV). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed sixty minutes following a 10min Object Location Memory training session.

overall_design: The objective of this study was to examine activity regulated gene expression in the dorsal hippocampus following a learning event in young (~3-m.o.) and old (~18-m.o.) wildtype and HDAC3flox/flox mutant mice. HDAC3 was deleted in dorsal hippocampus tissue of HDAC3flox/flox mice using AAV-CaMKII-Cre before behavior.

first: J

last: Kwapis

first: M

last: Wood

first: C

first: P

last: Baldi


title: RNA-seq analysis of microglia and infiltrating macrophages in the injured retina

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

summary:
The goal of this study is to identify genes differentially expressed between microglia and infiltrating macrophages in the injured retina

Methods: mRNA profiles of microglia (Cont) and infiltrating macrophages (GFP) at day 7 post-injry, quadruplicated, were generated by deep-sequencing using Illumina HiSeq 2500 sequencer.

Results: RNA-seq tags were mapped to the mouse mm9 reference genome assembly using Tophat2 ver. 2.0.8b, with FPKM values caluculated with Cufflinks ver. 2.1.1 with the default option.Comparison of gene expression between microglia and infiltrating macrophages identified genes specific to each subset.

Conclusions: Our study provides the detailed analysis of transcriptomes in microglia and infiltrating macrophages in the injured retina

overall_design: mRNA profiles of microglia (Cont) and infiltrating macrophages (GFP) harvested from the DTA-injured retina at day 7 post-injury were generated by deep-sequencing using Illumina HiSeq 2500.

first: Sumiko

last: Watanabe


title: Ribosome profiling of polysomes  from mouse  brains

status: Public on Jul 13 2018

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
We performed ribosome profiling of polysomes (Poly-RIBOseq) to monitor translation of  RNAs associated with polysomes in brain extracts from a mouse model
Keywords: ribosome profiling, translation, polysome profiling, Poly-RIBOseq

overall_design: We extracted polysomal  fractions from brains of a mouse model (Smn+/-; SMN2tg/0) and performed ribosome profiling (Poly-RIBOseq). Experiments were performed in biological duplicate.

first: Paola

last: Bernabò

first: Fabio

last: Lauria

first: Ewout

last: Groen

first: Elena

last: Perenthaler

first: Alessandro

last: Quattrone

first: Thomas

middle: H

last: Gillingwater

first: Gabriella

last: Viero


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [RNA-Seq]

first: Noa

last: Novershtern

overall_design: Mbd3f/-, Gatad2a-/- or wild-type (WT-1,WT-2) MEFs that carry DOX-inducible OKSM cassette were used,  and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/-, Gatad2a-/- and WT established iPSC line (after 3 passages or more), and Mbd3f/- or WT V6.5 mouse ESCs were used as positive controls. PolyA RNA-seq measured in each time point. WT-2 cell line is isogenic to Gatad2a-/-

first: Asaf

last: Zviran

first: Yoach

last: Rais

first: Nofar

last: Mor

first: Jacob

last: Hanna


title: Transcriptome-analysis of patient-derived normal and ulcerative colitis intestinal epithelial organoids

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Purpose: The objective of this study is to compare the transcriptome profile of intestinal epithelial organoids cultivated from distal colon tissue of patients with ulcerative colitis vs organoids cultivate from non-matched and otherwise healthy patient colon

first: Emina

last: Huang


title: The effect of CPPU on volatile compounds and transcriptome analysis of ‘Shine Muscat’ berries

city: nanjing

first: wu

last: wang

address: Weigang1 hao

institute: Nanjing Agricultural University

summary: Grape volatiles include a great number of compounds, among which monoterpenes, alcohols,esters and carbonyls were found.Grape may be divided into aromatic and non-aromatic varieties. ‘Shine Muscat’ belongs to the aromatic cultivar. The most abundant free compounds detected in Muscat grape were linalool, geraniol, citronellol, nerol. Grapevine (Vitis vinifera L.) is an economically important and widely cultivated fruit crop. Grape quality is important for its market value and is largely decided by its taste and aroma.Gas-chromatograph mass-spectrometry (GC-MS) was performed to observe changes of the volatile compounds.

overall_design: Three treated samples  (CPPU 0, CPPU 5ppm and CPPU 10 ppm) of grapevine were selected, and  total RNA was extracted from these samples for further library construction.

first: Wu

last: Wang

first: Jianmin

last: Tao


title: Change of 5hmC and 5mC landscapes in A2058-TET2WT cells cultured in high-g and normal-g

city: Boston

first: Di

last: Wu

state: MA

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Endocrinology

institute: The Brigham and Women's Hospital

summary: We report that high glucose can have a detrimental effect on the stability of TET2 protein, and thereby reduce the genome-wide 5hmC content. We use MeDIP and hMeDIP followed by sequencing to identify the change of 5hmC and 5mC landscapes in A2058-TET2WT over expressing cells cultured in high and normal glucose concentrations.

overall_design: A2058-TET2WT over expressing cells were cultured in high-g and normal-g for days. Their 5mC and 5hmC were profiled by MeDIP and hMeDIP sequencing.

first: Feizhen

first: Li

last: Tan

last: Hu

first: Hang

last: Liu


title: Expression data from PEG treated roots

status: Public on Jul 12 2018

city: Charleston

first: Yordan

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

summary: We study differences in gene expression between 5% PEG treated and control plants’ roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by water limitation mimicked by PEG treatment.treated

overall_design: Poplar roots from PEG treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 24, 48, 96 and 504h after transfer to control and 5% PEG media and RNA was extracted.

first: Victor

middle: B

last: Busov


title: Scc2 Is a Potent Activator of Cohesin's ATPase that Promotes Loading by Binding Scc1 without Pds5

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: In addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin’s ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin’s initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2’s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus
mixed sample

overall_design: Characterisation of the effect of WT and mutant cohesin complexes and associated factors on loading onto chromosomes in S. cerevisiae, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)

first: Naomi

last: Petela


title: Genome-wide analysis of 8-oxoguanine DNA glycosylase-1

city: Galveston

first: Istvan

last: Boldogh

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary: We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase (OGG1) which is a DNA base excision repair protein, after TNF exposure of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associate with peaks, and identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanine (primarily 8-oxoG). OGG1 increased highly significant (1e-09 to 1e-517) enrichment of 57  transcription factor binding sites including those for Sox(2, 3, 6, 10), RUNX, RUNX(1, 2), HOX(C, D), STAT(1, 3, 6), IRF(1 to 4), NF-κB. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. These and other data derived from further analysis, suggest that OGG1 modulates binding of transcription factors and gene expression.

overall_design: FLAG-tagged OGG1 expressing HEK293 cells were stimulated with TNF (20 ng/ml) for 0, 15, 30 and 60 min. After TNF exposure, protein-DNA complexes crosslinked using formalin according to standard Millipore® protocol. DNA was sheared with 10-sec pulses using a Cole-Parmer GEX 130 ultrasonic processor (average 300 bp) and chromatin was immunoprecipitated (IP) with antibody to FLAG or anti-RelA/p65 antibody using G-agarose beads (Millipore Corporation). After extraction, the DNA was subjected to high-throughput sequencing using Solexa/Illumina genome analyzer (Ambry Genetics)

first: L

last: Aguilera-Aguirre

first: I


title: H3K27 acetylation profiling of intestinal epithelial organoids cultivated from normal and colitic human primary colon mucosal tissue

summary: We report the results of ChIP-Seq profiling of H3K27 acetylation loci in intestinal epithelial organoids cultivated from primary patient colon tissue

overall_design: Examination of H3K27ac loci in 2 different types of intestinal epithelial organoids

first: E


title: Zearalenone exposure enhanced the expression of tumorigenesis genes in donkey granulosa cells via the PTEN/PI3K/AKT signaling pathway

city: QingDao

first: Zhang

middle: Rui

last: Qian

state: ShanDong

address: Great Wall Road

institute: Qingdao Agricultural University

summary: We investigated the biological effects of ZEA exposure on donkey granulosa cells by using RNA-seq analysis. ZEA at 10 and 30 μM were administered to granulosa cells within 72 hours of in vitro culture. ZEA at 10 μM significantly altered the tumorigenesis associated genes in donkey granulosa cells. Exposure to 10 and 30 μM ZEA treatment significantly reduced mRNA expression of PTEN, TGFβ, ATM, and CDK2 genes, particularly, the ZEA treatment significantly increased the expression of PI3K and AKT genes. Furthermore, immunofluorescence, RT-qPCR, and Western blot analysis verified the gene expression of ZEA-exposed granulosa cells. Collectively, these results demonstrated the deleterious effect of ZEA exposure on the induction of ovarian cancer related genes via the PTEN/PI3K/AKT signaling pathway in donkey granulosa cells in vitro.

overall_design: 9 mRNA profiles of donkey granulosa cells were generated by RNA sequencing.

first: Rui

middle: Q

last: Zhang

first: Guo

middle: L


title: A new axis linking diabetes to cancer: Glucose regulates tumor suppressor TET2 and 5hmC through AMPK

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

overall_design: Refer to individual Series


title: Whole Transcriptome RNASeq Data for Cell-Sorted Antibody Secreting Cells (ASC)

city: Atlanta

first: Greg

last: Gibson

state: GA

address: 950 Atlantic Dr. NW

department: Biological Sciences

institute: Georgia Institute of Technology

summary: We report whole transcriptome RNASeq data for cell-sorted pop2, pop3, and pop5 which are antibody-secreting cells from human peripheral blood

overall_design: 17 ASC samples, including 6 pop2 samples, 6 pop3 samples, and 5 pop5 samples across 6 individuals.

first: Doan

last: Nguyen

first: Swetha

last: Garimalla

first: Haopeng

last: Xiao

first: Shuya

last: Kyu

first: Igor

last: Albizua

first: Jacques

last: Galipeau

first: Kuang-Yeh

last: Chiang

first: Edmund

last: Waller

first: Ronghu

first: James

last: Roberson

first: Frances

middle: E

last: Lund

first: Troy

middle: D

last: Randall

first: Inaki

last: Sanz

last: Lee


title: Genetic determinants of chromatin accessibility in T cell activation across human individuals [ATAC-seq]

city: San Francisco

first: Rachel

last: Gate

state: CA

address: 533 Parnassus Ave

institute: UCSF

summary: We analyzed 105 chromatin accessibility (ATAC-seq) profiles in activated primary CD4+ T cells from healthy donors to identify genetic variants associated with variability in chromatin accessibility (ATAC-QTLs).

overall_design: ATAC-seq and RNA-seq on unstimulated and activated T cells from 105 and 96 individuals, respectively

first: Christine

last: Cheng


city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: Directed biomolecular evolution is widely used to tailor and enhance proteins but has hitherto not been applied in the reprogramming of mammalian cells. Here we describe a novel method to identify artificially enhanced and evolved reprogramming factors by pooled screens with randomised protein libraries, cell selection based on phenotypic readouts and genotyping by amplicon sequencing. We benchmark this approach by identifying artificially enhanced Sox2 and Sox17 factors in pluripotency reprogramming.

overall_design:
Mouse embryonic fibroblasts with a transgenic Oct4-GFP reporter (OG2-MEFs) were reprogrammed with Sox2,Oct4, Klf4 and c-Myc under Serum/LIF/Vitamin C conditions. Directed evolution of reprogramming factors by cell selection and sequencing (DERBY-seq) screens were performed by replacing Sox2 with eSox2 and eSox17 libraries. In the libraries three amino acids in the DNA binding HMG box were subjected to NNK randomisation. Cells were sorted by FACS and eSOX factors in GFP positive and GFP negative cell populations were genotyped by amplicon sequencing to identify variants with improved reprogramming activity.  Libraries were prepared by PCR amplifying genomically integrated retroviral transgenes. Sequencing adaptors and barcodes were added during the PCR.
Three independent biological replicates and two technical replicates (PCR and library prep ) were done for eSox2 DERBY-seq experiments. Three independent biological replicates were performed for eSox17 DERBY-seq experiments. Input pMX plasmid libraries were sequenced for both DERBY-seq experiments respectively.

We performed ChIP sequencing of wildtype Sox17 and an eSox17 mutant at  reprogramming  days 3 and 6.

RNA sequencing was performed for Sox17, Sox2, eSox2,eSox17 and GFP conditions at day 3, 6, 9 and iPSCs.

>>>Submitter states that they will update the GEO records with the nature of the mutants upon publication.<<<

first: Yogesh

last: Srivastava

first: Vikas

last: Malik

first: Mingxi

last: Weng

first: Ralf

last: Jauch


title: GRHL2-dependent enhancer switching maintains a pluripotent stem cell transcriptional subnetwork after exit from naïve pluripotency

city: Stanford

first: Amy

last: Chen

address: 279 Campus Drive West

institute: Stanford University


title: Genetic determinants of chromatin accessibility in T cell activation across human individuals


title: mRNA-seq data from adipose tissues of the great roundleaf bat (Hipposideros armiger) and mouse

city: Shenyang

first: Zhe

last: Wang

address: 120 Dongling Road

institute: Shenyang Agricultural University

summary: We performed transcriptomic profiling for two models of adipose browning, the classical mouse model and our newly described great roundleaf bat (H. armiger) model. Transcriptomes were generated from subcutaneous adipose tissue (sWAT), intra-abdominal adipose tissue (aWAT) and interscapular BAT (iBAT) from male and female bats, as well as sWAT and iBAT from male and female mice, which were acclimatized to 10°C and 30°C.  These 20 trascriptomes allowed us to identity genes, GO terms, and pathways that show significant expression changes and are shared by both species during the browning process.

sample_organism:
Mus musculus
Hipposideros armiger

platform_organism:
Mus musculus
Hipposideros armiger

overall_design: mRNA-seq data of 20 adipose tissues from the great roundleaf bat (H. armiger) and mouse were obtained by Illumina HiSeq 2000.

first: Yao

first: Shuyi

last: Zhang


title: Rapid genomic response after relief from nitrogen starvation of an enological strain of Saccharomyces cerevisiae

status: Public on Jul 10 2018

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

summary: The aim of this study was to determine how nitrogen repletion affected the genomic cell response of a Saccharomyces cerevisiae wine yeast strain, in particular within the first hour following relief from nutrient starvation. We found almost 4000 genes induced or repressed sometimes within minutes of nutrient changes. Some of the transcriptional responses to nitrogen depended on the TOR pathway which control positively ribosomal protein genes, amino acid and purine biosynthesis or amino acid permease genes and negatively stress-response genes, RTG specific TCA cycle genes and NCR sensitive genes. Some unexpected transcriptional responses concerned all the glycolytic genes, the starch and glucose metabolism and citrate cycle related genes which were down-regulated, as well as genes from the lipid metabolism.

overall_design: The yeast Saccharomyces cerevisiae EC1118 is a commercial wine yeast from Lallemand SA. Fermentation experiments were carried out in triplicates. The fermentation medium mimicks a standard natural must and has the same composition as the SM300 previously described (Bely et al. 1990), except for the total concentration of assimilable nitrogen which was 100 mg/L and the addition of 17 g/L FeCl3, 6H2O. Fermentations were conducted under constant stirring at 24°C in 1.2 L flasks equipped with locks to maintain anaerobiosis. Production of CO2 was monitored by weighing the flasks every 20 min, to determine weight loss. The rate of CO2 production was estimated using a polynomial smoothing as previously described in Sablayrolles et al. (1987). The number of cells was determined with a particle counter (Coulter counter, Beckman Coulter). Preliminary experiments have shown that under this condition, cells were starved for nitrogen (i.e. reached stationary phase) upon a release of 17 g of CO2. Some cells were collected at this stage as controls (t = 0), then diammonium phosphate (DAP) was added to the culture medium at a final concentration of 300 mg/L. Before DAP addition, an equivalent volume of medium was removed to keep the total volume unchanged. Samplings were then performed 15, 30, 45 and 60 min after DAP addition and cells were quickly recovered by filtration as previously described in Tesnière et al. (2017).

first: Catherine

last: Tesnière

first: Martine

last: Pradal

first: Chloé

last: Bessière

first: Isabelle

last: Sanchez

first: Frédéric

last: Bigey


title: GRHL2-dependent enhancer switching maintains a pluripotent stem cell transcriptional subnetwork after exit from naïve pluripotency [ChIP-Seq]

summary: During early development, pluripotent cells of the epiblast show extensive rewiring of enhancers with little associated change in gene expression. The mechanisms underlying and purpose of this rewiring are largely unknown. Here we identified a transcription factor, GRHL2, that is both necessary and sufficient to activate latent enhancers during the transition from naïve embryonic stem cells (ESC) to primed epiblast cells (EpiC). GRHL2 is necessary to maintain expression of its targets in EpiCs. However, these genes are already expressed at equivalent levels in ESCs, suggesting these genes switch enhancer usage during the transition. Identification of alternative enhancers driving these genes in ESCs uncovered an enrichment for the ESC-specific KLF transcription factors. While many KLF targets remain expressed in EpiCs, GRHL2 only regulates a specific subset promoting an epithelial program. These data suggest a model where a large naïve-specific transcriptional network is partitioned into smaller networks to uncouple their regulation in EpiCs, providing more flexibility in gene regulation during lineage specification.

overall_design: ATAC-seq in wildtype embryonic stem cells (ESCs) and epiblast cells (EpiCs); ATAC-seq and ChIP-seq for GRHL2, H3K4me1, H3K27Ac, and SMC1 in wildtype and GRHL2 knockout EpiCs; ChIP-seq for HA-tagged GRHL2, H3K4me1, H3K27Ac, and SMC1 in dox-inducible HA-GRHL2 ESCs and untargeted ESCs both treated with doxycyline for 24hrs.

first: Robert

last: Blelloch


title: Small RNA (sRNA), mRNA and SMRT sequencing data from pre-meiotic and meiotic anthers of Lilium Maculatum

status: Public on Jul 11 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots
Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of Lilium anthers.

overall_design: The L. maculatum plants were purchased from Home Depot (Newark, Delaware). Buds corresponding to pre-meiotic and meiotic stages were used to generate mRNA, full-length and sRNA libraries. Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies, so as to compensate for the lack of Lilium genome.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS" software package, and transcripts for protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).

first: Atul

last: Kakrana

first: Sandra

last: Mathioni

first: Olga

last: Shevchenko

first: Bruce

last: Kingham


title: Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]

status: Public on Jul 09 2018

city: Berlin

first: Dijun

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

summary: We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. To further investigate the downstream targets of REF6 represented H3K27me3 demethylase, we performed RNA-seq using single, double mutant and triple mutant. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.

overall_design: Expression profiling by RNA-seq in different genetic backgrounds of Arabidopsis.

first: Wenhao

last: Yan

first: Kerstin

last: Kaufmann


title: Genetic determinants of chromatin accessibility in T cell activation across human individuals [RNA-seq]

first: Rachel

last: Gate

summary: We analyzed 105 chromatin accessibility (ATAC-seq) profiles in activated primary CD4+ T cells from healthy donors to identify genetic variants associated with variability in chromatin accessibility (ATAC-QTLs).we analyzed 105 chromatin accessibility (ATAC-seq) profiles in activated primary CD4+ T cells from healthy donors to identify genetic variants associated with variability in chromatin accessibility (ATAC-QTLs)

first: Christine

last: Cheng


title: Targeting the HBZ Viral Oncoprotein Transcriptional Network in Adult T-cell leukemia/lymphoma (ChIP-Seq)

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Adult T-cell Leukemia/Lymphoma (ATLL) is a frequently incurable disease associated with the human lymphotropic virus type I (HTLV-I). The transcription factor HBZ is the only virally encoded gene that is expressed in all ATLL cases, but it is unclear why it may be essential in ATLL and how it might be targeted therapeutically. Here we performed RNA interference screening of ATLL lines and discovered that their proliferation depends on the transcription factors BATF3 and IRF4, which regulate the identity of normal immune cells. These factors, which are highly expressed in ATLL, cooperatively bind and transactivate genes that distinguish ATLL from other T cell malignancies, including BATF3 itself. HBZ binds to an ATLL-specific BATF3 super-enhancer and thereby regulates the expression of BATF3 and its downstream targets, including the oncogene MYC. The BET protein inhibitor JQ1 collapsed the transcriptional network directed by HBZ and BATF3, and was consequently toxic for ATLL lines and patient samples in vitro, and blocked growth of ATLL xenografts. Our study demonstrates that the HTLV-I virus exploits a regulatory module that can potentially be attacked therapeutically with BET protein inhibitors.

overall_design: For IRF4 ChIP-seq (n=4), KK1 and ST1 cell line chromatins were immuno-precipitated with normal rabbit IgG (Santa Cruz Biotechnology, sc2027) or IRF4 antibody (Santa Cruz Biotechnology, sc6059 and sc11450 (1:1 mix)). For BATF3 ChIP-seq (n=4), KK1 and ST1 cell line chromatins were immuno-precipitated with normal rabbit IgG (Santa Cruz Biotechnology, sc2027) or BATF3 antibody (R&D, AF7437). For BirA ChIP-seq (n=8), KK1 and ST1 cell lines were engineered to express BirA, transduced with Ctrl, HBZ (pRCMV/TO-flag-BIOTIN-HBZ-puro) or BATF3 (pRCMV/TO-flag-BIOTIN-BATF3-puro) Biotag constructs, and ChIP-seq performed using streptavidin to purify chromatin bound to these isoforms. For H3K27ac and BRD4 ChIP-seq (n=8), KK1 and ST1 cells were pre-treated with either DMSO or JQ1 before being cross-linked and chromatins were later immuno-precipitated with BRD4 antibody (Bethyl, Cat No. A301-985A) or H3K27ac antibody (Abcam, ab4729).


title: Transgenerational effect of Chlordecone

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

institute: Université de Rennes 1


title: Transgenerational effect of Chlordecone [RNA-seq]

summary: RNA seq project designed to understand the role of pesticide on transription of mRNA in the testis. We treated adult female mice with chlordecone with doses 0 (control),  100 Xg/kg/day and 1 mg/kg/day during gestation period E6- E15. Male born from Chlordecone- treated mice were crossed for a three generations. The testes from F3 generations were taken for mRNA extraction. For mRNA extraction we used columb. Three biological replicates used for each condition . We hypothesize that chlordecone cause changes in mRNA due to transgenerational effect of pesticides (Skinner et al, Science 2005). The changes in expression of certain genes can help us understand the effect of pesticides on many tissues. Number of sample :9 samples. We require Paired End sequencing and number of reads equal or more than 25M tags, strand specific sequencing

overall_design: RNA-seq of F3 testis of control and chlordecone-treated mice.

last: Hao

first: Fatima

last: Smagulova


title: Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds

last: Chen


title: Effect of liquid cultivations on N2 and AB1 strains of C. elegans

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: Abrupt environment changes can elicit an array of genetic effects. However, many of these effects can be overlooked by functional genomic studies conducted in static laboratory conditions. We studied the transcriptomic responses of Caenorhabditis elegans under single generation exposures to drastically different culturing conditions. In our experimental scheme, P0 worms were maintained on terrestrial environments (agar plates), F1 in aquatic cultures, and F2 back to terrestrial environments.  The laboratory N2 strain and the wild isolate AB1 strain were utilized to examine how the genotype contributes to the transcriptome dynamics. Significant variations were found in the gene expressions between the “domesticated” laboratory strain and the wild isolate in the different environments. The results showed that 20% - 27% of the transcriptional responses to the environment changes were transmitted to the subsequent generation. In aquatic conditions, the domesticated strain showed differential gene expression particularly for the genes functioning in the reproductive system and the cuticle development. In accordance with the transcriptomic responses, phenotypic abnormalities were detected in the germline and cuticle of the domesticated strain. Further studies showed that distinct groups of genes are exclusively expressed under specific environmental conditions, and many of these genes previously lacked supporting biochemical evidence.

overall_design: To induce an adaptive response and observe its sustained effects on the following generation, the P0 generation C. elegans was grown on bacteria-seeded agar plates, the F1 generation in liquid, and the F2 generation back on agar. We carried out three sets of experiments with different food sources and animal strains. For the first experiment, the F1 generation N2 strain was grown in axenic CeHR Medium. To examine the effect of dietary changes in the liquid cultures, we cultured F1 generation N2 strain in bacterial S-Medium for the second experiment. Finally, the adaptive response differences were investigated by growing F1 generation AB1 strain in CeHR Medium. For each generation, RNA-seq was performed on young adult animals to determine the transcriptional responses

first: Jung

last: Doh

first: Chandran

last: Sabanayagam


title: Transcriptome response of human skeletal muscle to divergent exercise stimuli

city: Phoenix

first: Jared

middle: M

last: Dickinson

address: 425 N 5th St

institute: Arizona State University

summary: While acute aerobic and resistance exercise stimulate a number of shared genes, each exercsie mode stimlutes a number of  uniquely responsive genes, thus highlighting that different forms of exercise facilitate distinct molecular responses in skeletal muscle.

overall_design: Randomized, counter-balanced, cross-over design (n=6) in which subjects performed an acute bout aerobic and resistance exercise separated by ~1 week.

first: Matthew

last: Huentelman

first: Chad

middle: C

last: Carroll

first: Andrew

last: D'Lugos

first: Marcus

middle: A

last: Naymik

first: Ashley

last: Siniard

first: Amanda

last: Wolfe

first: Donald

last: Curtis


title: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: human plasma pool

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed reproducibility and diversity of sequencing of mature miRNAs, generating libraries from RNA extracted from human plasma that was pooled from 11 healthy individuals. We find that protocol-specific biases are largely recapitulated in the biological samples, and that inter-protocol bias correction factors estimated from the more comprehensive equimolar synthetic pools can be applied to the biological samples to get more comparable, and in some cases, more accurate estimates of miRNA abundance.

overall_design: A common pool of human plasma RNA was sequenced by 6 different labs, using 1 common library construction protocol (TruSeq), and at least one additional protocol of their choice. A total of 15 sample libraries was produced, each in quadruplicate.


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export IV

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

summary: To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from HeLa cells.

overall_design: rRNA-depleted RNAs isolated from control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.

first: Xudong

last: Wu

first: Jungang

last: Gu


title: Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions in various Arabidopsis genetic backgrounds [ChIP-seq]

first: Dijun

summary: We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.

overall_design: Mapping of REF6 binding targets and H3K27me3 marked regions in different genetic backgrounds of Arabidopsis.

first: Wenhao

last: Yan

first: Kerstin

last: Kaufmann


title: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

summary:
Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied.  We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Nine labs prepared small RNA-seq libraries from 4 common RNA pools: a) 1 equimolar pool of 1,152 synthetic RNAs, b) 2 pools of synthetic RNAs at differing relative concentrations in pool A and B, and c) human plasma RNA pooled from 11 healthy individuals. Each lab prepared libraries from the samples in quadruplicate, using a standardized TruSeq protocol, as well as at least one other protocol of their choice. Refer to individual Series for details.


title: Gene expression changes after blockade of Frizzled7 in murine intestinal organoids

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
RNA was isolated from intestinal primary mouse organoids at 6h and 24h after treatment with dFz7-21 peptide, Fz7-21S (mock) peptide and DMSO.
These two time points were specifically selected to investigate early and late transcriptional responses after Fzd7 inhibition.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0010717

overall_design: Gene expression profiling of intestinal primary mouse organoids treated with dFz7-21 - a small molecule peptide that specifically and potently blocks Frizzled 7

first: Felipe

last: de Sousa e Melo

first: Aaron

last: Nile


title: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: synthetic ratiometric pools

summary: Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed reproducibility and accuracy of relative expression measurements using two pools of synthetic small RNA sequences, where subsets of the sRNAs vary in relative amount between pools A and B. The pools each contain 334 small RNAs, varying by 15 different ratios between pools A and B (10:1, 8:1, 5:1, 4:1, 3:1, 2:1, 1.5:1, 1:1, 1:1.5, 1:2, 1:3, 1:4 1:5, 1:8, 1:10). We find that although the sequencing bias varies extensively between protocols, the relative abundance measured between samples A and B is largely reproducible and accurate across labs and protocols. These results suggest that measurements of differential expression should be comparable across institutions and library preparation technologies.

overall_design: Two pools of synthetic RNAs were sequenced by 9 different labs, using 1 common library construction protocol (TruSeq), and at least one additional protocol of their choice. The RNA pools contain a common set of synthetic oligos at differing relative concentrations in the SynthA and SynthB pools. A total of 40 sample libraries was produced (20 each for SynthA and SynthB), each in quadruplicate.


title: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: synthetic equimolar pool

summary: Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed sequencing bias and reproducibility using an equimolar pool of 1,152 small RNA sequences ranging from 15-90 nt, and primarily comprised of annotated human microRNAs. We observed extensive protocol-specific and sequence-specific bias that was largely mitigated in protocols employing sequencing adapters with randomized end-nucleotides. We find that sequencing bias is highly reproducible across labs using the same library preparation technologies, and use the data to calculate inter-protocol bias correction factors. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.

overall_design: A single pool comprised of 1,152 synthetic RNAs was sequenced by 9 different labs, using 1 common library construction protocol (TruSeq), and at least one additional protocol of their choice. A total of 20 sample libraries was produced, each in quadruplicate.


title: H3K9me3 and H3K36me3 ChIP-seq in WT and H3.3 G34R mouse ES cells

status: Public on Jul 08 2018

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

institute: Monash University

summary: Sequencing of paediatric gliomas has identified two common substitution mutations (K27M and G34R) in genes encoding histone H3.3. We introduced a single-copy H3.3 G34R targeted mutation in mouse ES cells and observed gains in H3K36me3 and H3K9me3 across the genome. Altered chromatin profiles correlated with enrichment of KDM4 A/B/C, a histone lysine (K9/K36) demethylase. RNA-seq of H3.3 G34R mutant showed disrupted gene expression patterns which also correlated with KDM4 enrichment. Expression of a single copy of H3.3 G34R at endogenous levels was sufficient to genocopy KDM4 triple-KO cells as determined by ChIP-seq and RNA-seq.

overall_design: 4 samples - ChIP-seq of H3K9me3 and H3K36me3 in WT control and H3.3 G34R mutant cells

first: Hsiao

middle: P

first: Lee

last: Wong


title: ChIP sequencing of  intestinal cells in setd2f/f mice

status: Public on Jul 07 2018

first: Li

last: Li

address: 1954 Huashan Road

department: State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University

summary: ChIP sequencing for 2 samples and input.

overall_design: Examing the protein-DNA interaction sites

first: Wenjun

last: Liu


title: MTG1-RNA IP

status: Public on Jul 06 2018

city: Miami

first: Antonio

last: Barrientos

state: Florida

address: 1420NW 9th Street, NRB # 103

department: Neurology

institute: University of Miami Miller School of Medicine

summary: We report the interaction of MTG1 with mitochondrial RNAs.

overall_design: CLIP assay

first: Hyun-Jung

last: Kim

first: Antoni


title: RNA-seq in WT and H3.3 G34R mouse ES cells

overall_design: 2 samples - RNA-seq of WT control and H3.3 G34R mutant cells


title: ChIP-seq of intestinal cells and expression profiling of colon tissue after Setd2 disruption

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

overall_design: Refer to individual Series


title: Genome-wide analysis of 8-oxoguanine DNA glycosylase-1 after oxidative stress exposure

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary: We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase1 (OGG1, a DNA base excision repair protein), after oxidative stress exposure mediated by glucose oxidase (GOx) of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associated with peaks to identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanines (primarily 8-oxoG). OGG1 increased significantly at regulatory regions of CXC-, CC- chemokines, cytokines and growth factors. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. As expected NF-κB was enriched on gene regulatory regions including those of proinflammatory,cell proliferation ones. These and other data derived from further analysis, suggest that OGG1 modulates gene expression in coordination with NF-κB.

overall_design: FLAG-tagged OGG1 expressing HEK293 cells were stimulated with GOx (1 µU) for 0, 15, 30 and 60 min. After GOx exposure, protein-DNA complexes were crosslinked using formalin according to standard Millipore® protocol. DNA was sheared with 10-sec pulses using a Cole-Parmer GEX 130 ultrasonic processor (average 300 bp) and chromatin was immunoprecipitated (IP) with antibody to FLAG or anti-RelA/p65 antibody and IPs were collected using G-agarose beads (Millipore Corporation). After extraction, the DNA was subjected to high-throughput sequencing using Solexa/Illumina genome analyzer (Ambry Genetics).

first: L

last: Aguilera-Aguirre

first: I


title: The H3.3 G34R glioma-associated mutation alters H3K9me3 and H3K36me3 chromatin modifications


title: A versatile drug delivery system targeting senescent cells

status: Public on Jul 05 2018

city: Barcelona

first: Manuel

last: Serrano

state: Barcelona

address: Parc Científic de Barcelona, C/ Baldiri Reixac 10

department: Molecular Medicine

institute: IRB

summary: Senescent cells accumulate in many ageing-associated diseases such as pulmonary fibrosis, and targeting these cells has recently emerged as a promising therapeutic approach. Here, we take advantage of the high β-galactosidase activity of senescent cells to design a targeted drug delivery system based on the encapsulation of drugs with galacto-oligosaccharides (GalNP beads). In this experiment we show that gal-encapsulated rhodamine target senescent cells in the context of pulmonary fibrosis in mice.

overall_design: 8- to 10-week-old C57BL/6 wild-type mice were intratracheally inoculated with  bleomycin at 1.5 U/kg of body weight. Two weeks later mice were i.v. injected with 200 µl of a solution of GalNP beads loaded with rhodamine [GalNP(rho)] at 4 mg/ml, equivalent to 1 mg/kg of deliverable rhodamine. 6 hours later mice were sacrificed and lung cells were analysed by flow cytometry and sorted into Rho+ or Rho- cells, all CD45-CD31-.

first: Miguel

last: Rovira

first: Daniel

last: Muñoz-Espín

first: Coral

last: Fustero-Torre


title: Transcriptomics analysis in 3T3L1 preadipocytes with activation of p53 via Nutlin-3a treatment

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: 3T3L1 preadipocytes were treated with DMSO control and Nutlin-3a (prepared in DMSO) and total RNA  extracted from the treated cells were subjected to illumina based RNA-seq to  analyze and compare transcriptome to understand gene expression regulation influenced by p53 activation via Nutlin-3a treatment.

overall_design: Sample (3T3L1 cells treated with Nutlin-3a) and control (3T3L1 cells treated with DMSO) were taken in biological duplicates for high throuput sequencing based transcriptome analysis

first: Amit

middle: K

last: Behera

first: Madavan

last: Vasudevan

first: Tapas

last: Kundu


title: miR-222 regulation of the tolerized LPS response

city: New York

first: Sankar

last: Ghosh

institute: Columbia University

summary: The purpose of this study is to determine the effect miR-221/222 have on LPS-induced gene expression in macrophages.

overall_design: mRNA profiles of peritoneal macrophages from wildtype or miR-221/222 knockout mice that were untreated, stimulated with LPS, or tolerized and restimulated with LPS were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: John

middle: J

last: Seeley