title: The m7G tRNA methylome regulates embryonic stem cell self-renewal and differentiation

status: Public on Jul 01 2018

city: Boston

first: Shuibin

last: Lin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

summary: tRNAs are subject to numerous modifications including methylation. Mutations in the human N7-methylguanosine (m7G) methyltransferase complex METTL1-WDR4 cause primordial dwarfism and brain malformation yet the molecular and cellular function in mammals is not well understood. We developed m7G methylated tRNA immunoprecipitation sequencing (MeRIP-Seq) and tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome in mouse embryonic stem cells (mESCs). A subset of 22 tRNAs are modified at a ‘RAGGU’ motif within the variable loop. We observe increased ribosome occupancy at the corresponding codons in Mettl1 knockout mESCs implying widespread effects on tRNA function, ribosome pausing, and mRNA translation. Translation of cell cycle genes and those associated with brain abnormalities is particularly affected. Mettl1 or Wdr4 knockout mESCs display defective self-renewal and neural differentiation. Our study uncovers the complexity of the mammalian m7G tRNA methylome and highlights its essential role in ESCs with links to human disease.

overall_design: tRNA m7G MeRIP-Seq and TRAC-Seq were developed to identify the tRNA m7G methylome in mouse embryonic stem cells. RNA-seq was used to study the differential gene expression in the Mettl1 knockout and control cells. Riboseq was used to study the differentially translated genes in the Mettl1 knockout and control cells.

first: Richard

last: Gregory


title: Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations (RNA-Seq)

status: Public on Jun 19 2018

city: Stanford

first: Zhana

last: Duren

state: CA

address: 318 Campus Drive

country: USA

institute: Stanford university

type: Expression profiling by high throughput sequencing

summary: 464 scRNA-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

overall_design: We present a method(Coupled NMF) to cluster single cell chromatin accessibility data and single cell gene expression data simultaneously.

first: Xi

last: Chen

first: Mahdi

last: Zamanighomi

first: Wanwen

last: Zeng

first: Ansuman

middle: T

last: Satpathy

first: Howard

middle: Y

last: Chang

first: Yong

last: Wang

first: Wing

middle: H

last: Wong


title: Single-cell RNA sequencing resolves cellular heterogeneity throughout embryonic development of the thymus

status: Public on Jun 05 2018

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

summary: This dataset consists of single-cell RNA-seq (Drop-seq) data from eight days of mouse thymus development. Samples span from embryonic day 12.5, when the thymus coalesces, until birth. They cover the whole thymus, including mesenchyme, endothelium, epithelium, thymocytes, and other lymphocytes. The dataset also includes Drop-seq data on Rag1-/- embryos and on fetal thymic organ cultures (control and a retinoic acid perturbation).

overall_design: A single-cell atlas of the developing mouse thymus.

first: Eric

last: Kernfeld

first: Ryan

last: Genga

first: Margaret

last: Magaletta

first: Kashfia

last: Neherin

first: Ping

last: Xu

first: René


title: Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination

status: Public on Jul 02 2018

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

summary: Vaccines are among the most effective public health tools for combating certain infectious diseases such as influenza. The role of the humoral immune system in vaccine-induced protection is widely appreciated; however, our understanding of how antibody specificities relate to B cell function remains limited, due to the complexity of polyclonal antibody responses. To address this, we developed the Spec-seq framework, which allows for simultaneous monoclonal antibody (mAb) characterization and transcriptional profiling from the same single cell. Here, we present the first application of the Spec-seq framework, which we applied to human plasmablasts after influenza vaccination in order to characterize transcriptional differences governed by B cell receptor (BCR) isotype and vaccine reactivity. Our analysis did not find evidence of long-term transcriptional specialization between plasmablasts of different isotypes. However, we did find enhanced transcriptional similarity between clonally related B cells, as well as distinct transcriptional signatures ascribed by BCR vaccine recognition. These data suggest IgG and IgA vaccine positive plasmablasts are largely similar, whereas IgA vaccine negative cells appear to be transcriptionally distinct from conventional, terminally differentiated, antigen-induced peripheral blood plasmablasts.

overall_design: 295 single cells passed our quality control filters and were included in our analysis.

first: Karlynn

middle: E

last: Neu

first: Jenna

middle: J

last: Guthmiller

first: Min

last: Huang

first: Jennifer

last: La

first: Marcos

middle: C

last: Vieira

first: Kangchon

last: Kim

first: Nai-Ying

last: Zheng

first: Mario

last: Cortese

first: Micah

last: Tepora

first: Natalie

last: Hamel

first: Karla

last: Rojas

first: Carole

last: Henry

first: Dustin

last: Shaw

first: Charles

middle: L

last: Dulberger

first: Bali

last: Pulendran

first: Sarah

last: Cobey

middle: A

first: Patrick

last: Wilson


title: Transcriptomic analysis of A. baumannii during the course of a pneumonia infection

status: Public on May 23 2018

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Differentially expressed genes were detected during the mice infection in lungs

overall_design: Illumina RNA-seq analysis of bacteria grown during the lung infection versus bacteria grown in LB-flasks

first: Margarita

last: Poza


title: Transcriptional profiling of eosinophil subsets in Interleukin-5 transgenic mice

status: Public on Mar 20 2018

city: Parkville

first: Carolyn

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Eosinophils are important in fighting parasitic infections and are implicated in the pathogenesis of asthma and allergy. Interleukin-5 (IL-5) is a critical regulator of eosinophil development, controlling proliferation, differentiation and maturation of the lineage. Mice that constitutively express IL-5 have more than 10 fold more eosinophils in the haematopoietic organs than their wild type counterparts. We have identified that much of this expansion is in a population of Siglec-F high eosinophils, which are rare in wild type mice. In this study we assessed transcription in myeloid progenitors, eosinophil precursors and Siglec-F medium and Siglec-F high eosinophils from IL-5 transgenic mice and in doing so have created a useful resource for eosinophil biologists. We have then utilised these populations to construct an eosinophil trajectory based on gene expression and to identify gene sets that are associated with eosinophil lineage progression. Cell cycle genes were significantly associated with the trajectory, and we experimentally demonstrate an increasing trend towards quiescence along the trajectory. Additionally we found gene expression changes associated with constitutive IL-5 signalling in eosinophil progenitors, many of which were not observed in eosinophils.

overall_design: Total RNA was obtained from Eosinophil progenitors and subsets on a wild type and interleukin-5 transgenic background

first: Kirsten

last: Fairfax

first: Jessica

last: Bolden

first: Aaron

last: Robinson

first: Erin

last: Lucas

first: Tracey

middle: M

last: Baldwin

first: Kerry

last: Ramsay

first: Rebecca

last: Cole

first: Douglas

last: Hilton


title: Identification of peculiar gene expression profile in peripheral blood mononuclear cells (PBMC) of celiac patients on gluten free diet

status: Public on May 14 2018

city: Bari

first: Marica

last: Cariello

address: Pzza Giulio Cesare

country: Italy

institute: University of Bari

summary: The aim of the present study was to investigate changes in the whole-genome profile of the PBMCs of subjects with celiac disease (vs. controls).

overall_design: RNA obtained from PBMCs of the CTRL subjects and celiac patients. Comparisons: control vs celiac

first: Simona

last: D'amore

first: Giusi

last: Graziano


title: Transcriptome profiling identified a 3-lncRNA regulatory network in transthyretin against glucose induced hRECs dysfunction

status: Public on Jul 18 2018

city: Shanghai

first: Yunbin

last: Zhang

address: No. 320, Yueyang Road, Xuhui District

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

summary: Transcriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG) or high glucose with 4 uM TTR (HG+TTR) were conducted. Differentially expressed lncRNAs, mRNAs and TTR related lncRNAs and mRNA were acquired for further analysis. Functional annotation and enrichment including KEGG pathway, GO and GSEA were applied to analyze TTR regulated pathway and process. WGCNA analysis was implemented to obtain hub modules and genes. LncRNA-mRNA regulatory network were constructed based on cis, trans and ceRNA acting mode.

overall_design: Examination of Human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG), or high glucose with 4 uM TTR (HG+TTR)

first: Jun

last: Shao

first: Yong

last: Yao


title: Expression data of Glutarmatergic neuron and GABAergic neruon induced from iPSCs

status: Public on Jul 10 2018

city: shinjuku-ku, Tokyo

first: Takaya

last: Ishii

department: School of medicine

country: Japan

institute: Keio university

summary: We used microarrays to identify the differently expressed genes in disease model for bipolar disorder and schizophrenia.

overall_design: Expression profiling of neurons induced from iPSCs. Two neuron types: Glutamatergic and GABAergic. iPSCs came from healthy control, or patient with bipolar disorder or schizophrenia.

first: Hideyuki

last: Okano


title: Gene expression analysis of E16.5 Stk11-sufficient control and Sk11-/- lungs

status: Public on Jul 06 2018

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: Functional properties of mucosal surfaces are dependent on establishing the correct proportions of specialized epithelial cell types. In the mammalian airway, the proportions of ciliated and secretory cells types are tightly regulated to ensure efficient mucociliary clearance. Ciliated cells are one of the first mature cell types to be specified by differentiation of multipotent endodermal progenitors of the developing lung and can be replaced postnatally by differentiation of secretory progenitors. In each case, cell cycle exit is a necessary, early step that precedes differentiation. However, the relationship between cell cycle exit and cell fate determination is poorly understood. We show that the serine-threonine kinase Stk11 controls the cell cycle exit in airway stem/progenitor cells via phosphorylation and activation of the AMPK-related kinase Mark3, which directly suppresses Erk1/2 mediated Rb inactivation. Our study demonstrates that Stk11-dependent cell cycle exit accounts for the normal program of ciliated cell differentiation in developing and postnatal airways.

overall_design: Examination of gene expression in two E16.5 Stk11-sufficient control lungs, examination of gene expression in two E16.5 Stk11-/- lungs.

first: Qiqi

last: Chu

first: Huanwei

last: Huang

last: Tang


title: Deep-sequencing Identifies Prominent small RNA Profiles In Campthotecin-sensitive And Resistant Jurkat Cells

status: Public on Feb 12 2018

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: The balance between proliferation and apoptosis is essential to sustain homeostasis in T-cells. In addition to the well-documented transcriptional regulation, post-transcriptional gene regulatory networks have prominent effects on the regulation of T cell apoptosis. MicroRNAs (miRNAs) are non-coding small RNAs of about 17-25 nucleotides in length, which negatively regulate gene expression by translational inhibition or mRNA degradation. Although the comparison of healthy and cancerous tissues identified a number of miRNAs whose targets include apoptotic/anti-apoptotic genes, a more comprehensive screening is yet to be performed. We induced apoptosis with camptothecin, an inhibitor of DNA topoisomerase I, sorted the drug-sensitive pre-apoptotic Jurkat cells from the drug-insensitive ones, and deep-sequenced small RNAs in control, drug-sensitive and insensitive cells. Our results showed that drug-sensitive and –insensitive cells possess unique small RNA profiles, especially in miRNA and tRNA-derived ones. Additionally, they inversely express certain miRNAs such as miR-128, 720, and 425 compared to the untreated control cells.

overall_design: Apoptosis was induced in Jurkat T-cell Lymphocyte cells with  8 µg /mL camptothecin. The drug-sensitive pre-apoptotic Jurkat cells were sorted from the drug-insensitive ones using magnetic beads. small RNA profiles were obtained from control (JNN), drug-sensitive (JAP) and insensitive (JAN) cells through deep-sequencing with an Illumina platform.

first: Ipek

last: Erdogan

first: Mehmet

middle: I

last: Cosacak

first: Ayten

last: Nalbant


title: Single cell RNA sequencing of multiple myeloma II

status: Public on May 24 2018

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

summary: To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By combining allele frequency and expression magnitude deviations, HoneyBADGER is able to infer the presence of subclone-specific alterations in individual cells and reconstruct subclonal architecture. Also HoneyBADGER to analyze single cells from a progressive multiple myeloma (MM) patient to identify major genetic subclones that exhibit distinct transcriptional signatures relevant to cancer progression.

overall_design: We performed single cell RNA sequencing (RNA-seq) for multiple myeloma from the bone marrow and/or extramedullary sites from 3 patients. Data contain 173 and 1,339 single-cell RNA-seq from Fluidigm C1  and 10x Genomics respectively.

first: Jean

last: Fan

first: Peter

last: Kharchenko

first: Hae-Ock

last: Lee

first: Kihyun

last: Kim

first: Woong-Yang

last: Park


title: High-throughput sequencing  identify miRNAs involved in exosomes of MDA-MB-231 cocultivated with or without mature 3T3-L1

status: Public on Jan 31 2018

city: Wuhan

first: Wu

last: Qi

state: Hubei

address: 99 Zhang Zhidong Road

department: Department of Breast and Thyroid Surgery

institute: Renmin Hospital of Wuhan University

summary: To identify miRNAs involved in exosomes from MDA-MB-231 cultivated with mature 3T3-L1, small RNA libraries from exosomes stored at 20 °C for 0 and 24 h were constructed. A total of 432 small RNA sequences were generated, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 85 miRNAs were up-regulated and 300 were down-regulated in exosomes from MDA-MB-231 cultivated with mature 3T3-L1.


title: Genome -wide profile of SMRTER binding in Drosophila wing imaginal discs

status: Public on Dec 31 2017

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary: Several co-repressors interact directly with the DNA-binding protein CSL [Su(H) in Drosophila] and are proposed to keep target genes silenced in the absence of Notch activity.  To investigate co-repressor activity in the context of this well defined signalling pathway, we analysed the genome-wide binding profile of the best-characterized CSL co-repressor in Drosophila, Hairless, in Kc cells and in wing imaginal discs.  The binding profile in wing discs of a second CSL interacting repressor, SMRTER, was also analysed. There was significant overlap between Hairless and Su(H), both in Kc cells and in wing discs, where they were predominantly found in chromatin with active enhancer marks. The Hairless complex was widely present at some Notch regulated enhancers in the wing disc,but  no binding was detected at others, indicating that it is not essential for silencing per se. Analysis of target enhancers confirmed differential requirements for Hairless. SMRTER binding significantly overlapped with Hairless, rather than complementing it, and many enhancers were apparently co-bound by both factors. Our analysis indicates that the actions of Hairless and SMRTER gate the enhancers to Notch activity and to Ecdysone signalling respectively, to ensure that the appropriate levels and timing of target gene expression are achieved.

overall_design: Three replicates from Chromatin immunoprecipitation of SMRTER-YFP from wing imaginal discs, input and ChIP samples

first: Stephen

last: Chan

first: Bettina

last: Fischer

first: Steven

last: Russell


title: Response of Arabidopsis thaliana seedlings to acyl-CoAs

status: Public on Apr 30 2018

city: Antwerpen

first: Gerrit

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary: Floodings already have a nearly 60% share in the worldwide damage to crops provoked by natural disasters. Climate change will cause plants to be even more frequently exposed to oxygen limiting conditions (hypoxia) in the near future due to heavy precipitation and concomitant waterlogging or flooding events in large areas of the world. Although the homeostatic regulation of adaptive responses to low oxygen stress in plants is well described, it remained unknown by which initial trigger the molecular response to low-oxygen stress is activated. Here, we show that a hypoxia-induced decline of the ATP level of the cell reduces LONG-CHAIN ACYL-COA SYNTHETASE (LACS) activity, which leads to a shift in the composition of the acyl-CoA pool. High oleoyl-CoA levels release the transcription factor RELATED TO APETALA 2.12 (RAP2.12) from its interaction partner ACYL-COA BINDING PROTEIN (ACBP) at the plasma membrane to induce low oxygen-specific gene expression. We show that different acyl-CoAs provoke unique molecular responses revealing a novel role as cellular signalling component also in plants. In terms of hypoxia signalling, dynamic acyl-CoA levels integrate the cellular energy status into the oxygen signalling cascade with ACBP and RAP2.12 being the central hub. The conserved nature of the ACBP:RAP2.12 module in crops and the novel mechanistic understanding of how low-oxygen stress responses are initiated by oleoyl-CoA in plants provide useful leads for enhancing future food security.

overall_design: 1 control and 3 treatments with different forms of acyl-CoA in triplicate biological replicates

first: Romy

last: Schmidt

first: Marios

middle: N

last: Markakis

first: Jos

last: Schippers

first: Joost

last: van Dongen


title: Genomic profile of Hairless binding in Drosophila wing discs

overall_design: Three replicates from Chromatin immunoprecipitation of Hairless-GFP from wing imaginal discs, input and ChIP samples


title: Genome-wide profile of Notch pathway co-repressors and their role in shaping the Notch response

summary:
This SuperSeries is composed of the SubSeries listed below.
Several co-repressors interact directly with the DNA-binding protein CSL [Su(H) in Drosophila] and are proposed to keep target genes silenced in the absence of Notch activity.  To investigate co-repressor activity in the context of this well defined signalling pathway, we analysed the genome-wide binding profile of the best-characterized CSL co-repressor in Drosophila, Hairless, in Kc cells and in wing imaginal discs.  The binding profile in wing discs of a second CSL interacting repressor, SMRTER, was also analysed. There was significant overlap between Hairless and Su(H), both in Kc cells and in wing discs, where they were predominantly found in chromatin with active enhancer marks. The Hairless complex was widely present at some Notch regulated enhancers in the wing disc,but  no binding was detected at others, indicating that it is not essential for silencing per se. Analysis of target enhancers confirmed differential requirements for Hairless. SMRTER binding significantly overlapped with Hairless, rather than complementing it, and many enhancers were apparently co-bound by both factors. Our analysis indicates that the actions of Hairless and SMRTER gate the enhancers to Notch activity and to Ecdysone signalling respectively, to ensure that the appropriate levels and timing of target gene expression are achieved.

overall_design: Chromatin Immunoprecipitation (ChIP) and Transcription profiling of Kc cells, ChIP of wing discs

first: Gustavo

last: Cerda-Moya

last: Fisher


title: Unsupervised clustering and epigenetic classification of single cells

status: Public on Apr 20 2018

first: Mahdi

last: Zamanighomi

address: 390 Serra Mall

department: Statistics

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 96 scATAC-seq samples generated for the retinoic acid-induced mESC differentiation at day 4.

overall_design: We present a method that solely utilizes scATAC-seq data for the unsupervised clustering of cells and determination of cluster-specific open regions. The proposed procedure allows for the discovery of open chromatin regions specific to cell identity and the identification of transcription factors that drive the variation in cell identity.

first: Zhixiang

last: Lin

first: Timothy

last: Daley

first: Xi

last: Chen

first: Zhana

last: Duren

first: Alicia

last: Schep

first: William

last: Greenleaf

first: Wing

last: Wong


title: Expression changes in Hairless depleted Kc cells

first: Sarah

last: Bray

overall_design: RNAs were purified from replicates of two pairs of samples, Kc cells treated with control (white) dsRNA and Kc cells treated with Hairless dsRNA

first: Steve

last: Fischer


title: Endogenous RAC1 P29S in mouse melanoma

status: Public on Aug 10 2018

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

institute: The Francis Crick Institute

summary: We studied the effects of endogenous expression of the melanoma oncogene RAC1 P29S in BRAF V600E;PTEN hemizygous mouse melanomas.

overall_design: Transgenic mice with a conditional knock-in of the P29S mutation in the endogenous Rac1 locus were generated and crossed onto C57BL/6J, Tyr-CreER;BrafCA/wt;Ptenfl/wt mice. Melanomas were induced by topical 4OH-tamoxifen. We compared the gene expression profile in whole tumour lysates from Tyr-CreER+/-;Ptenfl/wt;BrafCA/wt;Rac1LSL-P29S/wt mice versus Tyr-CreER+/-;Ptenfl/wt;BrafCA/wt;Rac1wt/wt mice (n = 6 tumours from 5-6 animals per group).

first: Daniel

last: Lionarons

first: Julian

last: Downward


title: Genome-wide profiling of Notch corepressor Hairless in Kc cells using Dam-ID

overall_design: Three replicates from expression of Hairless-Dam fusion, 2 controls from DAM only

last: Russell

first: Bettina


title: DNA-binding pluripotency factors and DNA demethylases can cooperate to maintain pluripotent stem cell identity even in the absence of Brd4 [RNA-seq]

status: Public on Apr 10 2018

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Histone acetylation and the acetyl-lysine reader Brd4 have recently been implicated in embryonic stem cell (ESC) proliferation and self-renewal. We found that naïve pluripotent ESCs exhibit increased incorporation of glucose-derived carbons onto acetylated histones and elevations in H3K9ac and Brd4 recruitment at pluripotency gene promoters. Surprisingly, both H3K9 acetyltransferases, GCN5 and PCAF, and Brd4 recruitment were dispensable for proliferation, self-renewal and pluripotency of naïve ESCs. Naïve ESCs maintain gene expression by stabilizing Mediator at core pluripotency genes in a Brd4-independent manner. Brd4-independent proliferation could also be achieved in metastable ESCs by overexpression of pluripotency transcription factors. Under all conditions, self-renewal required the DNA methylcytosine oxidases Tet1 and Tet2. These data reveal that there is minimal dependence on Brd4 for self-renewal of naïve ESCs. Instead, the relative levels of DNA methylation and transcription factor abundance determine the requirement for bromodomain recognition of histone acetylation to the maintenance of stem cell identity.

overall_design: RNA sequencing of murine embryonic stem cells maintained in media containing fetal bovine serum and leukemia inhibitory factor (LIF) with or without inhibitors of GSK3b and MEK ('2i') and treated for 72h with JQ1 or vehicle control.

first: Lydia

middle: W

last: Finley

first: Santosha

last: Vardhana

first: Bryce

last: Carey

first: C

middle: D

last: Allis

first: Craig

middle: B

last: Thompson


title: Short trichome comparative genomic hybridization analysis in glycine max fast neutron mutants

status: Public on Aug 08 2018

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary: One short trichome mutant (family known by multiple names, including R59C46, FN0175946, and FNMN0409) was identified in a soybean fast neutron population (known as VP02 in Bolon et al. 2011). An advanced line of this mutant was compared to its wild-type parent (M92-220-Long) using CGH to identify the causative region/gene associated with the short trichome phenotype.

overall_design: One sample was analyzed. The sample was compared to its wild type parent (M92-220-Long) using Agilent CGH arrays.

first: Benjamin

last: Campbell

first: Adrian

last: Stec


title: Rat embryonic stem cells produce fertile offspring through tetraploid complementation

status: Public on Oct 11 2017

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Survival of pancreatic cancer cells lacking KRAS function

status: Public on Oct 23 2017

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Activating mutations in the proto-oncogene KRAS are a hallmark of pancreatic ductal adenocarcinoma (PDAC), an aggressive malignancy with few effective therapeutic options. Despite efforts to develop KRAS-targeted drugs, the absolute dependence of PDAC cells on KRAS remains incompletely understood. Here we modeled complete KRAS inhibition using CRISPR/Cas-mediated genome editing. While KRAS knockout led to decreased in vitro proliferation and impaired in vivo tumorigenic growth, KRAS was dispensable in a subset of human and mouse PDAC cells. KRAS knockout cells exhibited hyperactivation of the PI3K pathway and induced sensitivity to phosphoinositide 3-kinase (PI3K) inhibitors. Mechanistically, PI3K inhibition in KRAS knockout cells led to transient mitogen-activated protein kinase (MAPK) blockade while impeding AKT-dependent 4EBP1 phosphorylation and cap-dependent translation. Furthermore, comparison of gene expression profiles of cells retaining or lacking KRAS revealed a novel functional role of KRAS in the suppression of metastasis-related genes. Accordingly, KRAS knockout gene expression signatures correlated with PDAC circulating tumor cell (CTC) signatures, and human PDAC tumors with gene expression patterns enriched in signatures from KRAS knockout cells were associated with worse survival in patients. Together, these data underscore the potential for resistance of PDAC to even the very best of KRAS inhibitors and suggest combination therapies with PI3K inhibitors as a viable strategy to circumvent resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: KRAS intact and knockout subclones from human 8988T and mouse A13 parental cell lines. Biologic replicates include 4 intact and 3 knockout clones from 8988T and 2 intact and 2 knockout clones from A13.

first: Mandar

last: Muzumdar

first: Pan-Yu

last: Chen

first: Kimberly

last: Dorans

first: Arjun

first: Erin

last: Hong

first: Tyler

last: Jacks


title: Identification of differentially expressed genes by RNA-seq in AtGRP7 overexpression and knockdown lines

status: Public on Sep 28 2017

city: Bielefeld

first: Martin

last: Lewinski

address: Universitätsstraße 25

department: RNA Biology and Molecular Physiology

country: Germany

institute: Bielefeld University

summary: A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo regulatory landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNAseq to determine the genome-wide regulation repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.

overall_design: AtGRP7 RNA-seq

first: Katja

last: Meyer

first: Tino

last: Köster

first: Christine

last: Nolte

first: Claus

last: Weinholdt

first: Ivo

last: Grosse

first: Dorothee

last: Staiger


title: Rat embryonic stem cells produce fertile offspring through tetraploid complementation [RNA-Seq]

summary: Pluripotency of embryonic stem cells (ESCs) can be functionally assessed according to their developmental potency. Tetraploid complementation, through which an entire organism is produced from donor pluripotent cells, is taken as the most stringent test for pluripotency. It remains unclear whether ESCs from other species besides mice can pass this test. Here we show that the rat ESCs at very early passages are also capable to produce fertile offspring by tetraploid complementation, however, this capacity is rapidly lost during culture due to the loss of genomic imprinting. Our findings support that the naïve ground state pluripotency exists in rat and can be captured in rat ESCs, yet may be subjected to species-specific regulations, which have implications for the derivation and application of naïve pluripotent stem cells in other species including human.

overall_design: mRNA profiles of different passage rat embryonic stem cells

first: Tianda

last: Li

first: Guihai

last: Feng

first: Yufei

first: Mei

last: Wang

first: Wei


title: Rat embryonic stem cells produce fertile offspring through tetraploid complementation [RRBS]

first: Qi

last: Zhou

overall_design: RRBS profiles of different passage rat embryonic stem cells, tail tip, sperm.


title: Identification of the impact of RB status on chromatin accessibility [ATAC-seq]

status: Public on Feb 22 2018

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: The retinoblastoma protein (RB) is preferentially lost in the progression to castrate resistant prostate cancer (CRPC). However, the alterations associated with such loss have been scantly described.  Current findings have identified a novel E2F1 associated cistrome and transcriptome that is associated with RB loss in PCa.  In order to determine the contribution of chromatin accessibility to alterations in E2F1 activity, ATAC-Seq was performed.

overall_design: ATAC-Seq was performed on isogenic shCON and shRB LNCaP lines.  shCON cells were cultured and harvested in both hormone deficient and stimulated conditions, and shRB cells in hormone deficient conditions.

first: Karen

last: Knudsen


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [ATAC-Seq]

status: Public on Aug 29 2017

city: NYC

first: Marian

last: Mellen

address: 1230 York Avenue

institute: The Rockefeller University

summary: 5-hydroxymethylcytosine (5hmC) occurs at maximal levels in postmitotic neurons where its accumulation is cell specific and correlated with gene expression. Here we demonstrate that the distribution of 5hmC in CG and non-CG dinucleotides is distinct, and that it reflects the binding specificity and genome occupancy of methylcytosine binding protein 2 (MeCP2). In expressed gene bodies, accumulation of 5hmCG acts in opposition to 5mCG resulting in “functional” demethylation and diminished MeCP2 binding, thus facilitating transcription. Non-CG hydroxymethylation occurs predominantly in CA dinucleotides (5hmCA) and it accumulates in regions flanking active enhancers. In these domains, oxidation of 5mCA to 5hmCA does not alter MeCP2 binding or expression of adjacent genes. We conclude that the role of 5-hydroxymethylcytosine in postmitotic neurons is to functionally demethylate expressed gene bodies while retaining the role of MeCP2 in chromatin organization.

overall_design:
Examination of methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding.
ATAC-Seq dataset.

first: Nathaniel

last: Heintz


title: RNA seq of pancreatic cancer-associated fibroblasts

status: Public on Jan 20 2018

city: La Jolla

first: Paul

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

summary: Transcriptomic profiling of pancreatic cancer-associated fibroblasts (CAFs) was done to evaluate the expression of GPCRs. The same was also done for normal pancreatic stellate cells, so as to evaluate whether a population of GPCRs shows increased expression in CAFs vs their normal precursors. We report the discovery of a novel GPCR in CAFs; we demonstrate this GPCR helps to drive the cross-talk between CAFs and cancer cells, enhancing the growth of pancreatic cancer cells.

overall_design: Stranded mRNA sequencing of 3 lines of de-identified patient-derived, low-passage pancreatic CAFs and 1 line of normal pancreatic stellate cells (PSCs)

first: Shu

middle: Z

last: Wiley

first: Krishna

last: Sriram


title: Transcriptome analysis of gene expression in sec59-1∆ yeast cells

status: Public on Jan 15 2018

city: Tiruchirapalli

first: Vasanthi

last: Nachiappan

state: Tamil Nadu

address: School of Life Sciences

department: Biochemistry

country: India

institute: Bharathidasan University

summary: Microarray data revealed that, 1880 genes  were up regulated and 1430 genes were down regulated  among that  3310 genes, 92 lipidomic genes were up regulated and 17 genes were down regulated in sec59-1∆.  In sec59-1∆ cells, phospholipid, neutral lipid, sphingolipid and fatty acid metabolism genes were up regulated. N-Glycosylation defect affected various organelle functions such as mitochondria, peroxisome, vacuole and ER. Finally we can conclude from the microarray data, N-glycosylation   plays a crucial role in regulating the lipidome homeostasis  Microarray data revealed that, 1880 genes  were up regulated and 1430 genes were down regulated  among that  3310 genes, 92 lipidomic genes were up regulated and 17 genes were down regulated in sec59-1∆.  In sec59-1∆ cells, phospholipid, neutral lipid, sphingolipid and fatty acid metabolism genes were up regulated. N-Glycosylation defect affected various organelle functions such as mitochondria, peroxisome, vacuole and ER. Finally we can conclude from the microarray data, N-glycosylation   plays a crucial role in regulating the lipidome homeostasis

overall_design: Organism : Saccharomyces cerevisiae , Custom Saccharomyces cerevisiae 8x15k Gene expresssion Microarray (AMADID: 016333) designed by Genotypic Technology Private Limited

first: William

last: James


title: Genome-wide profile of Hairless occupancy in Kc cells

first: Sarah

last: Bray

overall_design: Three replicates of experiments immunoprecipitating Hairless GFP (Hairless) from Kc cells, input and ChIP from each experiment

first: Gustavo

last: Cerda-Moya

first: Steven

last: Russell

first: Bettina

last: Fischer


title: Isolation and culture of carotid atherosclerotic plaque inner mass cells

status: Public on Jun 26 2018

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

summary: To characterize atherosclerotic plaque cells we isolated cells from the body of vulnerable and stable human atherosclerotic plaques and performed RNA-Seq gene expression profiling of obtained samples.

overall_design: RNA-Seq gene expression profiling of stable and vulnerable plaque inner mass cells. We generated two biological replicates for each cell type, thus we obtained 4 RNA-Seq gene expression profiles.

first: Olga

last: Novikova

first: Joanna

last: Nazarkina

first: Anna

last: Cherepanova

first: Boris

last: Chelobanov

first: Roman

last: Deev

first: Evgeny

last: Pokushalov

first: Аndrey

last: Karpenko

first: Pavel


title: A cluster of miRNAs regulate MYB repressors to promote anthocyanin accumulation in grapes (sRNA-Seq)

status: Public on Dec 20 2017

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

institute: National Center for Biological Sciences

summary: MicroRNAs  are a class of endogeneously expressed non-coding small, ~21nt RNAs involved in the negative regulation of gene expression. In plants, miRNAs are known to play a critical role in developmental and metabolic pathways, as they predominantly target transcription factors. Studies in Arabidopsis and apple have shown that few microRNAs and small interfering (si) RNAs target MYB transcription factors, which are key regulators of phenylpropanoid pathway. However, it is not well-understood how miRNAs mediate regulation of MYBs to produce secondary metabolites such as anthocyanins and flavonoids. Here we show that, a cluster of abundant miRNAs target MYB transcription factors in anthocyanin rich fruits such as grapes. Using deep small RNA-sequencing we establish that grape varieties with high anthocyanin content express abundant MYB-targeting miRNAs resulting in differential expression of MYB proteins among grape varieties, thereby regulating the phenylpropanoid pathway.

overall_design: Deep sequencing of small RNA of three cultivars of grapes with varying levels of anthocyanin.

first: Padubidri

middle: V

last: Shivaprasad

first: Swetha

last: Chenna

first: Varsha

last: Tirumalai


title: NR2E3 gene networks are associated with AHR signaling pathways

status: Public on Oct 31 2017

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

summary: In order to identify NR2E3-specific gene expression pattern in liver cancer cell line, small hairpin RNA for NR2E3 was transfected in HepG2 human liver cancer cells.

overall_design: Two groups of samples are included: 1. sh control (shCT_1, shCT_2); 2. shNR2E3 (shNR2E3 KO_1 , shNR2E3 KO_2). Gene expression profiles of NR2E3 depleted cells were compared to that of shRNA controls. Experiments were performed in HepG2 cells.

first: Kyunghyun

first: Kwangmin

last: Choi


title: Genome-wide profile of Su(H) occupancy in Kc cells

first: Sarah

last: Bray

summary: Several co-repressors interact directly with the DNA-binding protein CSL [Su(H) in Drosophila] and are proposed to keep target genes silenced in the absence of Notch activity.  To investigate co-repressor activity in the context of this well defined signalling pathway, we analysed the genome-wide binding profile of the best-characterized CSL co-repressor in Drosophila, Hairless, in Kc cells and in wing imaginal discs.  The binding profile in wing discs of a second CSL interacting repressor, SMRTER, was also analysed. There was significant overlap between Hairless and Su(H), both in Kc cells and in wing discs, where they were predominantly found in chromatin with active enhancer marks. The Hairless complex was widely present at some Notch regulated enhancers in the wing disc,but  no binding was detected at others, indicating that it is not essential for silencing per se. Analysis of target enhancers confirmed differential requirements for Hairless. SMRTER binding significantly overlapped with Hairless, rather than complementing it, and many enhancers were apparently co-bound by both factors. Our analysis indicates that the actions of Hairless and SMRTER gate the enhancers to Notch activity and to Ecdysone signalling respectively, to ensure that the appropriate levels and timing of target gene expression are achieved.

overall_design: Three replicates of experiments immunoprecipitating Su(H) GFP (Suppressor of Hairless) from Kc cells, input and ChIP from each experiment

first: Gustavo

last: Cerda-Moya

first: Steven

first: Bettina


title: Identification of AtGRP7 targets by RIP-seq

first: Martin

last: Lewinski

summary: A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNA Immunoprecipitation (RIP-seq) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.

overall_design: AtGRP7 RIP-seq

first: Katja

last: Meyer

first: Tino

last: Köster

first: Christine

last: Nolte

first: Claus

last: Weinholdt

first: Ivo

last: Grosse

first: Dorothee

last: Staiger


title: A transcriptome survey of Trichophyton  rubrum exposed to undecanoic acid

status: Public on Feb 06 2018

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We assessed the transcriptome of the pathogenic fungus T. rubrum through RNA-seq analysis to identify transcriptome-wide changes in gene expression after challenge with undecanoic acid (UDA)
Methods: T. rubrum conidia (about 1x10^6 conidia per mL) were grown on Sabouraud medium for 96h, at 28ºC under shaking. The resulted mycelium   was transferred to RPMI 1640 medium in the absence or presence UDA (17.25 μg/mL) for 3h and 12h under shaking. Approximately 100 mg of frozen mycelia were used for total RNA extraction using  Illustra RNAspin Mini Isolation Kit (GE, USA)  and treated with RNAse-free DNAse I. RNA concentrations were estimated through NanoDrop ND-1000 spectrophotometer, and RNA integrity was verified using  Agilent Bioanalyser platform 2100. RNA libraries were prepared for sequencing according to Illumina guidelines.
Results:  We identified changes in specific functional categories, indicating that a significant number of genes respond to the stress induced by UDA, including those that determine fungal virulence. Moreover, the data generated provide evidence that UDA induces the alternative splicing of several genes involved in diverse metabolic pathways.
Conclusions: The general effect of UDA fungal toxicity involves changes to fungal metabolism and mechanisms for regulating pre-mRNA processing events.

overall_design: T. rubrum transcriptome in response to sublethal doses of undecanoic acid was assessed using a high-throughput RNA-sequencing (RNA-seq) technique in order to provide new insights about mechanism of UDA in the fungal toxicity.

first: Niege

middle: S

last: Mendes

first: Tamires

last: Bitencourt

middle: R

first: Rafael

last: Rocha

first: Nilce

last: Martinez-Rossi

first: Antonio

last: Rossi


title: A cluster of miRNAs regulate MYB repressors to promote anthocyanin accumulation in grapes (RNA-Seq)

first: Shivaprasad

last: Padubidri V.

summary: MicroRNAs  are a class of endogeneously expressed non-coding small, ~21nt RNAs involved in the negative regulation of gene expression. In plants, miRNAs are known to play a critical role in developmental and metabolic pathways, as they predominantly target transcription factors. Studies in Arabidopsis and apple have shown that few microRNAs and small interfering (si) RNAs target MYB transcription factors, which are key regulators of phenylpropanoid pathway. However, it is not well-understood how miRNAs mediate regulation of MYBs to produce secondary metabolites such as anthocyanins and flavonoids. Here we show that, a cluster of abundant miRNAs target MYB transcription factors in anthocyanin rich fruits such as grapes. Using RNA-sequencing we establish that grape varieties with high anthocyanin content express abundant MYB-targeting miRNAs resulting in differential expression of MYB proteins among grape varieties, thereby regulating the phenylpropanoid pathway.

overall_design: RNA-Seq of three cultivars of grapes with varying levels of anthocyanin.

first: Padubidri

last: Shivaprasad

first: Swetha

last: Chenna

first: Varsha

last: Tirumalai


title: Gene expression profiling in Dip G-treated HL-60 cells

status: Public on Jul 31 2017

city: Nanjing

first: Jian

last: Gao

state: Jiangsu

address: 22 Han Kou Road

institute: Nanjing university

summary: To understand the function of the small molecule Dip G, the gene expression profiles of HL-60 cells treated with Dip G were analyzed using the microarray.

overall_design: HL-60 cells were treated for 24 h in the absence or presence of Dip G (15 mM). Three replicates were performed in every independent experiment.

first: Yan

last: Shen

first: Minmin

last: Fan


title: Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent siRNAs in the nrpd1-3 mutant (sRNA).

status: Public on Jul 17 2017

city: Bloomington

first: Jered

last: Wendte

state: IN

address: 915 E. 3rd Street

institute: Indiana University

summary: The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.

overall_design: The Pol IV largest subunit DeCL domain deletion mutant, nrpd1 ΔDeCL, was assessed for sRNA expression across 24 nt siRNA clusters

first: Craig

last: Pikaard


title: An integrative network biology analysis identifies miR-508-3p as the determinant and a prognosis biomarker of the mesenchymal subtype ovarian cancer

status: Public on Jun 01 2018

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

institute: West China Second University Hospital

summary: Recently, several research groups have identified the mesenchymal subtype of serous OvCa on the basis of transcriptome data and its potential correlation with poor prognosis. We set out to define the regulatory mechanisms underlying the distinct gene expression profiles of serous OvCa using a network-based approach involving multiple molecular modalities such as gene expression and microRNA (miR) expression. Our study demonstrated that the mir-508-3p presented as the most powerful determinant of mesenchymal subtype-specific gene expression, tuning the majority of genes differentially expressed in the poor prognosis subtype, including genes associated with the epithelial–mesenchymal transition (EMT) program. Consequent functional experiments illustrate that miR-508-3p inhibition promoted EMT process, in vitro cell migration and invasion, and in vivo cancer metastasis.

overall_design: Total RNA was isolated after treatment with control miRNA or miR-508-3p inhibitor in OVTOKO and OVISE cell lines. Two independent experiments were carried out and gene expression profiles were analyzed.

first: Shengtao

first: Xin

last: Wang


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes

first: Marian

last: Mellen

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

overall_design: Refer to individual Series


title: Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast

status: Public on Jul 13 2017

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

institute: Waseda Institute for Advanced Study


title: Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent DNA methylation in the nrpd1-3 mutant (Bisulfite-Seq).

overall_design: The Pol IV largest subunit DeCL domain deletion mutant, nrpd1 ΔDeCL, was assessed for Pol IV-dependent DNA methylation with whole genome bisulfite sequencing.


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [MethylC-Seq and oxBS-Seq]

overall_design:
Examination of methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding.
MethylC-Seq oxBS-Seq dataset.

first: Nathaniel

last: Heintz


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [ORGANIC ChIP-Seq]

overall_design:
Examination of methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding.
ORGANIC ChIP-Seq dataset.


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [ChIP-Seq]

overall_design:
Examination of methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding.
ChIP-Seq dataset.


summary: Chromatin fibres dynamically change their organisation during cell cycle. In interphase nucleus, chromatin fibres are evenly distributed whereas their spatial occupancy are reorganised to form condensed chromosomes in mitosis. This process called chromosome condensation is necessary for an accomplishment of faithful chromosome segregation. One of the Structural Maintenance of Chromosomes complexes, Condensin, is indispensable for chromosome condensation. It remains, however, unknown how Condensin plays its role in shaping mitotic chromosome. Here we show that chromatin fibres change their interacting partners; short-range contacts in interphase nucleus are converted into long-range interactions to shape condensed chromosomes. This conversion of interactions among chromatin fibres results in the formation of larger domains within mitotic chromosomes. Condensin is solely in charge of the conversion and large domain formation in fission yeast mitosis. Our results show how fission yeast Condensin is involved in shaping mitotic chromosomes.

overall_design: Condensin ChIP-seq samples in mitosis.


title: Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis)

status: Public on Aug 01 2017

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

country: Canada

institute: The University of Victoria

summary: This study investigates transcriptomic responses of Pacific salmon lice, Lepeophtheirus salmonis, to infection with the microsporidian Facilispora margolisi and/or exposure to emamectin benzoate (EMB), an antiparasitic agent commonly used in salmon aquaculture.

overall_design: Copepodid larvae derived from individual egg strings were divided into control (0 ppb EMB) and treated (1 ppb EMB) groups, n = 14 pools for each group. Half of each group (i.e. control and treated) was derived from egg strings that tested positive for F. margolisi infection (n = 7 pools/group) and the other half of each group were derived from F. margolisi negative eggs.

first: Jordan

last: Poley

last: Sutherland

first: Mark

last: Fast

first: Simon

last: Jones


title: Expression profiling of NMuMG progression series

status: Public on Jun 17 2017

city: Charleston

first: Philip

middle: H

last: Howe

state: South Carolina

address: 173 Ashley Avenue

institute: Medical University of South Carolina

summary: We have developed a progression series of increasingly metastatic cell lines generated from the normal mammary epithelial cell line, NMuMG, to distinguish between early changes in cancer initiation and metastasis-promoting alterations.

overall_design: In the absence of hnRNP E1 expression, NMuMG cells become both tumorigenic and metastatic, with metastases identified in the lungs of mammary fat pad injected NOD/SCID mice. The metastatic potential of the E1KD cell line can be enhanced by in vivo passaging which allows for the artificial selection of cells capable of forming primary tumors and lung metastases. This technique led to the isolation of increasingly aggressive metastatic cell lines, termed L1P and L2P that metastasize to lung. In addition, the M1P cell line were isolated from a primary mammary tumor.

first: Breege

last: Howley

first: Laura

last: Link

last: Grelet

first: Maya

last: El-Sabban


title: 5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [nuclear RNA-Seq]

summary: 5-hydroxymethylcytosine (5hmC) occurs at maximal levels in postmitotic neurons where its accumulation is cell specific and correlated with gene expression. Here we demonstrate that the distribution of 5hmC in CG and non-CG dinucleotides is distinct, and that it reflects the binding specificity and genome occupancy of methylcytosine binding protein 2 (MeCP2). In expressed gene bodies, accumulation of 5hmCG acts in opposition to 5mCG resulting in “functional” demethylation and diminished MeCP2 binding, thus facilitating transcription. Non-CG hydroxymethylation occurs predominantly in CA dinucleotides (5hmCA) and it accumulates in regions flanking active enhancers. In these domains, oxidation of 5mCA to 5hmCA does not alter MeCP2 binding or expression of adjacent genes. We conclude that the role of 5-hydroxymethylcytosine in postmitotic neurons is to functionally demethylate expressed gene bodies while retaining the role of MeCP2 in chromatin organization.

overall_design:
Examination of genome wide cytosine methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding.
Nuclear RNA-Seq dataset.


title: PBMC transcriptome profiles identifies potential candidate genes and functional networks controlling the innate and the adaptive immune response to PRRSV vaccine in Pietrain pig

status: Public on Jun 13 2017

city: Bonn

first: Chritiane

last: Neuhoff

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

institute: University of Bonn

summary: In vivo microarray study of global gene expression changes in peripheral blood mononuclear cells (PBMCs) of Pietrain pigs during the stage of inatte immune and adaptive immune response to porcine reproductive and respiratory syndrome virus vaccination.

overall_design: PBMCs samples collected at three time points (0, 1 and 28 d post ) from PRRSV vaccinated Pietrain pigs were subjected for hybridization of 9 arrays. Samples from each of time points were hybridized with three biological replications. To characterize the gene expression changes, we compared the PBMCs transcriptome profiles in two contrast pairs: day 1 post vaccination versus day 0 or  just before vaccination (D1 vs. D0) and day 28 post vaccination versus day 0 or  just before vaccination (D28 vs. D0).

first: Aminul

last: Islam

first: Karl

last: Schellander

first: Christiane


title: Functional analysis of the Pol IV DeCL domain

status: Public on Jul 16 2017

first: Jered

last: Wendte


title: Sexual Divergence in Microtubule Function: The Novel Intranasal Microtubule Targeting SKIP Normalizes Axonal Transport and Enhances Memory

status: Public on Jun 29 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: Activity-dependent neuroprotective protein (ADNP), essential for brain formation, is a frequent autism spectrum disorder (ASD)-mutated gene. ADNP associates with microtubule end binding proteins (EBs) through its SxIP motif, to regulate dendritic spine formation and brain plasticity. Here, we reveal SKIP, a novel 4 amino acid peptide representing an EB-binding site, as a replacement therapy in an outbred Adnp-deficient mouse model. We discovered, for the first time, axonal transport deficits in Adnp+/- mice (measured by manganese-enhanced magnetic resonance imaging), with significant male-female differences. Furthermore, the Adnp+/- mice exhibited impaired hippocampal expression of key ASD-linked genes including the serotonin transporter (Slc6a4), the calcium channel (VDCC) and the autophagy regulator, BECN1 (Beclin1), in a sex-dependent manner. RNA-seq evaluations corroborated, in part, immunohistochemical and functional results. Intranasal SKIP treatment normalized social memory in 8-9-month-old Adnp+/--treated mice to placebo-control levels, while protecting axonal transport and ameliorating changes in ASD-like gene expression. SKIP presents a novel lead compound for ASD drug development, a prevalent unmet medical need.

overall_design: 8 different samples were used, all in biological triplicates except for one sample with duplicates. Samples include 1 month and 5 months mice hippocampus of males and females, wild-type and Adnp+\-.

first: Noy

last: Amram

first: Gal

last: Hacohen-Kleiman

first: Anna

last: Malishkevich

first: Jeny

last: Katz

first: Olga

last: Touloumi

first: Roza

last: Lagoudaki

first: Nikolaos

middle: C

last: Grigoriadis

first: Eliezer

last: Giladi

first: Adva

last: Yeheskel

first: Yan

last: Jouroukhin

first: Illana

last: Gozes


first: Yasutaka

last: Kakui

overall_design: Hi-C libraries of fission yeast chromosomes in interphase and in mitosis with or without chromosome condensation.


title: IL-33 and ST2 license beige and brown adipocytes for uncoupled respiration

status: Public on Jun 10 2017

city: San Francisco

first: minwoo

last: Lee

state: CA

address: 555 Mission bay blvd south

department: CVRI

institute: University of California, San Francisco

summary: For placental mammals, the transition from the in utero maternal environment to postnatal life requires the activation of thermogenesis to maintain their core temperature. This is primarily accomplished by induction of uncoupling protein 1 (UCP1) in brown and beige adipocytes, the principal sites for uncoupled respiration. Despite its importance, how placental mammals license their thermogenic adipocytes to participate in postnatal uncoupled respiration is not known. Here, we provide evidence that the 'alarmin' IL-33, a nuclear cytokine that activates type 2 immune responses, licenses brown and beige adipocytes for uncoupled respiration. We find that, in absence of IL-33 or ST2, beige and brown adipocytes develop normally but fail to express an appropriately spliced form of Ucp1 mRNA, resulting in absence of UCP1 protein, and impairment in uncoupled respiration and thermoregulation. Together, these data suggest that IL-33 and ST2 function as a developmental switch to license thermogenesis during the perinatal period.

overall_design: mRNA profiles of brown adipose tissues and inguinal white adipose tissues from postnatal day 0.5 and 24, respectively, WT and IL-33 knockout mice.

first: Ajay

last: Chawla

first: Justin

last: Odegaard

first: Min

first: Yoshitaka

last: Sogawa


title: Transcriptome profiling of resistant  NIL (PB1+Pi9) and susceptible rice line (PB1) 24 hours after M oryzae inoculation

status: Public on Jun 12 2017

city: New Delhi

first: T

last: Sharma

state: Delhi

address: Pusa Campus New

institute: NRCPB

summary:
Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of  rice leaf tissue infected with M.oryzae of resistant and suceptible line.  The results were validated using real time PCR.
Methods: Rice leaves were collected 24 hours  after M. Oryza (Mo-nwi-53) infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). RNA libraries were prepared for sequencing using standard Illumina protocols.
Results: Around 30 million pairs of filtered 101 base paired reads were obtained for each biological replicate. These reads were mapped against RGAP7 using Tophat and approximately 90% aligned to the RGAP 7 while 10% reads were unaligned. Approximately 1-2 million reads returned multiple hits to the RGAP7.  After alignment mapped reads were assembled using Cufflink and differentially expressed locus (DEL) were called using Cuffdiff. Statistical test was applied to find significant differentially expressed locus id after multiple corrections (FDR adjusted p value ≤0.05). We obtained 8,418  and 3336 significant (FDR adjusted p value ≤0.05) differentially expressed locus id in the resistant and susceptible rice line, respectively . The number of significant DEL with fold change value  greater and les than 2.0 were 1254 (850 upregulated  404 downregulated) and 781 (466 upregulated & 313 downregulated)in in resistance and susceptible lines, respectively. The final data represents the transcriptome of both resistant and susceptible line after mock and M.oryzae infection. The pathway and gene set enrichment analysis was performed to find changes in biological process and molecular function in resistant (PB1+ Pi9) and susceptible (PB1) rice line upon M.oryzae infection. The qRT PCR was performed to validate selected candidate genes playing important role in rice defense upon M.oryzae infection.
Conclusions: Our study represents the first detailed transcriptome analysis of resistant near isogenic line (PB1+ Pi9) and its susceptible control (PB1) with biological replicates upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis helps to expedite protein network analyses and dissection of complex biological functions. In summary we found that a single functional blast resistant gene Pi9 present in resistant NIL in the background of susceptible line (PB1) activates a cascade of defense response genes, leading to incompatible interaction.

overall_design: Transcriptome profiling of resistant  NIL (PB1+Pi9) and susceptible rice line (PB1), leaves after  mock and  M.oryzae infection with three biological replicate were generated  using Illumina Hiseq

first: Priyanka

last: Jain

first: Pankaj

middle: K

last: Singh

first: Ashok

first: Amol

last: Solanke

first: S

middle: G

last: Krishnan

first: Vinay


title: Gene expression in ATII cells transduced with adenovirus expressing constitutively active mutant HIF1a

status: Public on May 01 2017

city: Denver

first: Sonia

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

summary: To determine HIF1a target genes in ATII cells, we transduced freshly isolated rat ATII cells with an adenoviral vector expressing either GFP or a constitutively active mutant HIF1a construct. After 24 hours, RNA was extracted and subjected to microarray.

overall_design: There was one well transduced with AdGFP and one well transduced with AdHIF1a.  This was repeated four times, using four separate rats, on four separate dates. Therefore, there are 8 samples total, paired by extraction date.

first: Jazalle

last: McClendon

first: Nicole

last: Jansing

first: Elizabeth

last: Redente

first: Aneta

last: Gandjeva

first: Yoko

last: Ito

first: Sean

last: Colgan

first: Aftab

last: Ahmad

first: David

last: Riches

first: Robert

last: Mason

first: Rubin

last: Tuder

first: Rachel

last: Zemans


title: Patterns of Arabidopsis gene expression in the face of hypobaric stress [Experiment 2]

status: Public on May 11 2017

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: Extreme hypobaria is a novel abiotic stress that is outside the evolutionary experience of terrestrial plants. In natural environments, the practical limit of atmospheric pressure experienced by higher plants is about 50 kPa or ~.5 atmospheres; a limit that is primarily imposed by the combined stresses inherent to high altitude conditions of terrestrial mountains. However, in highly controlled chambers and within extra-terrestrial greenhouses the atmospheric pressure component can be isolated from other high altitude stresses such as temperature, desiccation, and even hypoxia. In addition, hypobaria can be carried to extremes beyond what is possible in terrestrial biomes, and explored as a single variable in the examination of plant responses to novel stress. Previous studies have shown that plants adjust to hypobaric stress by differentially expressing suites of genes in unique combinations that are not equal to the dissected components of hypobaric stress (such as hypoxia and desiccation). Here we examine the organ-specific progression of transcriptional strategies for physiological adaptation to hypobaric stress over time. An abrupt transition from a near-sea level pressure of 97 kPa to only 5 kPa is accompanied by the differential expression of hundreds of genes. However, the transcriptomic reaction to hypobaric conditions lying between these two extremes reveals complex, organ-specific responses that vary over a time course of hypobaric exposure, and that are also not linear with respect to a simple gradient of severity. It is also clear that plants adjust over time such that the gene expression patterns that are initially elicited to cope with hypobaria are mediated as plants adjust their metabolism to this environment. The patterns of genome-wide changes in gene expression across a gradient of atmospheric pressures, and over a time course of several days allows for the development of theories of how plant metabolisms may be adapting to changes in atmospheric pressures.

overall_design: The transcriptional profiles of Arabidopsis growing in atmospheric pressures of 75 kPa, 50 kPa, 25 kPa, 10 kPa or 5 kPa were used to evaluate the consequence of the hypobaric environment. In the first experimnent the 10 day old plants were transferred to The Low Pressure Growth Chambers (LPGC) (the Controlled Environment Systems Research Facility (CESRF) at University of Guelph, Ontario, Canada) and exposed to 97 kPa, 75 kPa, 50 kPa, 25 kPa, 10 kPa, 5 kPA for 24 hours, respectively. In the second experiment the 10 days old plants were transferred to the LPGCs and were exposed to an atmosphere of 10 kPa or 97 kPa.  The 97 kPa atmosphere was composed of a partial pressure of 21 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen. The 10 kPa samples were composed of a partial pressure of 2.1 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen.  The samples were harvested at: 1 hour, 3 hours, 6 hours, 12 hours, 48 hours and 72 hours. The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each.  At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots and the total RNA was extracted and subjected to the The Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays.

first: Anna-Lisa

last: Paul

first: Mingqi

last: Zhou

first: Jordan

last: Callaham

first: Matthew

last: Reyes

first: Michael

last: Stasiak

first: Alberto

last: Riva

first: Agata

last: Zupanska

first: Mike

middle: A

last: Dixon

middle: J


title: Patterns of Arabidopsis gene expression in the face of hypobaric stress [Experiment 1]

overall_design: The transcriptional profiles of Arabidopsis growing in atmospheric pressures of 75 kPa, 50 kPa, 25 kPa, 10 kPa or 5 kPa were used to evaluate the consequence of the hypobaric environment. In the first experimnent the 10 day old plants were transferred to The Low Pressure Growth Chambers (LPGC) (the Controlled Environment Systems Research Facility (CESRF) at University of Guelph, Ontario, Canada) and exposed to 97 kPa, 75 kPa, 50 kPa, 25 kPa, 10 kPa, 5 kPa for 24 hours, respectively. In the second experiment the 10 days old plants were transferred to the LPGCs and were exposed to an atmosphere of 10 kPa or 97 kPa.  The 97 kPa atmosphere was composed of a partial pressure of 21 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen. The 10 kPa samples were composed of a partial pressure of 2.1 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen.  The samples were harvested at: 1 hour, 3 hours, 6 hours, 12 hours, 48 hours and 72 hours. The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each.  At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots and the total RNA was extracted and subjected to the The Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays.


title: Children with neuroblastoma show altered erythrocyte’s maturation in bone marrow and decreased number of erythrocytes in peripheral blood

status: Public on May 31 2017

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

institute: IRCCS AOU San Martino-IST

summary: Neuroblastoma (NB) is a pediatric tumor with a heterogeneous presentation at diagnosis. Fifty per cent of patients present with localized disease (stage L1/L2) whereas the other half have metastatic disease (stage M), mainly involving the bone marrow (BM). In these latter patients the physical occupancy of the BM space by metastatic NB cells has been thought to be responsible for impairment of BM function. Here, based on gene expression profiles of BM resident cells obtained in a large number of stage L and stage M NB patients, as compared to gene expression profiles of BM resident cells from healthy subjects, we investigated whether the tumor growth, either at distance or locally, affected hematopoietic lineages' maturation and release of mature hematopoietic cells in the periphery (PB). Our investigation clearly demonstrated that in children with NB, regardless of the presence of metastatic cells in the BM, there was a selective impairment of erythrocyte maturation at the ortho-chromic stage. In the BM, all the other cell lineages were un-affected. The altered erythrocyte maturation resulted in a reduced amount, and increased RWD, of PB erythrocytes. In PB samples from patients with stage L disease a significant increase in the number of mature neutrophils was observed, suggesting that in these NB patients innate immunity was activated. No increase occurred in PB of stage M NB patients. Although the cause of the selective impairment of erythrocyte maturation, as well as that of the activation of innate immunity in stage L NB patients remained elusive, our observations allowed to fully refusing the tenet that BM-infiltrating NB cells affected physiological BM functions due to physical occupancy of the BM space. In addition, these findings open the way to a new area of research not only in NB and other clinically similar pediatric cancers, such as rhabdos and sarcomas, but also in adult cancers metastasizing in the BM. Looking more carefully to the BM microenvironment could help discovering novel targets for innovative therapeutic approaches.

overall_design: We performed a gene expression analysis on 57 samples: 13 BM (bone marrow) from healthy donors, 20 BM from localized NB, 14 GD2 negative cells from localized NB and 10 GD2 negative cells from metastatic NB

first: Fabio

last: Morandi

first: Paola

last: Scaruffi

first: Luca

last: Persico

first: Corrado

last: Lagazio

first: Maria

last: Corrias


title: Transcriptional and accessible chromatin profiles during conversion process of alternatively activated macrophages (RNA-Seq)

status: Public on Apr 24 2017

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

summary: Whether inflammatory macrophages can adopt features of the tissue resident niche and what mechanisms mediate phenotypic conversion remain unclear. In this study, we show by cell surface phenotyping, as well as by RNA-Seq transcriptional profiling and ATAC-Seq open chromatin regions profiling, that inflammatory monocyte can adopt a tissue resident phenotype, which is also accompanied by re-programming of the transcriptional profiles and remodeling of the open chromatin landscape. The conversion process is dependent on Vitamin A, suggesting that Vitamin A deficiency may lead to the failure to resolve inflammation, as inflammatory macrophages accumulate without adopting a tissue residency phenotype.

overall_design: Monocyte-derived (N=3), tissue converted (N=3) and tissue resident (N=3) mouse peritoneal macrophages were FACS-sorted for RNASeq and ATACSeq.

first: Uma

last: Mahesh Gundra

first: Natasha

middle: M

last: Girgis

last: Gonzalez

first: Mei

last: San Tang

first: P'ng

last: Loke


title: KLF1 directly activates expression of the novel fetal globin repressor, ZBTB7A/LRF, in erythroid cells

status: Public on Apr 13 2017

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

institute: University of New South Wales

summary: Genes encoding the human β-like hemoglobin proteins undergo a developmental switch from fetal γ-globin to adult β-globin expression at around the time of birth. β-hemoglobinopathies, such  as  sickle  cell  disease  and  β-thalassemia, result  from  mutations affecting  the  adult  β-globin gene.  The  only  treatment  options  currently available  carry  significant  side-effects. Analyses of heritable variations in fetal hemoglobin (HbF) levels have provided evidence that reactivation of the silenced fetal γ-globin genes in adult erythroid cells is a promising therapy. The γ-globin repressor BCL11A has become the major focus with several studies investigating its  regulation and  function as a  first  step  to inhibiting its expression  or activity. However, a second repression mechanism has recently been shown to be mediated by the transcription factor  ZBTB7A/LRF,  suggesting  that  understanding  the  regulation  of  ZBTB7A  may  also  be useful.  Here  we  show  that  KLF1  directly  drives  expression  of  ZBTB7A in  erythroid  cells  by binding  to  its  proximal  promoter.  We  have  also  uncovered  an  erythroid-specific  regulation   mechanism,  leading  to  the upregulation  of  a  novel  ZBTB7A transcript  in  the  erythroid compartment.  The  demonstration that  ZBTB7A,  like  BCL11A, is  a  KLF1  target  gene  also  fits with  the  observation  that  reduced KLF1  expression  or  activity  is  associated  with  HbF  derepression.

overall_design: ChIP-seq was undetaken in duplicate on two different cell lines against KLF1. Input controls were inncluded

first: Laura

last: Norton

first: Alister

middle: P

last: Funnell

first: Beeke

last: Wienert

first: Ryo

last: Kurita

first: Yukio

last: Nakamura

first: Sjaak

last: Philipsen

first: Richard

last: Pearson

first: Kate

last: Quinlan

first: Merlin

last: Crossley


title: Transcriptional and accessible chromatin profiles during conversion process of alternatively activated macrophages

overall_design: Refer to individual Series


title: Patterns of Arabidopsis gene expression in the face of hypobaric stress

first: Robert

last: Ferl


title: Comparative analysis of the microRNA transcriptome revealed high altitude adaptation in yak (Bos grunniens)

status: Public on Mar 31 2017

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

summary:
Purpose:  The goal of this study was to reveal epigenetic differences in the microRNA transcriptomes of two organs (heart and lung) between yak and cattle.
Methods: Three unrelated 2-year old adult females for both of yaks and cattle (Luxi Huang cattle) were used in this study. Two of significant hypoxia-responsive tissues (heart and lung) were rapidly collected from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen. All frozen samples were stored at –80 °C until RNA extraction.The total RNA were extracted with Trizol (Ambion, USA). NanoDrop ND-2000 spectrophotometer (Nano Drop, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) were used to monitor the concentration and integrity of RNA, respectively. In brief, several successive steps consist the Illumina sequencing. The small RNA with length of 14-40 nt were first purified by polyacrylamide gel electrophoresis (PAGE), and then specific adapters were ligated to the purified small RNA. The ligated RNA were reverse transcribed to cDNA libraries. Finally, each library were sequenced on Genome Analyzer.
Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation.
Conclusions: In this study, we illustrated the differences in the microRNA transcriptomes level for heart and lung between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation. The work performed here will provide a typical demonstration for future deciphering the mechanism of high altitude adaptation

sample_organism:
Bos taurus
Bos grunniens

platform_organism:
Bos taurus
Bos grunniens

overall_design: Lung and heart miRNA profiles of yak and cattle were generated by deep sequencing, in triplicate , using Illumina Hiseq2000 .

first: Jiuqiang

last: Guan

first: Keren

last: Long

first: Jideng

last: Ma

first: Jinwei

last: Zhang

first: Long

last: Jin

first: Qianzi

last: Tang

first: Anan

last: Jiang

first: Xun

last: Wang

first: Xuewei

last: Li

first: Mingzhou

first: Xiaolin

last: Luo


title: Comparative genome hybridization between grapevine white-berried somatic variants and ancestral black-berried cultivars

status: Public on Apr 01 2017

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

institute: CSIC

summary:
Somatic variants spontaneously appear during the vegetative multiplication of woody crops. The new white-berried grapevine cultivar Tempranillo Blanco (TB) originally appeared as a bud sport of the black skin-berried Tempranillo Tinto (TT) cultivar. To understand the origin of this variation, TT and TB genomes were sequenced. Structural variation and genetic segregation analyses uncovered that complex chromosome rearrangements consistent with chromothripsis, a catastrophic phenomenon recently described in human cancer, generated the variant genome of TB and the deletion of the color locus functional allele. Loss of heterozygosity and decreased copy number delimited alternating monosomic and disomic fragments in the distal arms of TB’s linkage groups 2 and 5. Hemizygous fragments collectively extended over 8.1 Mb and comprised 313 annotated genes. Clustered breakpoints for complex chromosome rearrangements disrupting linkage groups 2 and 5 were identified and junctions involved unbalanced inter- and intra-chromosome translocations and one unbalanced inversion. Signatures of blunt fusions or microhomology-mediated end joining mechanisms were detected at breakpoint junction flanks. Segregation distortion in TB-derived selfed progeny indicated linkage of rearrangements in a single copy of the affected chromosomes that was barely transmitted. Additionally to berry color loss, these dramatic changes have further viticultural consequences in TB associated to a decreased sexual fitness. Our findings show that chromothripsis spontaneously arise during mitotic multiplication of grapevine, evidencing that this phenomenon could contribute to clonal variation in woody crops and to the evolution of plant genomes.

Grapevine GrapeGen GeneChips(R) were used for partial comparative genome hybridization between black-berried cultivars and their respective white-berried somatic variants. Differences in copy number were used to estimate chromosome deletions associated to the loss of berry color.

overall_design: Young grapevine leaves from each variant line were used for gDNA extraction. Fragmented DNA was amplified, labelled and hybridized to GrapeGen Affymetrix microarrays. Three pairs of white- and black-berried variants were compared with two biological replicates per variant.

first: José

last: Martínez-Zapater


title: Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing

status: Public on May 17 2017

city: Beijing

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

summary: Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on single T cells isolated from peripheral blood, tumor and adjacent normal tissues from hepatocellular carcinoma patients.

overall_design:
T cells from HCC patients were sorted, profiled by Smart-seq2 and Tang2010 protocol (for patient P1202, the suffix "t" indicate cells from this patient were processed using Tang2010 protocol; cells from other patients were processed using SMART-Seq2) and sequenced on Illumina HiSeq2500 and HiSeq4000. Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high) were sorted to perform RNA sequencing. The categories （"sampleType" column in the SAMPLES section） contain PTC(CD8+ T cells from peripheral blood), NTC(CD8+ T cells from adjacent normal liver tissues) ,TTC (CD8+ T cells from tumor), PTH(CD3+, CD4+ and CD25- T cells from peripheral blood), NTH(CD3+, CD4+ and CD25- T cells from adjacent normal liver tissues), TTH(CD3+, CD4+ and CD25- T cells from tumor), PTR(CD3+, CD4+ and CD25high T cells from peripheral blood), NTR(CD3+, CD4+ and CD25high T cells from adjacent normal liver tissues), TTR(CD3+, CD4+ and CD25high T cells from tumor), JTH(CD3+, CD4+ and CD25- T cells from joint area between the tumor and the adjacent normal tissue),JTR(CD3+, CD4+ and CD25high T cells from joint area between the tumor and the adjacent normal tissue), JTC(CD3+CD8+ T cells from joint area between the tumor and the adjacent normal tissue)
Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002072

first: Chunhong

last: Zheng

first: Liangtao

first: Jae-Kwang

last: Yoo

first: Huahu

last: Guo

first: Yuanyuan

first: Xinyi

first: Boxi

last: Kang

first: Ruozhen

last: Hu

first: Julie

last: Huang

first: Qiming

first: Zhouzerui

last: Liu

first: Minghui

last: Dong

first: Xueda

first: Wenjun

last: Ouyang

first: Jirun

last: Peng

first: Zemin


title: Epithelial-to-mesenchymal transition defines feedback activation of receptor tyrosine kinase signaling induced by MEK inhibition in KRAS mutant lung cancer

status: Public on Mar 15 2017

city: Kanazawa

first: Hiromichi

last: Ebi

state: Ishikawa

address: 13-1 Takaramachi

department: Institute for Frontier Science Initiative and Cancer Research Institute

institute: Kanazawa University

summary: To determine the difference of gene expression profile in epithelial and mesenchymal KRAS mutant lung cancers, epithelial NCI-H358 cells were treated with TGFβ1 (4 ng/mL) or PBS for 14 days in order to induce epithelial to mesenchymal transition (EMT). Gene expression was determined in NCI-H358 cells before and after EMT induction. In addition, in order to investigate the effect of a MEK inhibitor trametinib on gene expression, mesenchymal NCI-H1792 cells were treated with 50 nM trametinib for 48 hours. Gene expression of H1792 cells for pre- and post-trametinib treatement was determined.

overall_design: H358 was induced EMT by treated with TGF-beta. H1792 were treated with trametinib for 48 hours. Two independent experiments were performed

first: Hidenori

last: Kitai

first: Shuta

last: Tomida


title: Circular RNA expression profiling of human granulosa cells during maternal aging

status: Public on Mar 30 2017

city: Wuhan

first: Jing

last: Cheng

state: Hubei

address: Jiefang Avenue 1095

department: Obstetrics and Gynecology

institute: Tongji Hospital

summary: Advanced maternal age was closely associated with decreased pregnancy rates and increased spontaneous miscarriages. Even seeking assisted reproductive technology (ART), only 12.2% of women aged 41-42, and 4.2% of women older than 42 years achieved live births with their own oocytes, which were remarkably lower than that of women younger than 35 years (40.1%). Elucidating underlying molecular signatures that link maternal age and fecundity decline is particularly important for developing predictive markers and therapeutic targets for improving reproductive outcomes in aging women. Circular RNAs are a unique class of non-coding RNAs with a stable structure formed by special loop splicing, and they contribute to post-transcriptional regulation of gene expression by binding specifically to miRNAs and sequestering miRNAs to terminate suppression of their targets. Increasing evidences indicate that circular RNAs play important roles in many age-related diseases, such as cardiovascular disease, nervous system disorders, and cancer. However, the role of circular RNAs in reproduction and their contribution to ovarian aging remains to be discovered. The aim of this study was to characterize circRNA expression profiles of granulosa cells according to maternal age, identify age-related changes that could potentially reflect oocyte competence, and constitute non-invasive tools to explore follicular micro-environment quality and to predict ART outcomes, thus improving the personalized patient’s care. Circular RNAs profiles in granulosa cells obtained from IVF patients (n=6) was analyzed by a human circRNA microarray. Samples from women with advanced age (AA,≥ 38 years) were compared to those from women with young age (YA,≤ 30 years). Significantly differentially expressed circular RNAs discovered in the microarray were validated in additional 20 AA and 20 YA samples by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Granulosa cells from another independent cohort (80 women range from 22 to 48 years old) were analyzed by qRT-PCR to further verify the association of diminished ovarian function with candidate circular RNAs. Our results indicated that circRNA_103827 and circRNA_104816 expressions in granulosa cells were negatively correlated with the number of top quality embryos and pregnancy outcomes. Bioinformatics analysis revealed that both circular RNAs were potentially involved in glucose metabolism, mitotic cell cycle, and ovarian steroidogenesis. Therefore, age-related up-regulation of circRNA_103827 and circRNA_104816 might be potential indicators of compromised follicular micro-environment which could be used to predict IVF prognosis, and improve female infertility management.

overall_design: Six samples were analysed. Three samples of granulosa cells from women with advanced age (AA, ≥ 38 years) were compared to three samples from women with young age (YA, ≤ 30 years).

first: Jia

first: Suzhen

last: Yuan

first: Su

last: Zhou

first: Wei

last: Yan

last: Shen

first: Aiyue

last: Luo

first: Da

last: Zhu

first: Shixuan

last: Wang


title: Preoperative short-term hormone therapy for hormone receptor positive breast cancer

status: Public on Apr 19 2017

city: Okayama

first: TAKAYUKI

last: IWAMOTO

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

institute: Okayama university hospital

summary: Core needle biopsy (Cx) primary cancer specimens were collected at Okayama University Hospital in Japan from hormone receptor positive /HER2 negative patients that subsequently received two weeks of neoadjuvant hormone therapy. Thirty clinical TNM stage I and II women were enrolled in this study. The study was approved by the Institutional Review Board and all patients signed informed consent forms. Patients received preoperative hormone therapy daily for two weeks before surgery. Premenopausal patients received tamoxifen (40 mg) and postmenopausal patients received letrozole (2.5 mg). All patients underwent a mastectomy or breast-conserving surgery. Surgical samples after treatment were also collected. Hormone and HER2 receptor statuses were determined in the diagnostic Cx specimens before hormone therapy. Cases with ≥1% positive nuclear staining for estrogen receptors (ER) or progesterone receptors (PgR) with IHC were considered hormone receptor-positive. Cases with either 0 or 1 positive IHC staining for HER2 or with an HER2 gene copy number < 2.0 by fluorescent in situ hybridization (FISH) analysis were considered HER2−. Specimens for gene expression analysis were collected into RNA and later stored at -80°C. Gene expression profiling was performed using Affymetrix U133A gene chips. Expression data were normalized using the MAS5 algorithm, mean centered to 600, and log2 transformed before further analysis.

first: Takayuki

last: Iwamoto

first: Junji

last: Matsuoka


title: Factors regulating subcutaneous adipose tissue storage, fibrosis, and inflammation may underlie low systemic rates of fatty acid mobilization in insulin sensitive obese adults

status: Public on Mar 08 2017

city: Ann Arbor

first: Jeffrey

last: Horowitz

state: Michigan

address: CCRB, 401 Washtenaw Ave

institute: University of Michigan

summary: Although the rate of fatty acid release from adipose tissue into the systemic circulation is very high in most obese adults, some obese adults maintain relatively low rates of fatty acid release, which helps protect them against the development of systemic insulin resistance.  The primary aim of this study was to identify factors in adipose tissue that may underlie low vs. high rates of fatty acid mobilization in a relatively homogeneous cohort of obese adults. We obtained subcutaneous abdominal adipose tissue samples from 30 obese adults (BMI: 38±1 kg/m2, age: 30±2 yr) after an overnight fast.  We performed microarray analysis on the adiose tissue samples.

overall_design: We obtained subcutaneous adipose tissue biopsies from obese adults after an overnight fast.

first: Douglas

middle: W

last: Van Pelt

first: Lisa

last: Guth

first: Abigail

middle: Y


title: Generation and functional characterization of MDSC-like cells

status: Public on Apr 03 2017

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Myeloid derived suppressor cells (MDSC) are critical in regulating immune responses by suppressing antigen presenting cells (APC) and T cells. We previously observed that incubation of peripheral blood monocytes with IL-10 during their differentiation to dendritic cells (moDC) results in the generation of an APC population with a CD14+HLA-DRlow phenotype (IL-10-APC) with reduced stimulatory capacity similar to human MDSC. Here, we show that co-incubation of IL-10-APC and moDC caused a reduction of DC-induced T cell proliferation, of the expression of maturation markers and of secreted cytokines and chemokines. Furthermore, addition of IL-10-APC increased the immunosuppressive molecule osteoactivin and its corresponding receptor syndecan-4 on moDC. Using transcriptome analysis, we could identify a set of molecules and pathways  mediating the immunosuppressive effects of IL-10-APCs. In addition, we found that IL-10-APC as well as human isolated MDSC, expressed higher levels of programmed death (PD)-1, PD-ligand-1, glucocorticoid-induced-tumor-necrosis-factor-receptor-related-protein (GITR) and GITR-ligand. Inhibition of osteoactivin, syndecan-4, PD-1 or PD-L1 on MDSC using blocking antibodies restored the stimulatory capacity of DC in co-incubation experiments. Our results demonstrate that osteoactivin/syndecan-4 and PD-/PD-L1 are key molecules that are profoundly involved in the inhibitory effects of MDSC on DC function and might be promising tools for an application in the clinics.

overall_design: Isolated human monocytes from peripheral blood were differentiated to monocyte-derived dendritic cells (moDC) in presence or absence of interleukin-10 (IL-10). Additional cell maturation by application of LPS leads to a total number of 4 conditions with 3 samples each.

first: Annkristin

last: Heine

first: Stefanie

last: Held

first: Jonas

last: Schulte-Schrepping

first: Kathrin

last: Klee

middle: L

first: Brossart

last: Peter


title: Genome profiles of chickens infected with infectious bursal disease virus by RNA-seq

status: Public on Mar 09 2017

city: Xinxiang

first: Changbo

last: Ou

state: Henan

address: No.90 Hualan Road

institute: Henan Institute of Science and Technology

summary:
Purpose: To explore the interaction between host and IBDV, RNA-Seq was applied to analyse the transcriptional profiles of the responses of chickens' bursas of Fabricius in the early stage of IBDV infection.

Method: Eighteen SPF white leghorn chickens were randomly divided into two groups with 9 chickens for each group: the mock group (the healthy group) and the IBDV-inoculated group (the infection group). Chickens from the infection group were inoculated with 0.1 mL of 103 EID50 IBDV CJ801 stock through eye-nose drops. The chickens from the mock group were kept in a separate isolator and mock challenged with PBS. On days 1, 3 and 7 after infection, 3 chickens from each group were killed for bursa collection. Each bursa was immediately put into liquid nitrogen and then stored in 80 ℃ refrigerator. RNA sequencing was performed with total RNA from bursae from each group at the first two time points and completed by a commercial company.

Results: The results displayed that a total of 15546 genes were identified in the chicken bursa libraries. Among the annotated genes, there were 2006 and 4668 differentially expressed genes in the infection group compared with the mock group on day 1 and day 3 post inoculation (1 and 3 dpi), respectively. Moreover, there were 676 common up-regulated and 83 common down-regulated genes in the bursae taken from the chickens infected with IBDV on both 1 and 3 dpi. Meanwhile, there were also some characteristic differentially expressed genes on 1 and 3 dpi. On day 1 after inoculation with IBDV, host responses mainly displayed immune response processes, while metabolic pathways played an important role on day three post infection. Six genes were confirmed by quantitative reverse transcription-PCR.

Conclusions: In conclusion, the differential gene expression profile demonstrated with RNA-Seq might offer a better understanding of the molecular interactions between host and IBDV during the early stage of infection.

overall_design: Gene expression profiles of chickens infected with IBDV on 1 and 3 dpi when compared to mock infected chickens.

first: Xingyou

last: Liu