title: RNA-seq data of effects of DCPS inhibition in mouse AML cells (CALM/AF10) and in normal GMP cells. Overall mRNA profiles of CALM/AF10 (#1/#2) and MLL/AF9 (#1/#2).

city: Fukuoka

first: Takuji

last: Yamauchi

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

summary: Purpose: The goals of this study are to assess the possibility whether DCPS inhibition would impair pre-mRNA splicing in AML cells/normal GMP, and to assess overall effects of DCPS inhibition.

overall_design:
Methods: mRNA profiles of AML (CALM/AF10) and normal GMP cells at 0h, 6h and 10h after RG3039 treatment were generated by deep sequencing, in triplicate, using NextSeq. RNA-seq data were analyzed using a bioinformatic pipeline enabling quantification of exon-exon junctions without predetermining alternative aplicing models of annotating splice junctions as described (Darman et al., 2015).
Methods: RNA-seq experiments were performed using 4 indicated AML lines.


title: T47D RNA-seq and ChrRNA-seq data

status: Public on Nov 21 2018

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

type: Expression profiling by high throughput sequencing

summary: We performed genome-wide RNA-seq and ChrRNA-seq experiments in T47D cell lines  after PADI2 knock down . Both the mRNA and  chromatin RNA seq  peformed in sicontrol  and siPADI2  as in biological replicates . Also we performed  mRNA seq in T47D cells expressing HA Tagged amanitin resistant wild type in comparison to R1810A mutant form of RNAP2.

overall_design: We designed experiment to perform   mRNA  sequencing in T47D after PADI2 knock down as in biological replicate experiemnt .  Given the fact we found significant number of genes differentailly expressed after PADI2 knockdown in T47D cells, we designed to perform Chromatin RNA seq in  T47D cells after PADI2 knock down as in biological replicates.  We find that PADI2 deiminates R1810 at CTD (C-terminal domian)  of RNAP2 , So in order to analyse the mRNA  gene expression level in T47D cells expressing amanitin resistant  HA - tagged wild type and mutant form of RNAP2 , we performed mRNA seq as in biological replicate in T47D cells expressing   amanitin resistant  HA - tagged wild type and mutant form of RNAP2.

first: Priyanka

last: Sharma

first: Antonios

last: Lioutas

first: Javier

last: Quilez

first: Roni

middle: H

last: Wright

first: Chiara

last: Di Vona

first: Roland

last: Schüller

first: Dirk

last: Eick

first: Miguel

last: Beato


title: Ten-eleven translocation proteins modulate the response to environmental stress in mice

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

country: USA

institute: Emory University

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 5-hydroxymethylcytosine (5hmC) is enriched in brain and has been recognized as an important DNA modification. However, the roles of 5hmC and its “writers”, Ten-eleven translocation (Tet) proteins, in stress-induced response have yet to be elucidated. Here, we show that chronic restraint stress (CRS) induced the depression-like behavior in mice and resulted in a 5hmC reduction in prefrontal cortex (PFC). Interestingly, we found that the loss of Tet1 (Tet1 KO) led to the resistance to CRS while the loss of Tet2 (Tet2 KO) increased the susceptibility of mice to CRS. Genome-wide 5hmC profiling identified the phenotype associated stress-induced dynamically hydroxymethylated loci (PA-SI-DhML), which are strongly enriched with hypoxia-induced factor (HIF) binding motifs. We demonstrated the physical interaction between TET1 and HIF1α induced by CRS, and revealed that the increased HIF1α binding under CRS is associated with SI-DhML. These results together suggest that TET1 could regulate stress-induced response by interacting with HIF1α.

overall_design: Chronic restraint stress were applied to wildtype, Tet1 KO and Tet2 KO mice to investigate the role of 5hmC/TET-protein in stress response

first: Peng

last: Jin


title: Arginine citrullination at the C-terminal domain controls RNA Polymerase II  transcription

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

overall_design: Refer to individual Series


title: Regeneration time course of a larval sea star, Patiria miniata

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

summary: Regeneration is pervasive among the metazoa, but to vastly varying degrees. Platyhelminthes, Cnidaria, and Echinodermata are examples of phyla whose members are capable of whole-body regeneration (WBR). While planaria and hydra have been exemplary models of this phenomenon, the molecular details of echinoderm WBR are less established. It remains unclear to what degree such a dramatic regenerative capacity is due to the operation of conserved mechanisms and, in particular, whether any of these are involved in a regenerating Deuterostome. We characterize regeneration in the larval sea star (Patiria miniata) via transcriptome assessment. Transcriptome profiling highlight functions common to regeneration, such as wound healing, axis patterning and proliferation. This dataset was used as a basis for comparison to published Platyhelminth and Cnidarian regeneration datasets. These analyses show that sea star larvae undergo regeneration through a trajectory including wound response, axis respecification, and blastemal proliferation. Commonalities between this Deuterostome model and other WBR models suggest a deep conservation of whole-body regeneration among the metazoa.

overall_design: Regenerating anterior and posterior segments were measured at three separate time points during regeneration along with sibling, non-bisected control larvae. Two replicate measurements were made for a total of 18 samples.

middle: A

first: Veronica

middle: F

last: Hinman


title: Transcriptome analysis of L.lactis F44 and G423: insights into adaptation to acidic environment

status: Public on Nov 20 2018

city: TianJin

first: Kairen

last: Tian

address: No. 135, YaGuan Road, JinNan District

country: China

institute: Tianjin university


title: T47D Breast cancer cell line ChIP-seq data

summary: We performed genome-wide  PADI2 ChIP seq experiments in T47D cell lines and also RNP2 ChIP seq in T47D cells  only expressing HA Tagged amanitin resistant wild type in comparison to R1810A mutant form of RNAP2.

overall_design: We designed experiment to perform genome wide PADI2 ChIP sequencing in T47D cells as in biological replicates .We find that PADI2 deiminates R1810 at CTD (C-terminal domian ) of RNAP2 , Therefore in order to investigate precise effect of the RNAP2  R1810A mutantion , we performed the RNAP2 ChIP seq by using the  HA tagged antibody after expressing the amanitin resistant  HA - tagged wild type and mutant form of RNAP2 .


title: Effects of acid stress on gene transcription of L.lactis strain G423

summary: Bacteria that live in the acidic environment face number of growth-related challenges from the intracellular pH changes. In order to survive under acidic environment, Lactic acid bacteria must employ multiple genes and proteins to regulate the relative pathways.

overall_design: 2 samples,  the treatment and the control

first: Hao

last: Wu

first: Jianjun

last: Qiao


title: Effects of acid stress on gene transcription of L.lactis strain F44


title: Impact of CD22 CAR T-cell therapy on leukemia cell transcriptome

status: Public on Nov 18 2018

city: Tianjin

first: Qing

last: Niu

address: No. 288, Nanjing Road, Heping District

institute: Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Although CD19 CAR T therapy has attained encouraging clinical outcomes worldwide, leukemia relapse after this therapy is associated with particular poor prognosis and has become an urgent problem to be solved. In consideration of the possible genetic or transcriptomic mechanisms underlying relapse, leukemia samples before CAR T cell infusion and after relapse were subjected to transcriptome sequencing

overall_design: Two B-ALL samples from the same patient, collected respectively at his pre-treatment stage and after the tumor relapse

first: Jing

last: Pan

first: Xiaoming

last: Feng

first: Chunrong

last: Tong


title: Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations [Hi-C]

status: Public on Nov 19 2018

city: Berlin

first: Andreas

last: Magg

state: Berlin

address: Ihnestraße 63-73

department: Development and Disease

country: Germany

institute: Max-Planck-Institute for Molecular Genetics

summary: Here we study the effect of balanced chromosomal rearrangements (BCRs) on gene expression in vivo in mouse embryos by generating a series of genomic inversions that place an active enhancer cluster located in the Epha4 regulatory domain at different positions within a neighboring gene dense region. Expression studies in embryonic limb buds show that the inverted enhancer cluster was able to activate several genes downstream of its new position, resulting in gene misexpression and limb phenotypes. Capture Hi-C from mutant limb buds showed that the activated genes were located within a region of asymmetric three-dimensional contacts, so called architectural stripes. Deletion of the CTCF binding site at that position of the stripe anchor resulted in a collapse of the stripes, down regulation of ectopic gene expression, and a rescue of the skeletal phenotype. In cells in which the enhancers are not active, such as mouse embryonic stem cells (mESCs), stripes do not form, indicating that their formation is also dependent on enhancer activity. Based on HiC from limb buds we show that architectural stripes are a frequent feature in the genome often associated with developmentally active enhancers. Thus, BCRs can induce ectopic gene expression via the formation of asymmetric chromatin contacts. The formation of these stripes is dependent on CTCF anchors and enhancer activity.

overall_design: We used Hi-C to identify assymetric structures (architectural stripes) genome-wide in vivo in forelimb and hindlimb tissue (Embryonic stage E11.5). Limb buds of ten embryos were pooled and, subsequently, three independent Hi-C libraries were generated and sequenced. We also used the Hi-C data to correlate the occurrence of architectural stripes with distinct chromatin states (determined with EpiCSeg, Mammana and Chung, 2015).

first: Katerina

last: Kraft

first: Verena

last: Heinrich


title: Combinatory RNA sequencing analyses reveal RNA editing-dependent and -independent gene regulation by ADAR1 in gastric cancer

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing were performed in AGS and MKN-45 cells with stable ADAR1 knock-down. Changed frequencies of editing and messenger RNA (mRNA) and microRNA (miRNA) expression were then identified by bioinformatic analyses.

overall_design: mRNA and miRNA sequencing were performed before and after stable knockdown of ADAR1 in AGS and MKN-45 cell line

first: Charles

middle: J

last: Cho


title: Kmt2b conveys monovalent and bivalent H3K4me3 in spermatogonial stem cells at germline and embryonic promoters

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

summary: The mammalian male germline is sustained by a pool of spermatogonial stem cells (SSCs) that can transmit both genetic and epigenetic information to offspring. However, the mechanisms underlying epigenetic transmission remain unclear. The histone methyltransferase Kmt2b is highly expressed in SSCs and required for the SSC-to-progenitor transition. At the stem cell stage, Kmt2b catalyzes H3K4me3 at bivalent H3K27me3-marked promoters as well as at promoters of a new class of genes lacking H3K27me3, which we call monovalent. Monovalent genes are mainly activated in late spermatogenesis while the bivalent genes are mainly not expressed until embryonic development. These data suggest that SSCs are epigenetically primed by Kmt2b in two distinguishable ways for the upregulation of gene expression during the spermatogenic program and through the male germline into the embryo. Because Kmt2b is also the major H3K4 methyltransferase for bivalent promoters in embryonic stem cells, we also propose that Kmt2b has the capacity to epigenetically prime stem cells.

overall_design: ChIP-seq (H3K4me3 and H3K27me3) and RNA-seq were performed using Kmt2b control (F/F) and knockout (FC/FC) germline stem cells (GSCs). H3K9me3 ChIP-seq was performed using Kmt2bF/F samples. All experiments were done using duplicate cell lines.

first: Yuki

last: Kobayashi

first: Takayuki

last: Shirakawa

first: Kumiko

last: Watanabe

first: Keita

last: Mizoguchi

first: Ikue

last: Hoshi

first: Kuniko

last: Nakajima

first: Jun

last: Nakabayashi

first: Sukhdeep

last: Singh

last: Dahl

first: Dimitra

last: Alexopoulou

first: Masahide

last: Seki

first: Yutaka

last: Suzuki

first: Hélène

last: Royo

first: Antoine

last: Peters

first: Konstantinos

last: Anastassiadis

first: A

last: Stewart

first: Kazuyuki

last: Ohbo


title: Dynamic Reorganization of the Genome Shapes the Recombination Landscape in Meiotic Prophase

status: Public on Nov 17 2018

city: La Jolla

first: Kevin

last: Corbett

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: In meiotic prophase, chromosomes are organized into compacted loop arrays to promote homolog pairing and recombination. Here, we probe the architecture of the mouse spermatocyte genome in early and late meiotic prophase using Hi-C. We show that early-prophase chromosomes are arranged as linear arrays of 0.8-1 Mb loops, which extend to 1.5-2 Mb in late prophase as chromosomes compact and homologs undergo synapsis. Topologically associating domains (TADs) are lost in meiotic prophase, suggesting that assembly of the meiotic chromosome axis dramatically reduces the dynamics of chromosome-associated cohesin complexes. While TADs are lost, physically-separated A and B compartments are maintained in meiotic prophase. Moreover, meiotic DNA breaks and inter-homolog crossovers preferentially form in the gene-dense A compartment, revealing a role for chromatin organization in meiotic recombination. Finally, direct detection of inter-homolog contacts genome-wide reveals the structural basis for homolog alignment and juxtaposition by the synaptonemal complex.

overall_design: Hi-C detection of intra- and inter-homolog contacts in B6 x CAST F1 hybrid mouse spermatocytes. Two independent biological replicates of zygonema-stage spermatocytes, and three independent biological replicates of pachynema-stage spermatocytes.

first: L

last: Patel

first: K

middle: D


title: STAT3 binding to DNA in wildtype vs B cell specific STAT3 knockout mice

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: A mutation in the Signal Transducer and Activator of Transcription 3 (STAT3) has been linked to incidence of Autosomal Dominant Hyper Immunoglobulin E Syndrome (AD-HIES), a disease characterized by elevated serum IgE antibody. However, how this genetic mutation leads to the phenotype has not been fully understood. We investigated the specific role of STAT3 in the germinal center (GC) B cells and plasma cells for IgE class switching. Through the use of STAT3 conditional knockout mice in a Th2-type immunization model, we demonstrated that CD2-Cre driven STAT3 cKO mice showed elevated IgE and decreased IgG1 in the serum, and a reduction in GC formation. Within the GC, IgG1+ GC B cells were decreased while IgE+ GC B cells were more prevalent. Additionally, these mice exhibited reduced IgG1 and elevated IgE populations of antibody-producing plasma cells. Subsequent experiments using a CD19-Cre B-cell specific cKO mouse established this effect to be B-cell intrinsic. Transcription factors critical for GC and plasma cell differentiation, including Bcl-6 and Aicda, were shown to function as downstream signals of STAT3 regulation. Further ChIP-seq analysis revealed that many genes including Bcl3 and Crtc2 were among the direct STAT3 regulated targets. Mice with STAT3 deficiency in B cells also demonstrated an increase in lung inflammation when used in an asthma-like disease model. This model suggests a negative role for STAT3 in regulating class switching of the GC B cells from the IgG1 to the IgE producing state, which may serve as a therapeutic target for treatment of AD-HIES and other immune disorders.

overall_design: Chip-seq peaks from two biological replicates of STAT3 knockout mouse DNA were compared to the ChIP-Seq peaks from wild type mouse DNA

first: Paul

last: Dascani

first: Chuanlin

last: Ding

first: Xiangyu

last: Kong

first: David

last: Tieri

first: Xioling

last: Hu

first: Huang-ge

last: Zhang

first: Kitamura

last: Daisuke

first: Roberto

last: Bolli

middle: C

last: Yan


title: Next Generation Sequencing for Genome-wide Maps of DNA Methylaton in mES Cells

city: Shanghai

first: Jin

last: Li

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

institute: Fudan University

summary: Aberrant DNA methylation is a distinguished feature of cancer. We introduce a novel method of Guide Positioning Sequencing (GPS) for precisely detecting whole genome DNA methylation and applied GPS as well as WGBS in mouse embryonic stem cells.

overall_design: Epigenetic information of mES cells

first: Wenqiang

last: Yu

first: Yan

first: Wei

first: Ming

last: Gao

first: Huaibing

last: Luo

first: Shihua

last: Dong


title: Transcriptome analysis of control and miR-200a overexpressed TF-1 cells

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: RNA-seq and analysis was perfprmed was performed to identify the affection caused by miR-200a overexpression in TF-1 cells.

overall_design: poly(A) RNA were enriched and submitted to seq on a proton platform. Differentially expressed genes, functional networks and signalling pathways were analyzed.

first: Xiangdong

last: Fang


title: Integrated Analysis of LncRNA-mRNA Co-Expression in the Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs

status: Public on Nov 16 2018

first: Yang

address: No.10, west end of right 'an gate, fengtai district, Beijing

institute: Capital Medical University

summary: Miniature pigs, a valuable alternative model for understanding human tooth development, have deciduous teeth from all four tooth families that are replaced once by permanent molars. The extracellular matrix (ECM) supports cells and maintains the integrity of tooth germs during tooth development. However, details on the role of the ECM in tooth development are poorly understood. Here, we performed long non- coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the ECM components of deciduous tooth germs by RNA sequencing in miniature pigs. From the early-cap to the late-bell stages, we identified 4,562 and 3,238 differentially expressed genes (DEGs) from E40 to E50 and E50 to E60, respectively. In addition, a total of 1,464 differentially expressed lncRNAs from E40 to E50, and 969 differentially expressed lncRNAs from E50 to E60 were obtained. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were enriched significantly for multiple signaling pathways, especially for the ECM pathway. We then outlined the detailed dynamic gene expression profiling of ECM components during deciduous molar development. Comparison of the cap and bell stages revealed that the structure and functions of the ECM dynamically changed. The ECM-related genes, including THBS1, COL4A5, COL4A6, COL1A1, CHAD, TNR, GP1BA, and ITGA3, were significantly changed, and some were shown to enrich during the bell stage development. Finally, we outlined the co-expression of lncRNAs and ECM properties during tooth development. We showed that the interplay of key lncRNAs could change ECM processes and influence the ECM establishment of tooth patterns to accomplish full tooth formation. These results might provide information to elucidate the regulation network of the lncRNA and ECM in tooth development.

first: Songlin

last: Wang


title: Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains (mRNA-seq)

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

summary: MicroRNAs (miRNAs) regulate many neurodevelopmental events, including proliferation, neurogenesis, neuronal migration, and cell survival. Individual miRNAs interact with hundreds of mRNA transcripts, but the precise landscape of these interactions in the context of cell-type-specificity has not been determined. Here, we used multiple parallel approaches, including AGO2-HITS-CLIP, combined mRNA and miRNA single-cell profiling and bipartite network analysis, to reveal a non-uniformity of miRNA-mRNA interactions that supports both defined cell-type identities as well as their dynamic transitions during human brain development at stages of peak neurogenesis. miRNA-mRNA clusters dynamically exploit the redundancy of the miRNA target code to differentially cluster across transitions in brain development. Using cell-type-specific functional properties of miRNA-mRNA interactions, we identify the role of great ape-specific miR-2115 in regulating cortical progenitor cell proliferation by targeting a radial glia enriched gene, origin recognition complex subunit 4 (ORC4). Together, our study suggests that miRNAs contribute to cell identity by regulating the expression of cell-type-specific transcripts.

overall_design: AGO2-HITS-CLIP was performed on human prenatal brain tissue samples and miRNA and mRNA libraries were prepared separately from the band corresponding to AGO2:miRNA:mRNA complex (130 kDa). Libraries were sequenced on Ion Torrent platform.

first: Neha

last: Rani

first: Tomasz

last: Nowakowski

first: Hongjun

last: Zhou

middle: S


title: Long-range epigenetic concordance revealed by simultaneous profiling of DNA methylation and chromosomal conformation changes in bulk and single cell Methyl-HiC

first: Guoqiang

state: Beijing

address: No.5 Yiheyuan Rd

institute: Biomedical Pioneering Innovation Center,Peking University

summary: Genomic sequences, as well as its covalent epigenetic modifications, are spatially organized into three-dimensional structures. Here, we developed Methyl-HiC by combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture genome-wide chromosome conformation changes and DNA methylation within the same DNA molecule. Methyl-HiC generated consistent information compared with in situ Hi-C and WGBS from the same cell line. We detected long-range DNA methylation concordance in general but varied in different chromatin states. We extended Methyl-HiC to single cell level and applied it on 103 primed and 47 naïve mouse embryonic stem cells (mESCs). We revealed the heterogeneity of chromosomal conformation changes by grouping cells in their DNA methylation level alone. We also observed increases of DNA methylation stochasticity and decreases of contact frequency together in late replication timing regions. Our method here paves the road to evaluate the direct long-range effect of epigenetic alterations in different pathological and healthy conditions at genome-wide and single cell level.

overall_design: Methyl-HiC and single cell Methyl-HiC experiments applied to mouse embryonic stem cell (F123).

first: Yaping

last: Liu

first: Manolis

last: Kellis

first: Bing

last: Ren


title: Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

city: Cambridge

first: Hugo

last: Brandao

state: MA

address: 77 Massachusetts Ave. E25-526C

institute: Massachusetts Institute of Technology

summary: Several general principles of global 3D genome organization have recently been established, including non-random positioning of chromosomes and genes in the cell nucleus, distinct chromatin compartments, and topologically associating domains (TADs). However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are still poorly characterized. Here, we systematically probe heterogeneity in genome organization. High-throughput optical mapping of several hundred intra-chromosomal interactions in individual human fibroblasts demonstrates low association frequencies, which are determined by genomic distance, higher-order chromatin architecture, and chromatin environment. The structure of TADs is variable between individual cells, and inter-TAD associations are common. Furthermore, single-cell analysis reveals independent behavior of individual alleles in single nuclei. Our observations reveal extensive variability and heterogeneity in genome organization at the level of individual alleles and demonstrate the coexistence of a broad spectrum of genome configurations in a cell population.

overall_design: We generated Hi-C libraries of the immortalized human cell line HFF-hTERT and performed dilution Hi-C

first: Elizabeth

last: Finn

first: Gianluca

last: Pegoraro

middle: B

first: Anne-Laure

last: Valton

first: Marlies

middle: E

last: Oomen

first: Job

last: Dekker

first: Leonid

last: Mirny

first: Tom

last: Mistelli


title: Histone H3-G34V and H3-G34R mutant fission yeast exhibit distinct chromatin changes and different DNA damage sensitivities.

status: Public on Nov 15 2018

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R mutant histone H3.3.  H3.3-G34R mutants are common in tumors additionally mutant for p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, but minimally affects transcriptional control. H3-G34R mutants exhibit genomic instability and increased replicative stress including slowed replication fork restart although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and on damage have altered HR protein dynamics suggestive that H3-G34R slows resolution of HR-mediated repair.  In summary our analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.

overall_design: H3.3 mutations in fission yeast are examined with a panel of 3 H3 WT samples, 3 G34V, 3 G34R mutants and 3 Set2D mutants

first: Brandon

middle: R

last: Lowe

first: Rajesh

middle: K

last: Yadav

first: Atsushi

last: Matsuda

first: Ryan

last: Henry

first: Alfonso

middle: G

last: Fernandez

first: Joshua

last: Hamey

first: Satish

last: Kallappagoudar

first: Carolyn

middle: M

last: Jablonowski

first: Marc

middle: W

last: Wilkins

first: Andrew

last: Andrews

first: Yasushi

last: Hiraoka

first: Janet

last: Partridge


title: Transcriptional profiling in the anterior pituitary gland of juvenile broiler chickens genetically selected for high or low body weight

city: Athens

first: Laura

last: Ellestad

address: 110 Cedar Street

department: Department of Poultry Science

institute: Unviversity of Georgia

summary: Several processes governing growth and metabolism are regulated by the neuroendocrine system, particularly the trophic hormones produced in the anterior pituitary gland. However, many of the differences that exist in pituitary gene expression and functional gene networks associated with divergent growth characteristics are still largely unknown. Using the Del-Mar 14K Chicken Integrated Systems microarray, this experiment evaluated global gene expression in the anterior pituitary gland during the first 7 weeks of post-hatch growth in two lines of chickens genetically selected for high growth (HG) or low growth (LG) at SRA-INRA, France. The HG and LG chickens differ in body weight, abdominal fat content, and plasma hormone and metabolite levels, making them a valuable model for both biomedical and agricultural traits. Amplified total RNA extracted from individual anterior pituitary glands collected from 4 birds from each line at each age (n=4) was produced. Cy-3 labeled cDNA from these samples was hybridized with an aliquot of Cy-5 labeled cDNA made from a pool of total RNA from all 32 samples. Data were analyzed as log2-(Cy3intensity (norm)/Cy5intensity (raw)) by two-way ANOVA using a linear mixed model procedure (PROC MIXED; SAS institute Inc., Cary, NC), and a total of 2,310 spots were significantly different (P<0.05) by line (1,100), age (1,058), or the line-by-age interaction (353). Of these, we identified 291 spots representing 263 genes as differentially expressed between HG and LG birds, where there was a >160% difference between the highest expression in one line and the lowest expression in the other and a significant line-by-age (110) or line (181) effect. Four anterior pituitary hormones were contained in this set of differentially expressed genes: thyroid-stimulating hormone ?-subunit, luteinizing hormone ?-subunit, and follicle-stimulating hormone ?-subunit mRNA levels were higher in the HG line; and growth hormone mRNA was elevated in the LG line. Pathway analysis revealed differences in expression between HG and LG lines associated with molecular transport, endocrine system development and function, organ and tissue morphology, and cellular compromise. Potential alteration in pituitary function between the two lines was highlighted in a network containing genes associated with hormone expression and secretion, as well as those potentially involved in pituitary gland morphology and vascularization.

overall_design: A reference design was used to analyze amplified antisense RNA from four biological replicates of each line (HG or LG) at each age (weeks 1, 3, 5, and 7). Each Cy3-labeled experimental sample was hybridized with an aliquot of the Cy5-labeled reference pool, which was generated from equal amounts of all 32 individual samples.

last: Porter


title: Identifying deer antler proliferation and mineralization genes using comparative RNA-seq

city: Stanford

first: Peter

last: Yang

address: 300 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford University

summary:
Purpose: The goal of this study is to compare (RNA-seq) transcriptomes of in vitro cultured human bone marrow-derived mesenchymal stem cells (hMSCs) and fallow deer antler-derived skeletal progenitors (FD RM Cells) under multiple conditions to identify candidate proliferation and mineralization genes responsible for fast antler regeneration
Methods: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads were analyzed at the transcript isoform level STARS followed by Cufflinks. Validation for genes of interest was performed using immunofluorescence staining.
Results: Comparison of human and fallow deer skeletal progenitor datasets yielded proliferation and mineralization gene candidates
Conclusions: Our study represents the first detailed analysis of human and fallow deer transcriptomes of skeletal progenitor cells under proliferation and mineralization conditions, with biologic replicates, generated by RNA-seq technology. Our in vitro comparative approach circumvent some of the logistical and technical challenges in identifying candidate proliferation and mineralization genes responsible for rapid deer antler regeneration. We conclude that in vitro comparison of RNA-seq based transcriptomes identified candidate proliferaiton and mineralization genes to advance bone biology and holds promise to rapidly regenerate large bone volumes for regenerative medicine. The comparative approach utilized here can be adapted for almost any tissue to study a specific phenomenon of interest.

sample_organism:
Homo sapiens
Dama dama

platform_organism:
Homo sapiens
Dama dama

overall_design: Design: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Dai Fei Elmer

last: Ker

first: Dan

last: Wang

first: Rashmi

last: Sharma

first: Bin

last: Zhang

first: Ben

last: Passarelli

first: Norma

last: Neff

first: Chunyi

last: Li

first: William

last: Maloney

first: Steve

last: Quake

first: Yunzhi

middle: P


title: The in vitro influence of adiponectin on the porcine endometrium on days 15 to 16 of gestation.

status: Public on Nov 14 2018

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

summary: Adiponectin is a hormone secreted primarily by white adipose tissue. Recent studies have shown that adiponectin and its receptors (AdipoR1 and AdipoR2) are expressed in different reproductive tissues, including the ovary and uterus. This newly discovered endocrine system plays an important role in the regulation of reproductive processes. The aim of this study was to explore the influence of adiponectin on global gene expression in the porcine endometrium during early gestation, on days 15 to 16 of pregnancy (implantation period).

overall_design: We analized samples obtained from 4 indyviduals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and adiponectin treated grous. The concentration of adiponectin in the culture medium was 10 µg/ml. In vitro tissue cultures were cultivated with treatments for 24 hours.

first: Nina

last: Smolinska

first: Karol

last: Szeszko

first: Marta

last: Kiezun

first: Edyta

last: Rytelewska

first: Katarzyna

last: Kisielewska

first: Marlena

last: Gudelska

first: Tadeusz

last: Kaminski


title: Lung resident mesenchymal stromal cells reveal transcriptional dynamics of lung

city: boston

first: ruggero

last: spadafora

address: 55 fruit street

department: newborn medicine

institute: MGH

summary: We report the correlation between lung-derived neonatal MSCs and 2 clinical variables among preterm newborns: corrected gestational age (CGA) at collection and the severity of bronchopulmonary dysplasia (BPD)

overall_design: To test the correlation between the transcriptional profiles of tracheal aspirate-derived mesenchymal stromal cells with late stage lung development and with bronchopulmonary dysplasia.

first: Ruggero

last: Spadafora

first: Paul

last: Lerou


title: Oncogenic Enhancers Inform Therapeutic Leads in Lethal Infant Ependymoma

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

summary: Genome sequencing studies have uncovered the most frequent mutations in cancer and novel targets for therapy. While successful in many tumors, this approach has failed in others. Lethal infant ependymomas (Group A) lies at the far end of this spectrum with no recurrent focal genomic alterations, no recurrent somatic mutations, and no clear driver for targeted therapy. Despite a paucity of genetic aberrations, Group A ependymomas demonstrate widespread epigenetic alterations. We therefore sought to interrogate the oncogenic drivers of ependymoma by characterizing the enhancer landscapes of 30 primary tumors. Super enhancer (SE) mapping revealed novel ependymoma oncogenes such as PAX6, SKI, and FGFRL1 and uncovered subgroup specific SE lesions across ependymoma, specifically, in Group A such as PAX3, MEIS1, and IGF2BP1. Finally, we identified SE associated gene dependencies that maintain FGFR1 and WEE1 expression in ependymoma, demonstrating the utility of SE lesions to predict novel targets for cancer therapy.

overall_design: H3K27ac ChIP seq using the antibody (Abcam catalog #AB4729, Lot #GR184557) was performed on 30 flash frozen primary ependymoma specimens

last: Mack

first: Michael

last: Taylor

first: Jeremy

middle: N

last: Rich


title: Global gene expression profile of primary mouse lung and small cell lung cancer (SCLC) tissues

first: Yifeng

last: Xia

address: 10010 North Torrey Pines Road

department: Laboratory of Genetics

institute: Salk Insitute

summary: Mouse SCLCs were induced by lentiviral vector expressing luciferase-Mycl-shp53-shRb or IkBaM-Mycl-shp53-shRb. Tumor tissues were isolated from mice that reached clinical endpoints. RNA was isolated using the RNeasy kit according to manufacturer’s protocol with the addition of DNase (Direct-zol). cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina). RNA sequencing was performed using a HiSeq 2500 Sequencing System (Illumina).

overall_design: 8 normal mouse lung samples, 6 luciferase-Mycl-shp53-shRb tumor samples and 6 IkBaM-Mycl-shp53-shRb were compared by standard RNAseq method.


title: Ribonomic identification of mRNAs associated with RNA binding proteins TcRBP7 and TcRBP40 from Trypanosoma cruzi

city: Lund

first: Saloe

middle: Bispo

last: Poubel

state: skane

address: Building 404:B3 Scheelevägen 2

country: Sweden

institute: Lund University

summary: TcRBP7 and TcRBP40 proteins are adjacent paralogs in T. cruzi with a conserved RRM structure and similar protein localization at specific foci at the posterior region. We identified their targets in order to compare their function, infering about the evolutionary implication of regulatory proteins duplication. Surprisingly, the mRNA targets co-immunoprecipitated with each RBP were distinct, pointing to a subfunctionalization outcome. In addition, TcRBP40 bound to transcripts of mucin-associated surface proteins (MASPs), which work in T. cruzi’s host-cell invasion. Both proteins recognize similar putative target sequences despite showing different binding behavior. This study shows the rearrangement potential in gene expression networks in the face of duplication of regulatory proteins.

overall_design: mRNAs isolated in vivo by co-immunoprecipitation of GFP-tagged TcRBP7 and TcRBP40, in triplicates. GFP-tag alone was used as a control, in triplicate. mRNAs were sequenced in SOLiD4 System.


title: Functional analysis of Mpk1-mediated cell wall integrity signaling pathway in the thermotolerant methylotrophic yeast Hansenula polymorpha

city: Seoul

first: Eun Jung

last: Thak

address: 84, Heukseok-ro, Dongjak-gu

institute: CHUNG-ANG University

summary:
Purpose: To identify the downstream gene sets regulated by Mpk1p in H. polymorpha under normal and caffeine-treated conditions, we compared the RNA-seq based transcriptional profiles.
Methods: Total RNA was isolated according to the hot phenol extraction method and all procedure for RNA sequencing were conducted by ChunLab. More than 1.5-fold regulated genes are functionally classified using the Munich Information Center for Protein Sequences (MIPS) FunCat.
Results: Transcriptome analysis of the DL1-L strain revealed that caffeine significantly increased expression of a subset of cell-wall related genes in an Mpk1p-dependent manner, but most of which were not Rlm1-target genes.
Conclusion: Our results support the essential role of Mpk1p in maintaining cell wall integrity upon several stress conditions of H. polymorpha.

overall_design: mRNA profiles of cells grown at normal and caffeine-treated conditions were generated by RNA-seq using Illumina.

first: Hyun

middle: A

last: Kang

first: Hyunah

last: Kim

first: Eun

middle: J


title: KDM5A regulates p53 function

first: Lance

last: Palmer

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: KDM5A regulates p53 expression by modulating the expression of a subgroup of translation iniation genes.

overall_design: CRISPR-CAS9 mediated knockout of KDM5A in HCT116 cells were subject to ChIP-seq for KDM5A and H3K4me3.

first: Jun

last: Yang

first: Yiping

last: Fan


title: Genome-wide Ezh2 and Tcf1 occupance in follicular helper T cells

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: mapping Ezh2 and Tcf1 binding sites in follicular helper T cells

overall_design: C57BL/6 mice were then infected with vaccine virus, and 8 days later, CD44-high, CD62L-negative CD4+ T cells were further stained, and CXCR5+, SLAM-low follicular helper T cells were sorted and used for ChIPseq of Tcf1 or Ezh2. For negative control, CD62L+CD44-low naïve CD4+ T cells were sorted from CD4-Cre, Tcf1 fl/fl mice, or from CD4-Cre, Ezh2 fl/fl mice as Tcf1-deficient, or Ezh2-deficient naive CD4+ T cells, respectively.

first: Hai-Hui

last: Xue


title: The splicing factor SRSF1 regulates the radio-resistance of cancer cells through modulating the alternative splicing of PTPMT1

status: Public on Nov 12 2018

city: Dalian

first: Yang

last: Wang

address: No.9 West section, South Lv Road

institute: Dalian Medical University

summary: RNA-seq was performed on H1299 cells that stably knocking down SRSF1 or control, as well as these cells that were treated with ionizing radiation, in order to profile the alternative splicing events that were regulated by SRSF1 upon ionizing radiation.

overall_design: Examination of different alternative splicing events in 4 types of cells

first: Wang

first: Sun

last: Bing


title: Transcriptomic dataset after cisplatin induced acute kidney injury

city: Cologne

first: Andreas

last: Beyer

address: Joseph-Stelzmann-Str. 26

department: System Biology

institute: University of Cologne

summary: Cisplatin-induced acute kidney injury (AKI) is one of the most common and severe side effects and can prevent the use of this important agent. Unfortunately, preventive or therapeutic tools to address cisplatin-induced AKI are lacking. Interestingly, in the last decades a row of preconditioning strategies that employ the activation of cellular stress resistance pathways have been shown to be promising approaches to protect from organ injury in rodent models. Here, we characterized both the protective potential and the underlying molecular patterns of two strategies – caloric restriction and hypoxic preconditioning – in mice treated with cisplatin.

overall_design: mRNA profiles of mouse kidney after cisplatin injection with preconditioning baseline, caloric restriction and hypoxia.

first: Martin

last: Späth

first: Malte

last: Bartram

first: Nicolàs

last: Palacio-Escat

first: K. Johanna

last: Hoyer

first: Cedric

last: Debes

first: Christina

last: Schroeter

first: Thomas

last: Benzing

first: Bernhard

last: Schermer

first: Volker

last: Burst

first: Julio

last: Saez-Rodriguez

first: Pitter

middle: F

last: Huesgen

first: Roman-Ulrich

last: Müller

first: Markus

last: Rinschen

first: Fatih

last: Demir

first: Amrei

last: Mandel

first: Franziska

last: Grundmann

first: Giuliano

last: Ciarimboli

first: Jaychandran

last: Kizhakkedathu

first: Susanne

last: Brodesser

first: Heike

last: Göbel

first: Jan

middle: U

last: Becker

last: Höhne


title: Ribosome profiling analysis of heat effect on rice

city: University Park

first: Zhao

last: SU

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: To impose the heat treatment similar to the Structure-seq experiment, we applied Ribo-seq to 14-day-old rice (Oryza sativa) shoot tissue to investigate the effect of heat stress (42°C) as compared to control condition (22°C).

overall_design: Two-week-old rice plants in pots were inverted and the shoots were immersed in a water bath at 22°C or 42°C for 10 min treatment, and ten shoots were harvested for each individual sample. Two biological replicates were obtained for each treatment and time-point. Ribosome profiling libraries were then made using these four sets of materials to determine the translational efficiency changes under different temperatures.

last: Su

first: Yin

last: Tang

first: Philip

last: Bevilacqua

first: Sarah

last: Assmann


title: Knockdown of HP1γ in H1792 cells

status: Public on Nov 13 2018

first: JIE

last: Lv

department: Department of Computational Biology

summary: For analysis of genes regulated by HP1γ in LUAD, we used microarray analysis to determine the global changes in gene expression upon HP1γ knockdown in H1792 cells and identified distinct sets of up-regulated and down-regulated genes upon depletion of HP1γ.

overall_design: H1792 cells were infected with 2 different shRNAs of HP1γ (shHP1γ-16 and -17). After 96 hours of selection in 1ug/ml puromycin-containing medium, cells were harvested for RNA extraction. Global gene expression levels of  HP1γ knockdown cells were measured by Affymetrix U133P and compared with those of control (shLuc) cells. Experiments were peformed in duplicate. Microarray adat was processed by RAMA and heat map was generated by MeV software.

first: Hunain

last: Alam

first: Jie

first: Kaifu

last: Chen

first: MinGyu

last: Lee


title: Rice RNA secondary structurome under heat stress

summary: We used the Structure-seq2 protocol and applied it to 14-day-old rice (Oryza sativa) shoot tissue for genome-wide RNA structure probing to investigate the effect of heat stress on the RNA structurome.

overall_design: We applied our newly optimized pipeline of Structure-seq2 on two weeks old rice shoot. 1 g of shoot tissue were collected right before each treatment. -/+DMS treatments  (3 biological replicates for each) was applied for room temperature treatment as the control. For the heat shock treatment, −DMS and +DMS samples were similarly prepared but under 42°C. Total 12 individual libraries was labeled with unique Illumina TruSeq barcode and were sequenced by HiSeq2500.

first: Laura

last: Ritchey


title: Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome

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

overall_design: Refer to individual Series


title: Genome-wide analysis of heat effect on rice transcriptome by RNA-seq

summary: To impose the heat treatment similar to the Structure-seq experiment, we applied RNA-seq to 14-day-old rice (Oryza sativa) shoot tissue to investigate the effect of heat stress (42°C) as compared to control condition (22°C).

overall_design: Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22°C or 42°C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30°C) for ease of sampling during the recovery period (0 min, 10 min, 50 min, 1 h 50 min, 9 h 50min). Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.


title: Long-term expansion of functional pancreatic islets on a laminin-521 matrix and curative transplantation into diabetic mice

status: Public on Nov 09 2018

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: In this study we show, for the first time, that whole islets can be cultured and significantly expanded long-term in vitro on specific basement membrane (BM) laminin LN-521 which is a normal component of islet BMs. Isolated islets adhere and flatten to form 2-3 cell layer entities with ~10 % of all endocrine cell types proliferating after 2-5 weeks in culture. Time-lapse imaging of freshly isolated islets in suspension labeled with hypoxia and DNA degradation indicators reveals that spherical islets on LN-111 rapidly develop hypoxia and central necrosis, in contrast to islets attached to LN-521, which normal b-cell glucose responsiveness. RNA sequencing analyses reveal that freshly isolated islets express LN-521 binding integrins. Compared to other matrices, islets grown on LN-521 develop a unique expression signature, including expression of specific integrins, involved in cell adhesion and matrix production as well as proliferation. The results reveal specific LN-521-mediated effects into islet cells and suggest that use of in vitro expanded islets may significantly enhance the efficacy of islet transplantation treatment of T1D.

overall_design: Isolated mouse pancreatic islets were cultured in wells coated with 3 different matrices, either laminin-521, laminin-421 or laminin-111, for either 0, 3 or 12 days. Islets were seeded to triplicate wells (A, B and C), 20 islets per well. After each time point the islets were collected and stored in RNAlater in -80C until RNA isolation. Total RNA was extracted and sequencing libraries were constructed with 2 ng of total RNA. Barcoded libraries were multiplexed and sequenced as pair-end 75bp reads on HiSeq2000.

first: Miina

last: Öhman

first: Xiaoran

last: Chai

first: Su

middle: T

last: Tay

first: Sujoy

last: Ghosh

first: Enrico

last: Petretto

first: Karl

last: Tryggvason


title: ETV5 silencing in bladder cancer cell line 97-7

city: Leeds

first: Erica

last: di Martino

address: Becket Street

department: Experimental Oncology

country: United Kingdom

institute: University of Leeds

summary:
We hypothesized that ETV5 may be a mediator of the oncogenic effects of mutant FGFR3 in bladder cancer cells
ETV5 was silenced by shRNA in the bladder cancer cell line 97-7 to investigate effect on phenotype. To identify downstream gene targets of ETV5 we compared gene expression profiles in silenced and control cells.

overall_design: Two different hairpins targeting ETV5 were used (sh155 and sh1189) and expressed in 97-7 cells using a retroviral system. The gene expression profile of silenced cells was compared to the profile of the empty vector and scrambled controls. Each condition was repeated in triplicate. sh115 and sh1189 were pooled together for analysis; empty vector and scrambled controls were pooled together for analysis

first: Margaret

last: Knowles

first: Carolyn

last: Hurst

first: Olivia

last: Alder


title: The mechanism research of differentially expressed circRNAs in ALV-J-induced tumor chickens

status: Public on Nov 10 2018

city: Guangzhou

first: Xinheng

last: Zhang

state: Guangdong

address: No.483, Wushan Road, Tianhe District

department: Animal Science

institute: South China Agricultural University

summary: In this study, we want to screen differentially expressed circRNAs in ALV-J-induced tumor chickens by circRNA-seq, and then conduct the mechanism research of those important circRNAs in ALV-J-induced tumor chickens

overall_design: Firstly, one-day old chicks were injected ALV-J, and then cultivated ALV-J-susceptible chickens and ALV-J-resistant chickens. Secondly, at 10 weeks, we collected livers of ALV-J-resistant chickens and ALV-J -susceptible chickens, three livers as three replications were collected from ALV-J -resistant chickens and ALV-J-susceptible chickens. Those collected livers were used for circRNA-seq. Thirdly, analyzed differentially expressed circRNAs in ALV-J-susceptible chickens and ALV-J-resistant chickens. Lastly, research the function of those differentially expressed circRNAs in ALV-J -susceptible chickens which was the model of ALV-J-induced tumor chickens.

first: Qingmei

last: Xie


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-EUCGR]

status: Public on Nov 08 2018

city: montpellier

first: Laurent

last: Maggia

address: TA A-108 / 03 Av. Agropolis

department: BIOS

country: France

institute: Cirad

summary:
Finding predictive molecular markers for resistance against Myrtle rust may help to identify resistant plants and provide a means of maintaining Myrtaceae production in nursery, especially for ecosystems restoration purposes. Sequence polymorphism involving in differentiate expressed genes are particularly relevant for disease resistance marker design.
We sequenced the transcriptomes of resistant and susceptible individuals of three endemic host species: Arillastrum gummiferum, Tristaniopsis glauca and Syzygium longifolium. The rust phenotype of the individuals of each species was defined as "infected" (considered as susceptible) and "healthy" (considered as resistant). We described here a pre-breeding methodology to find disease resistance markers by combining next-generation sequencing, differential gene expression (DGE) and SNP calling. DGE was conducted in parallel using the only one available sequenced Myrtaceae genome (Eucalyptus grandis) and a de novo assembly transcriptome from each species. The edgeR tests if a gene is DE between “infected” individuals versus “healthy” ones. If the fold change log (FC = infected/healthy) is greater than 0, the gene is thus overexpressed in the infected individuals (considered as susceptible).

overall_design: Five individuals of Tristaniopsis glauca (One healthy/Four infected)

first: Julia

last: Soewarto

first: Stéphanie

last: Bocs

first: Chantal

last: Hamelin

first: Pierre

last: Mournet

first: Hélène

last: Vignes

first: Angélique

last: Berger

first: Alix

last: Armero

first: Guillaume

last: Martin

first: Alexis

last: Dereeper

first: Sarah

last: Gautier

first: Fabian

last: Carriconde


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-EUCGR]

overall_design: Seven individuals of Syzygium longifolium (five healthy/two infected)


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-DENOVO]


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-EUCGR]

overall_design: Six individuals of Arillastrum gummiferum (Three healthy/three infected)


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-EUCGR]

overall_design: Six individuals of Tristaniopsis glauca (Two healthy/Four infected)


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-DENOVO]


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-DENOVO]


title: Nucleobindin-2 controls insulin-sensitivity in obesity without impacting food intake and adiposity

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: We performed whole transcriptome profiling on sorted tissue macrophages from adipose of wild-type or Nucb2-/- mice on high fat diet

overall_design: Profiles were generated on fluorescence-activated-cells (FACs) sorted F480+CD11b+ cells from adipose tissue, using sequencing analysis

first: Anthony

last: Ravussin

first: Jil

last: Sander

first: Yun-Hee

last: Youm

first: Bolorma

last: Vandanmagsar

first: Gerald

middle: I

last: Shulman

first: Matthew

middle: S

last: Rodeheffer

first: Kim

middle: Y

last: Nguyen

middle: L

first: Vishwa

middle: D

last: Dixit


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii)

first: Laurent

last: Maggia

sample_organism:
Arillastrum gummiferum
Tristaniopsis glauca
Syzygium longifolium


title: Mandibular dysmorphogenesis due to abnormal osteogenic activity in FGFR2-related craniosynostosis mouse models

status: Public on Nov 07 2018

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn Institute of Medicine at Mount Sinai

summary: Mutations within FGFR2 are causative for various craniosynostosis syndromes. The mandibular dysmorphogenesis in these syndromes has rarely been quantitatively characterized prenatally and the cellular and molecular mechanism involved is unclear. To investigate the effects of FGFR2 mutations on development of the mandible, micro-computed tomography (μCT) images were acquired using newborn mice of three Fgfr2-mutant lines associated with Apert and Crouzon craniosynostosis syndromes. Euclidean Distance Matrix Analysis and analysis of relative bone mineral density (BMD) of 3D μCT images revealed differences in mandible morphology and BMD between the mice carrying the Fgfr2 mutations and their unaffected littermates. We further investigated the mechanism for mandibular dysgenesis in the Fgfr2+/S252W (Fgfr2S252W) mouse model that showed the most severe phenotypes. At E16.5, Fgfr2S252W embryos showed an increase in the size of the osteogenic anlagen and Meckel’s cartilage (MC) and altered microarchitecture and mineralization in the mandible relative to unaffected littermates. Laser capture microdissection and RNA-Seq analysis revealed transcriptomic changes in the mandibular bone, highlighting increased expression of genes undergoing osteoclast differentiation and dysregulated genes active in bone mineralization. Increased osteoclastic activity in the mandible of Fgfr2S252W embryos was confirmed and elevated inorganic pyrophosphate concentration was identified due to upregulated expression of Enpp1 and Ank. In contrast, increased proliferation in MC was observed at E12.5. These findings provide evidence that gain-of-function mutations in FGFRs differentially affect intramembranous ossification of dermal bone and cartilage formation contributing to mandibular dysmorphogenesis in craniosynostosis syndromes.

overall_design: Quantitative high-resolution micro-computed tomography (µCT) images of the mandible were acquired for 182 newborn (P0) mice to investigate the effects of three FGFR2 mutations associated with Apert and Crouzon syndromes. Samples for histological and transcriptome analysis consisted of 66 embryos of Fgfr2+/S252W model. Laser Capture Microdissection was used on embryos at E16.5 (3 Fgfr2S252W embryos and 3 unaffected littermates, all were female) to isolate tissues in Meckels cartilage, mandibular bone and mandibular condylar cartilage, respectively. Libraries were prepared with NuGEN Ovation RNA-Seq System v2 (amplification) and Illumina Nextera XT Library Prep kit. Fragments were sequenced using paired end reads (2×100 bp) on the Illumina HiSeq platform.

first: Susan

last: Motch Perrine

first: Meng

last: Wu

first: Nicholas

middle: B

last: Stephens

first: Divya

last: Kriti

last: van Bakel

first: Ethylin

last: Wang Jabs

first: Joan

last: Richtsmeier


title: Germline competency of human embryonic stem cells depends on eomesodermin

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: In humans, germline competency and the specification of primordial germ cells (PGCs) are thought to occur in a restricted developmental window during early embryogenesis. Despite the importance of specifying the appropriate number of PGCs for human reproduction, the molecular mechanisms governing PGC formation remain largely unexplored. Here, we compared PGC-like cell (PGCLC) differentiation from 18 independently derived human embryonic stem cell (hESC) lines, and discovered that the expression of primitive streak genes were positively associated with hESC germline competency. Furthermore, we show that chemical inhibition of TGFβ and WNT signaling, which are required for primitive streak formation and CRISPR/Cas9 deletion of Eomesodermin (EOMES), significantly impacts PGCLC differentiation from hESCs. Taken together, our results suggest that human PGC formation involves signaling and transcriptional programs associated with somatic germ layer induction and expression of EOMES.

overall_design: There are 91 RNAseq samples  in total.

first: Chen

last: Di

first: Anastasia

last: Lukianchikov


title: Genome-wide DNA methylation analysis of the whole blood of individuals with Coffin-Siris and Nicolaides-Baraitser syndromes

city: London

first: Bekim

last: Sadikovic

state: Ontario

address: 800 Commissioners Rd E

department: Pathology and Laboratory Medicine

country: Canada

institute: University of Western Ontario

type: Methylation profiling by genome tiling array

summary: Coffin-Siris and Nicolaides-Baraitser syndromes (CSS and NCBRS) are Mendelian disorders caused by mutations in subunits of the BAF chromatin remodeling complex. We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2). We demonstrate that the degree of similarity in the epi-signatures of some CSS subtypes and NCBRS can be greater than that within CSS, indicating a link in the functional basis of the two syndromes. We show that chromosome 6q25 microdeletion syndrome, harboring ARID1B deletions, exhibits a similar CSS/NCBRS methylation profile. Specificity of this epi-signature was confirmed across a wide range of neurodevelopmental conditions including other chromatin remodeling and epigenetic machinery disorders. We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening.

overall_design: Following bisulfite conversion of DNA extracted from blood, methylation analysis was performed using the Illumina Infinium bead chip arrays (San Diego, CA), according to the manufacturer’s protocol. The resulting methylated and unmethylated signal intensity data were imported into R 3.4.2 for analysis. Normalization was performed using Illumina normalization method with background correction using the minfi package in R 3.4.2.

first: Erfan

last: Aref-Eshghi


title: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-DENOVO]

first: Julia

last: Soewarto

first: Stéphanie

last: Bocs

first: Chantal

last: Hamelin

first: Pierre

last: Mournet

first: Hélène

last: Vignes

first: Angélique

last: Berger

first: Alix

last: Armero

first: Guillaume

last: Martin

first: Alexis

last: Dereeper

first: Sarah

last: Gautier

first: Fabian

last: Carriconde


title: Generation of nephronal cells from human pluripotent stem cells via renal-vesicle formation

city: Berlin

first: Nancy

last: Mah

address: Augustenburger Platz 1

department: Berlin-Brandenburger Centrum für Regenerative Therapien (BCRT)

institute: Charité - Universitätsmedizin Berlin

summary: Human pluripotent stem cells (hPSC) provide a possible source for generation of kidney cells and organoids applicable in regenerative medicine, disease modeling and drug screening. By analyzing the effect of different factors on renal differentiation, we established an 8-day-protocol that steered hPSCs to the renal lineage by a step-wise process, segmented into mesoderm induction, intermediate mesoderm specification and metanephric induction outlining renal organogenesis. The differentiated cells contain populations of SIX2+/CITED1+ metanephric mesenchyme- (MM) and of HOXB7+/GRHL2+ ureteric bud (UB)-like cells at the end of 6 days. Transcriptome analysis corroborated that the in vitro generated precursor cell types at day 8 resemble their renal vesicle counterparts in vivo. The cells were further differentiated in 2-dimensional culture into podocyte- and diverse tubular epithelial-like cell types, showing their nephrogenic potential. In 3-dimensional culture, the progenitors gave rise to renal vesicles, and upon mouse embryonic kidney re-aggregation they form tubular structures.

overall_design: Assessment of the progress of pluripotent stem cells towards a renal lineage at regular time points of a novel differentiation protocol.

first: Krithika

last: Hariharan

first: Harald

last: Stachelscheid

first: Bella

last: Rossbach

first: Su-Jun

last: Oh

first: Petra

last: Reinke

first: Andreas

last: Kurtz


title: Genome wide expression change by RNF168 knocking down in MCF-7 cells

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

summary: We aim to the investigate the role of RNF168 in breast cancer progression. MCF-7 cells were used as the model and RNF168 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM stramble siRNA and siSMURF1. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Jian

last: Zhu


title: lncRAN and mRNA expression signatures in SKOV3 cells: control vs. β-HCG transfected

status: Public on Nov 06 2018

city: Shanghai

first: Xiaoqing

last: Guo

address: 2699 west gaoke road

department: Obstetrics and Gynecology

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

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

summary: To further development of the effects of β-HCG in ovarian cancer SKOV3 cells，we have employed lncRNA and mRNA microarray as a discovery platform to identify lncRNA and mRNA expression in β-HCG overexpressing ovarian cancer cells. SKOV3 cells were transfected with lentiviral vector with eGFP, encoding β-HCG and negative control vector (LV- β-HCG and LV-CON,) by using polybrene. The dysregulation of β-HCG was confirmed by using RT-PCR. RNA was extracted and detected by a lncRNA and mRNA microarray in LV-β-HCG and LV-CON SKOV3 cells. The different expression of lncRNA and mRNA in LV-β-HCG and LV-CON SKOV3 cells was analyzed to explore the mechanism that β-HCG affect ovarain cancer cells.

overall_design: β-HCG overexpression induced lncRNA and mRNA expression in SKOV3 cells was measured in β-HCG and LV-CON groups.  3 control replicates at each group.


title: Gene expression profiling of CD301b+ macrophages and F4/80 negative immune cells from day 5 mouse wound beds

first: Brett

middle: Adam

last: Shook

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

institute: George Washington University

summary: Cells were isolated from day 5wounds from dorsal skin wound beds of 7-9 weeks old using FACS. This experiment describes the gene expression profile associated with different immune cell subsets during tissue repair.

overall_design: Cells were isolated by FACS.

first: Valerie

last: Horsley


title: Gene expression profiling of myofibroblasts in young and aged day 5 wound beds

summary: Mesenchymal cells were isolated from day 5 dorsal skin wound beds of 7-weeks old and >24-months old using FACS. This experiment describes multiple unique subsets of wound bed myofibrolbasts capable of contributing to tissue repair.

overall_design: Myofibroblast subsets were isolated by FACS. Cells were sorted based on CD34 and CD29 expression, where APs are CD34+ and CD29+; CD29 cells have high levels of CD29; and DN is CD34- and CD29 Low.


title: Gene expression profiling of adipocyte precursor cells (AP) nonwounded and day 5 wound beds

summary: APs were isolated from naïve skin and day 5wounds from dorsal skin wound beds of 7-9 weeks old using FACS. This experiment describes changes in AP gene expression associated with injury and subsequent tissue repair.

overall_design: APs were isolated by FACS.


title: RNAseq analysis of ruxolitinib treated breast cancers

status: Public on Nov 05 2018

city: Nashville

first: Justin

middle: M.

last: Balko

address: 2220 Pierce Avenue

department: Cancer Biology

institute: Vanderbilt University Medical Center

summary: We performed RNA sequencing analysis on fresh-frozen biopsies of metastatic triple-negative breast cancer prior to undergoing therapy with ruxolitinib, or after 2 cycles of therapy in a subset of patients.

overall_design: Seventeen samples were successfully sequenced, including two pairs of baseline and cycle 2, two unmatched cycle 2 samples, and eleven unmatched baseline samples.

first: Yaomin

last: Xu

last: Lin

first: Daniel

last: Stover

first: Yu

last: Wang


title: Gene expression profile of postnatal lung development in the marsupial opossum (Monodelphis domestica)

city: Melbourne

first: Amit

last: Kumar

state: VIC

address: 2 St Andrews Place, East Melbourne, Victoria

country: Australia

institute: Peter MacCallum Cancer Centre

summary: RNA-seq of lung tissue at 7 time points of postnatal development

first: Vengamanaidu

last: Modepalli

first: Julie

last: Sharp

first: Norman

middle: R

last: Saunders

first: Kevin

last: Nicholas

first: Christophe

last: Lefèvre


title: Single-cell and bulk RNA-seq of Th2

first: Weijie

last: Yin

address: 320 Yue Yang Road

institute: Shanghai Institutes for Biological Sciences

summary: Th2 cell is a subset of CD4+ T helper (Th) cells, which regulates the immunity to extracellular parasites and allergic inflammation. Th2 cells specifically secrete Type 2 cytokines such as IL-4, IL-5, IL-13, and also express many universal cytokines like IL-2 and GM-CSF. While theses cytokines are indispensable for Th2 cell mediated response, there is complex heterogeneity in the pattern of cytokine production among Th2 cell population. As previous studies were mainly conducted at population levelref, here we took advantage of single-cell RNA-seq to explore heterogeneity in in vitro differentiated Th2 cells. Although a few single cell researches about Th2 cells was conducted, there is no comprehensive understanding of the heterogeneity of Th2 lineage yet, inspiring us to make some difference on this issue. Our studies identify that cytokine genes contributed most to the transcriptome heterogeneity of Th2 cells; expression of universal cytokines showed bimodality, but not Th2 specific cytokines.

overall_design: 56 Single Th2 cells for single-cell RNA-seq. Pooled 10,000 Th2 cells for bulk RNA-seq.


title: Identification of immune-activated Hematopoietic Stem Cells

city: Beer-Sheva

first: Nir

last: Bujanover

address: Ben Gurion 1

department: Immunology

country: Israel

institute: Ben-Gurion University

summary: We utilized our transgenic Fgd5-mCherry mouse to sort and RNAseq for HSCs under acute immune activation (with pIC) to reveal a complex cell cycle gene expression and an upregulated IFN I/II signature

overall_design: RNAseq of bone marrow Lineage-Sca1+cKit+CD150+mCherry+ cells (1000) 24hrs after pIC was administered and control (PBS treated)

first: Roi

last: Gazit


title: Maintenance of human hematopoietic stem cells in vitro using chemical cocktails

status: Public on Nov 04 2018

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

summary: Single cell RNA-seq is a powerful tool for studying complex biological systems such as HSPCs cultured in vitro. We detected 11, 3, 4, 8 and 8 subpopulations in uncultured CD34+ cells,control cells, CD34+ cells with the treatment of CFO, cytokines and CFO + cytokines using t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis.

overall_design: We applied our homemade microwell single cell RNA-seq platform to perform analysis with uncultured human CD34+ cells, control cells, CFO cultured CD34+ cells, cytokine cultured CD34+ cells as well as CFO + cytokines cultured CD34+ cells.

first: Guoji

last: Guo


title: mRNA expression files of spermatogonial stem cells in response to Bisphnel A

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We isolated mouse spermatogonial stem cells (SSCs) and employed the in vitro propagation of mouse SSCs.We got patterns of mRNA expression of Bisphnel A (BPA)- treated SSCs and untreated SSCs by RNA-sequencing (RNA-seq).GO and KEGG pathway enrichment analyses were executed to determine the principal function of the differential expressiongenes (DEGs).“Regulation of programmed cell death” and “regulation of apoptotic process” were enriched in the BPA-treated SSCs by GO analysis, and “apoptosis” pathway was clustered by KEGG analysis.Among the genes involved in “apoptosis”pathway, Atf4 (Activating transcription factor 4,an apoptotic transcription factor) and Ddit3 (DNA damage inducible transcript 3,also referred to as Chop) were significantly up-regulated in BPA-treated SSCs groups, which were proved by qPCR.

overall_design: mRNA profiles of  groups of Bisphnel A treated SSCs and  groups of untreated SSCs

first: Hui

last: Xie

first: Xiaowen

last: Gong


title: Drosophila intestinal stem and progenitor cells are major sources and regulators of homeostatic niche signals

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

institute: Menzies Institute for Medical Research

summary: Epithelial homeostasis requires the precise balance of epithelial stem/progenitor proliferation and differentiation. While many of the signaling pathways that regulate epithelial stem cells have been identified, less is known about their targets or crosstalk between them. Here, we use gene expression profiling by targeted DamID to identify the stem/progenitor specific transcription and signaling factors in the Drosophila midgut. Many signaling pathway components, including ligands of most major pathways, exhibit stem/progenitor specific expression and have regulatory regions bound by both intrinsic and extrinsic transcription factors. In addition to previously identified stem/progenitor-derived ligands, we show that both the insulin-like factor Ilp6 and TNF ligand egr are specifically expressed in the stem/progenitors and regulate normal tissue homeostasis. We propose that intestinal stem cells not only integrate multiple signals but also contribute to and regulate the homeostatic signaling micro-environmental niche through the expression of autocrine and paracrine factors.

overall_design: Targeted DamID with RNA pol II and Sox21a.  Pol II: two conditions (ISCs/Ebs, esg driver; ECs, myo driver), two replicates per protein per condition; Sox21a: one condition (ISCs/EBs, esg driver), three replicates.

first: David

middle: P

last: Doupé

first: Hannah

last: Dayton

first: Andrea

middle: H

last: Brand

first: Norbert

last: Perrimon


title: Epigenetic correction of defective plasticity in a tauopathy mouse model with an acetyltransferase activator [RNA-Seq]

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

summary: In the adult brain, histone acetylation is associated with activity-regulated transcriptional changes that are required for synaptic plasticity and memory. These processes are dismantled in neurodegenerative diseases. Here, we demonstrate that synaptic plasticity and memory deficiencies can be restored in a mouse model of tauopathy following treatment with CSP-TTK21, a small molecule activator of CBP/p300 histone acetyltransferases (HAT). CSP-TTK21 normalized the H2B acetylation levels in many genes, including a series of super-enhancer –regulated genes, associated with plasticity and neuronal function in resting tauopathic mice. CSP-TTK21 re-established part of the learning-induced hippocampal transcriptome, including the induction of immediate early genes and memory-related genes, and the down-regulation of neuronal identity genes that bear super-enhancers. This study is the first to provide in vivo proof-of-concept evidence that direct activation of CBP/p300 HAT efficiently and selectively reverses epigenetic, transcriptional, synaptic plasticity, and behavioral deficits associated to Alzheimer’s disease lesions in mice.

overall_design: RNA profiles by deep sequencing using Illumina HiSeq 2500 obtained from  Dorsal Hippocampus of WT and THY-Tau22 mice, not treated or treated with either Saline (S), CSP (C) ors CSP-TTK21 (T), in basal (resting, no training) or behavior (spatial training) conditions, as noted.


title: ARv7 represses tumor suppressors genes in castration-resistant prostate cancer  [RNA-Seq]

status: Public on Nov 02 2018

city: Boston

first: Myles

last: Brown

address: 450 Brookline Ave., D730

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Endocrine therapies in prostate cancer (PCa) treatment block androgen receptor (AR) function, but are palliative as tumors progress to a lethal, castration-resistant state (CRPC). CRPC remains dependent on AR signaling, which can act through the full-length AR (ARfl) or constitutively active splice variants, e.g. ARv7. We show here that both ARfl and ARv7 bind to the same genomic region and heterodimerize in a CRPC cell line model, but regulate distinct transcriptomes. ARv7, unlike ARfl, preferentially represses transcription and demonstrates an increased affinity for co-repressors, decreased chromatin residence time and lower dependence on FOXA1 binding. We identified a group of ARv7-repressed genes, including the UDP-galactosyltransferase B4GALT1 that are down-regulated during PCa progression and important for CRPC growth. In conclusion, we propose that ARv7 acts as a transcriptional repressor of genes that limit proliferation, a function that should be targeted in CRPC patients.

overall_design: RNA-seq from shRNA-mediated knock-down experiments in prostate cancer cell lines

first: Anna

middle: C

last: Groner

first: Laura

last: Cato

first: Irene

last: Lee

first: Jaice

last: Rottenberg

first: Jonas

last: de Tribolet-Hardy


title: RNA-seq of HIV bnAb and control individuals PBMC

status: Public on Nov 01 2018

city: Durham

first: Todd

last: Bradley

address: 2 Genome Court

institute: Duke University Medical Center

summary: We sought to determine differences in transcript expression between a cohort of HIV-infected individuals that either developed broadly neutralizing antibodies (bnAb) or did not develop them (control). With the ultimate goal to identify transcripts that are associated with the development of bnAbs that would identify novel pathways that could be targeted in future vaccine strategies to increase the frequency of individuals that develop bnAbs against HIV. Using this approach we identified that Rab11 recycling endosomes, particularly in dysfunctional natural killer cells are associated with the development of HIV-1 bnAbs.

overall_design: RNA extracted from peripheral blood mononuclear cells of 95 subjects was subject to RNA-seq for transcriptome analysis comparing individuals that developed HIV-1 broadly neutralizing antibodies to those that did not develop them (control).


title: Molecular profiling of reticular gigantocellularis neurons

first: Inna

last: Tabansky

state: NY

address: 1230 York Ave, Box 275

department: Neurobiology and Behavior

institute: The Rockefeller University

summary: we used technique that allows the molecular characterization of particular neuronal subpopulations based on their neuroanatomical projections and the locations of their cell bodies.  This ‘retro-TRAP’ (translating ribosome affinity purification from retrogradely labeled neurons) approach relies on viral injection into an anatomical area targeted by the neurons of interest, followed by selective precipitation of ribosomes from retrogradely labeled cell bodies, and subsequent RNAseq analysis.

overall_design: By comparing the mRNAs enriched in the NGC neurons which are retrogradely labeled due to viral injection into central thalamus, to gene expression of non-labeled surrounding cells in NGC, and then performing a comprehensive bioinformatics analysis of these results, we were able to identify genes enriched in these cells. This procedure allowed us to highlight genes and pathways unique to these neurons with projections ascending to thalamus, as compared to other cells in reticular NucleusGigantocellularis.

first: Yupu

last: Liang


title: Rainbow-seq: combining cell division lineage tracking with single-cell RNA sequencing for understanding cell fate decision in preimplantation development

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

summary: Our main question is whether there are reproducible cell-to-cell transcriptome differences in 4-cell embryos that are attributable to their different progenitor cells at the 2-cell stage. If the answer is negative, we wish to test whether there are reproducible cell-to-cell transcriptome differences in 8-cell embryos that are attributable to their different progenitor cells at the 2-cell stage. To address these questions, we developed the Rainbow-seq method that uses fluorescent protein genes to trace cell divisions in preimplantation embryonic development (PED) embryos

overall_design: Mouse strains STOCK Gt(ROSA)26Sortm1(CAG-Brainbow2.1)Cle/J (stock number 013731)  and STOCK Tg(CAG-cre/Esr1*)5Amc/J (stock number 004453) were crossed for the production of embryos containing one copy of the Rainbow  construct 2.1 and one copy of the gene coding for the CRE protein.  Two-cell embryos were collected 46hpi and treated in vitro with 4-Hydroxytamoxifen for two hours, followed by in vitro culture in KSOM media (37°C, 5%CO2, 100% humidity). Embryos were cultured until reaching 4-cell, 8-cell or early blastocyst . stage. The cells of 4- and 8-cell embryos were dissociated for single cell sequencing.

first: Fernando

last: Biase


title: Transcriptional profiling of MDA-MB-231 and its ρ0 cells (lacking mtDNA) after 48h arginine depletion by arginine deiminase (ADI).

city: Duarte

middle: K.

last: Ann

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

summary: In this study, the effect of arginine deprivation on global gene expression in MDA-MB-231 and its ρ0 cells were examined. MDA-MB-231 ρ0 cells lack mitochondrial DNA and therefore have impaired OXPHOS function. Both parental and ρ0 cells were cultured in complete or arginine depleted medium for 48 hours. Comparative transcriptome analysis of both cell lines in complete growth medium versus arginine depleted medium were performed.

overall_design: Examination of gene expression in parental MDA-MB-231 cells and its ρ0 cells after 48 hour arginine depletion.

first: Chun-Ting

last: Cheng

first: Yue

last: Qi

middle: K


title: Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections.

city: Edinburgh

first: Liam

last: Morrison

state: Midlothian

address: Easter Bush

institute: The Roslin Institute, The University of Edinburgh

summary: Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ~2,000 alleles. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving allelic differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12, providing further evidence for hierarchical VSG expression, a conclusion that was confirmed by the novel application of diversity analysis to VSG expression. Our results indicate that long read analysis is a reliable tool for resolving diverse allele expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and identifying mosaic gene formation unprecedentedly early during the infection process.

overall_design: We used PacBio to sequence long read cDNA amplicons from 20 blood samples enriched for VSG transcripts from replicate in vivo T. brucei TREU927 infections in batches (n=5) mice at 3, 6, 10 and 12 days post infection.

first: Siddharth

last: Jayaraman

first: Claire

last: Harris

first: Edith

last: Paxton

first: Anne-Marie

last: Donachie

first: Heli

last: Vaikkinen

first: Richard

last: McCulloch

first: James

last: Hall

first: John

last: Kenny

first: Luca

last: Lenzi

first: Christiane

last: Hertz-Fowler

first: Christina

last: Cobbold

last: Reeve

first: Tom

last: Michoel

last: JMorrison


title: RNA Sequence Analysis of postnatal day 7 (P7) control and Tgfbr2-deleted dental pulp mesenchymal cells

city: Birmingham

first: Sarah

last: Peters

state: AL

address: 1918 University Blvd, MCLM 643

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: We report on P7 dental pulp root and crown genetics and pathways altered by the deletion of Tgfbr2 in the dental pulp and odontoblast cells to investigate the short tooth root phenotype demonstrated in the Tgfbr2 conditional knockout mice.

overall_design: Roots and crowns were harvested and RNA was isolated separately and analyzed for genetic alterations.

first: Rosa

last: Serra


title: Transcriptome analysis by RNA sequencing after treatment with JIB-04 in colorectal cancer

city: Seoul

first: Hyein

last: Cho

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of systems biology

institute: Yonsei university

summary: We investigate RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, apoptosis, and DNA replication and are also related to several cancers including colorectal cancer. JIB-04 also altered the expression of genes involved in various signaling pathways such as the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the Wnt signaling pathway, which is crucial for the proliferation and maintenance of colorectal cancer cells.

overall_design: Examination of RNA sequencing profile in DMSO or 2µM of JIB-04 treated HCT116.

first: Min-Seong

last: Kim

first: Hye-In


title: Programed cell removal of Neutrophils regulated by calreticulin

city: Palo Alto

first: Kristopher

middle: David

last: Marjon

address: 265 Campus

department: ISCBRM

institute: Stanford

summary: RNA seq analysis for pathwayidentification  to identify

overall_design: RNA Seq analysis of apoptotic resistant and WT neutrophils isolated from bone marrow and peritoneum after thiglycollate induced inflammation

first: Mingye

last: Feng


title: Setdb1 is essential for meiotic sex chromosome inactivation in mice

city: London

first: Takayuki

last: Hirota

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Meiotic synapsis and recombination ensure correct homologous segregation and genetic diversity. Asynapsed homologues are transcriptionally inactivated by meiotic silencing, which serves a surveillance function and in males drives meiotic sex chromosome inactivation. Silencing depends on the DNA damage response (DDR) network, but how DDR proteins engage repressive chromatin marks is unknown. We identify the histone H3-lysine-9 methyltransferase SETDB1 as the bridge linking the DDR to silencing in male mice. At the onset of silencing, X-chromosome H3K9 trimethylation (H3K9me3) enrichment is downstream of DDR factors. Without Setdb1, the X chromosome accrues DDR proteins but not H3K9me3. Consequently, sex chromosome remodelling and silencing fails, causing germ cell apoptosis. Our data implicate TRIM28 in linking the DDR to SETDB1, and uncover additional factors with putative meiotic XY-silencing functions. Furthermore, we show that SETDB1 imposes timely expression of meiotic and post-meiotic genes. Setdb1 thus unites the DDR network, asynapsis and meiotic chromosome silencing.

overall_design: Transcriptome and H3K9me3 ChIP-seq profiles in Setdb1 wildtype and cKO pachytene spermatocytes

first: Paul

last: Blakeley

first: Mahesh

middle: N

last: Sangrithi

first: Shantha

last: Mahadevaiah

first: Vesela

last: Encheva

first: Ambrosius

last: Snijders

first: Elias

last: ElInati

first: Obah

middle: A

last: Ojarikre

first: Dirk

middle: G

last: de Rooij

first: Kathy

last: Niakan

middle: M

last: Turner


title: PTEN loss in the fallopian tube induces hyperplasia and ovarian tumor formation

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary: The goals of this study are to compare mouse oviductal transcriptome profiling (RNA-seq) of PTEN-depleted cells by shRNA versus a scr shRNA control expressing PTEN.

overall_design: mRNA profiles of PTEN-deficient and control scramble Mouse oviductal cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Angela

last: Russo


title: Isogenic mouse model of Kras G12D mutation in Acute Lymphoblastic Leukemia

city: New York

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary:
RAS-MAPK activating mutations in NRAS, KRAS and PTPN11 were present in 24/55 (44%) cases in our series of diangosis and relapsed ALL. To evaluate the specific role of RAS-MAPK activating mutations in chemotherapy resistance in ALL we used primary isogenic leukemia cells expressing either Kras wild type or a mutant oncogenic form of Kras (Kras G12D)
Mechanistically, functional dissection of Kras wild type and mutant Kras (Kras G12D) isogenic ALL cells demonstrated induction of methotrexate resistance, but also improved response to vincristine, in mutant Kras-expressing ALL cells.
These results pave the road for the development of tailored personalized therapies for the treatment of relapsed ALL

overall_design: We analyzed mRNA expression profiles of primary isogenic leukemia cells expressing either Kras wild type or Kras G12D, in triplicate.

first: Koichi

last: Oshima

first: Hossein

last: Khiabanian

first: Ana

last: da Silva-Almeida

first: Gannie

last: Tzoneva

first: Francesco

last: Abate

first: Marta

last: Sanchez-Martin

first: Zachary

last: Carpenter

first: Alex

last: Penson

first: Arianne

last: Perez-Garcia

first: Concepción

last: Nicolas

first: Milagros

last: Balbin

first: Maria

middle: L

last: Sulis

first: Motohiro

last: Kato

first: Katsuyoshi

last: Koh

first: Maddalena

last: Paganin

first: Giuseppe

last: Basso

first: Julie

last: Gastier-Foster

first: Meenakshi

last: Devidas

first: Mignon

last: Loh

first: Renate

last: Kirschner-Schwabe

first: Teresa

last: Palomero

first: Raul

last: Rabadan

first: Adolfo

last: Ferrando


title: Exploring the sound-modulated delay in tomato ripening through expression analysis of RNA.

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: We evaluated the molecular mechanism underlying this delaying fruit ripening by performing RNA-sequencing analysis of tomato fruits at 6 h, 2 days (d), 5 d and 7 d after 1 kHz sound vibration treatment. Differentially expressed genes revealed that some of these genes are involved in plant hormone and cell wall modification processes. Ethylene and cytokinin biosynthesis and signalling genes were downregulated by sound vibration treatment, whereas genes involved in flavonoid, phenylpropanoid and glucan biosynthesis were upregulated. Our results indicate that sound vibration helps delay fruit ripening through the sophisticated regulation of RNAs and transcription factor genes.

overall_design: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR. Sequencing was performed on paired end reads (2×150 bp) using the HiSeq-2000 platform (Illumina).

first: Joo-Yeol

first: Jihye

last: Jung

first: Choong-Min

last: Ryu

first: Mi-Jeong

last: Jeong


title: RNAseq anaysis of ventral striatum cholinergic cells of p11 cKO mice

first: Yotam

last: Sagi

address: 1230 York Ave.

institute: Rockefeller University

summary:
Purpose: To identify gene expression changes in cholinergic neurons of the ventral striatum of p11 cKO mice
Method: Translating Ribosome Affinity Purification (TRAP) to isolate RNA from ChAT+ cells and, cDNA synthesisi and next generation RNAseq using Illumina Hiseq sequencer.
Results: Biostatistical analysis identified 113 genes that were altered by p11. 59 genes were up-regulated and 54 down-regulated.

overall_design: 6 ventral striata from 3 ChAT bacTRAP mice   were pooled for one translating ribosome affinity purification sample. We used mice that were ChAT BacTRAP crossed with ChAT Cre and p11 fl/fl and littermates without Cre as controls.

first: Paul

last: Greengard


title: Essential functions of the transcription factors TCF1 and SOX13 in gdT cell development (Sox13tg_Sox13lo)

city: Worcester

first: OK HYUN

last: CHO

state: MA

address: 368 Plantation Street

department: Pathology

institute: University of Massachusetts Medical School

summary: Innate-like gd T effector subsets are exported from the thymus as “memory-like” cells prewired for rapid, specialized function. Previously, we showed that emergent gd subsets distinguished by TCRg and TCRd usage in the fetal and adult thymus possess distinct global transcriptomes and the subset-specific combinatorial expression of High Mobility Group box transcription factors (HMG TFs) shown as a primary determinant of gd effector differentiation. While the detailed mechanism of HMG TFs cooperativity and counter-regulations are not fully understood, a key feature for IL-17 producing gd T effectors (Tgd17) is predicted to be context-dependent interactions between SOX13 and TCF1 that result in diversified target gene regulation. More SOX13 allow more TCF1 dockings on DNA. TCF1 chromatin occupancy in the Tgd17 gene cluster (V2 set) mimics when the amount of SOX13 is enhanced like the Sox13 transgenic system. Globally 75% of SOX13 binding is overlapped with TCF1 binding and V2 set-specifically 85% of SOX13 targets are overlapped with TCF1 targets. The genome-wide analysis between TCF1 and SOX13 indicates cooperative and active SOX13-dependent-TCF1-modulations on V2 sets.

overall_design: Performed ChIPseq using antibodies specific for TCF1 will establish global positioning of TCF1 on chromatin as a basal state of cells undergoing effector programming

first: O

last: Cho

first: H

last: Shin

first: J

last: Kang


title: Essential functions of the transcription factors TCF1 and SOX13 in gdT cell development