title: Phenotypes and niche adaptation of bloom forming Microcystis aerruginosa in a heterogeneous environment revealed by RNA-seq

status: Public on Dec 15 2017

first: Haeyoung

last: Jeong

institute: KRIBB

summary: RNA-seq was applied to compare the changes in transcriptional patterns for these morphotypes of M. aeruginosa KW strain in spatially heterogeneous environment. The main objective was to identify the differentially expressed transcripts and get meaningful information about the molecular mechanism that could be the regulators of this differing morphological and physiological states of these morphs.

overall_design: mRNA profiles of S-morphotype and W-morphotype of Microcystis aeruginosa strain KW using Illumina HiSeq 2500, without replicates.

first: Ankita

last: Srivastava

first: Chi-Yong

last: Ahn


title: RNA-seq of tumor residing CD8+ T cells overexpressing Runx3

city: La Jolla

first: John

middle: Justin

last: Milner

state: CA

address: 9500 Gilman Dr. MC0377

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses1,2. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer.

overall_design: 6 samples: 2 Runx3-overexpressing tumor P14 samples, 2 control tumor P14 samples, 2 control spleen samples

first: J

middle: J

first: A

middle: W

last: Goldrath


title: H3K27me3 localization during B cell differentiation

status: Public on Dec 16 2017

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: B cells are poised to differentiate into antibody secreting plasma cells however the remodeling of repressive epigenetic modifciations are not well understood during this cell fate transition.  Therefore, ChIP-seq was performed for H3K27me3 in naive splenic B cells and LPS induced splenic antibody secreting plasmablasts.  These data define a role for Ezh2 dependent H3K27me3 in the regulation of murine B cell differentiation in vivo.

overall_design: H3K27me3 ChIP-seq insplenic B cells and LPS induced splenic plasmablasts

first: C

middle: D

middle: M

last: Boss


title: DSB-induced transcription of pLac-Tet plasmid in cell-free extracts.

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

summary: Raw reads of RNA products generated upon incubation of circular and linear pLac-Tet plasmid in human cell-free extract.

overall_design: RNA profiles of products generated upon incubation of circular and linear pLac-Tet plasmid in human cell-free extract obtained by deep sequencing using Ion Proton.  pLac-Tet plasmid sequence prepared by cloning a fragment of 556 bp which contains an I-SceI site flanked by 3 Tet and 8 Lac repetitive elements into SfiI site of pMK-RQ vector (GENEART).

first: Fabio

last: Iannelli

first: Sheetal

last: Sharma

first: Flavia

last: Michelini


title: Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions

city: Cambridge

first: Joseph

middle: Robert

last: Piechura

state: Massachusetts

address: 52 Oxford Street

department: FAS Center for Systems Biology

institute: Harvard University

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

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Refer to individual Series


title: Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]

summary: We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions

platform_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cyanobacteria were grown under either a Low Light, Clear Day, High Light pulse, or Shade pulse condition, and gene expression was measured periodically using RNA sequencing

middle: R

first: Kapil

last: Amarnath

first: Erin

middle: K

last: O'Shea


title: Class I histone deacetylases HDAC1, 2 and 3 are histone decrotonylases

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: We characterize histone crotonylation in intestinal epithelium-derived cells through Mass spectrometry, ChIp-Seq and RNA-Seq approaches and show that this modification is removed by class I histone deacetylases, HDAC1, 2 and 3.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq profile from mouse colon epithelium. ChIP-Seq experiments for H3K18crotonylation and H3K4me3 on mouse colon epithelium. ChIP-Seq experiments for H3K18 crotonylation and H3K18 acetylation on HCT116 cell line treated or not with the HDAC inhibitor MS275 (5 µM) for 18h. All the experiments were performed in triplicate.

first: Jeremy

last: Denizot

first: Rachel

last: Fellows

first: Claudia

last: Stellato

first: Payal

last: Jain

first: Alessandro

last: Cuomo

first: Szabina

last: Balázsi

first: Zoltán

last: Hajnády

first: Anke

last: Liebert

first: Elena

last: Stoyanova

first: Juri

last: Kazakevych

first: Hector

last: Blackburn

first: Renan

middle: O

last: Corrêa

first: Hélène

last: Perée

first: Mariangela

last: Spagnuolo

first: Raphael

last: Mattiuz

first: Csaba

last: Matolcsi

first: Joana

last: Guedes

first: Jonathan

last: Clark

first: Marc

last: Veldhoen

first: Marco

middle: A

last: Vinolo

first: Tiziana

last: Bonaldi

first: Patrick

last: Varga-Weisz


title: ATAC-Seq of CD8+ T cell subsets during LCMV infection

first: John

last: Milner

summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer.

overall_design: 6 samples, 2 replicates each, Day 7 LCMV infection CD8+ T cell subsets

first: J

first: A

last: Goldrath


title: Determining mRNA half-lives on a transcriptome-wide scale

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

summary: Translation and mRNA decay are intimately connected processes, and translational inhibition often precedes and stimulates transcript degradation. Here, we have focused on methods that allow determination of mRNA stability on a transcriptome-wide scale. We describe experimental and computational methods for the two most commonly used approaches (transcriptional inhibition and metabolic labeling), and we discuss associated caveats.

overall_design: Metabolic labeling time courses (1, 2, 4, 8, 12, 24 hr) using 4SU were performed in HEK293.

first: Andrew

last: Lugowski

first: Nicholson

last: Beth

middle: S


title: Subcellular genomics shows pervasive within-mitochondrion single nucleotide variant heteroplasmy as revealed by single mitochondrion sequencing

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

summary: We performed single cell RNA-seq on the cell somas of mouse neurons and astrocytes. The transcriptomes were bioinformatically screened for RNA sequences that were generated in the mitochondria of the cell. These data were used to confirm the presence and expression of DNA SNVs.

overall_design: We cultured cells from mouse cortical brain tissue and performed RNA-seq after 3 rounds of aRNA amplification.

first: Jacqueline

last: Morris

first: Young

first: Hua

last: Zhu

first: Jai

middle: H

last: Lee

first: Hoa

last: Giang

first: Alexandra

middle: V

last: Ulyanova

first: Gordon

last: Baltuch

first: Steven

last: Brem

first: H

middle: I

last: Chen

first: David

last: Kung

first: Timothy

last: Lucas

first: Donald

last: O'Rouke

last: Wolf

first: M

last: Grady

middle: Y

last: Sul

first: James

last: Eberwine


title: HNF1B controls epithelial organization and cell polarity during ureteric bud branching and collecting duct morphogenesis

city: PARIS

first: Silvia

last: Cereghini

address: 9 Quai Saint Bernard BatC 7ET

department: Developmental Biology

country: France

institute: IBPS- UMR7622 CNRS -UPMC

summary: Kidney development depends critically on proper ureteric bud branching giving rise to the entire collecting duct system. The transcription factor HNF1B is required for the early steps of ureteric bud branching. Yet, the molecular and cellular events regulated by HNF1B are poorly understood. We report that specific removal of Hnf1b from the ureteric bud leads to defective cell-cell contacts and apico-basal polarity during the early branching events. High resolution ex vivo imaging combined with a membranous fluorescent reporter strategy show decreased mutant cell-rearrangements during mitosis-associated cell dispersal and severe epithelial disorganisation. Molecular analysis reveals downregulation of Gdnf-Ret pathway components and suggests that HNF1B acts both upstream and downstream of Ret-signaling by directly regulating Gfrα1 and Etv5. Subsequently, Hnf1b-deletion leads to massively mispatterned ureteric tree network, defective collecting duct differentiation and disrupted tissue architecture leading to cystogenesis. Consistently, mRNA-seq analysis performed from E15.5 control and mutant kidneys shows that the most impacted genes encode intrinsic cell-membrane components with transporter activity. Our study uncovers a fundamental and recurrring role of HNF1B in epithelial organization during early ureteric bud branching and further patterning and differentiation of the collecting duct system. Article submitted to Development. Authors: Audrey Desgrange, Claire Heliot,Ilya Skovorodkin, Saad U. Akram, Janne Heikkilä, Veli-Pekka Ronkainen, Ilkka Miinalainen I., Seppo J. Vainio and Silvia Cereghini

overall_design: We examine the function of Hnf1b during renal branching morphogenesis by conditional inactivation in the UB and its derivatives using the Hoxb7cre reporter mouse line. We crossed mice homozygous for a Hnf1b floxed allele (Hnf1bfl/fl ) (Heliot el al., Development 2013 (4):873-885.) with males HoxB7-Cre;Hnf1bLacZ/+ heterozygous for the Hoxb7-cre and for the Hnf1b null allele (Hnf1blacZ/+), (Barbacci et al., Development 1999 21, 4795-805.) to generate HoxB7-Cre;Hnf1bLacZ/fl embryos designed as mutants.  Hnf1bLacZ/fl and Hnf1b+/fl embryos without the HoxB7-Cre transgene were considered as controls, due to the lack of a phenotype in heterozygous embryos for the Hnf1b LacZ-null allele (Barbacci et al., Development 1999 21, 4795-805.).The two kidneys from E15.5 mutant and control embryos were microdissected from the same litter. This requirement limited the number of samples used to 2 controls and 2 mutants, independently of the sex since we found a similar phenotype in males and females. RNA was extracted by Tryzol using the miRNA mini kit Qiagen for extraction of total and miRNAs. The quality of the RNA samples was assessed on the Agilent Bioanalyzer system using the Agilent RNA 6000 Nano Kit  (Agilent Technologies) and RNA with a RIN higher than 8 was used. 1-2 μg of total RNA were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (ThermoFisher Scientific). mRNA was digested with RNase III, purified, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA‐Seq Kit v2 (ThermoFisher Scientific).

first: Audrey

last: Desgrange

first: Pantelis

last: Hatzis

first: Martin

last: Reczko

first: Vaggelis

last: Harokopos


title: RNA-seq analysis of genes under control of Burkholderia thailandensis E264 MftR

city: Baton Rouge

first: Anne

last: Grove

state: LA

address: 131 LSB

department: Biological Sciences

institute: Louisiana State University

summary: Comparison of transcriptomes of wild-type cells and cells deleted for MftR as well as both strain grown in absence and presence of 5 mM urate

overall_design: Four different samples, each analyzed in triplicate

first: Ashish

last: Gupta

first: Renesh

last: Bedre


title: Genome-wide H3K27 trimethylation patterns when AMPKa1 and AMPKa2 (AMPKa DKO) were deleted in mouse embryonic fibroblast cells

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: H3K27me3 signals on the chromatin were determined using ChIP-seq assay to assess if deletin of AMPKa1 and AMPKa2, which inactivates the AMPK kinase, affected global H3K27me3 abundance and distribution on the chromatin.

overall_design: AMPKa WT and DKO MEFs were used for the ChIP-seq assays in order to directly compare the H3K27me3 signals between these two cell lines.

first: Lixin

last: Wan

first: Zhao

last: Zhang

first: Wenyi

last: Wei


title: Expression profiling of AMPK-regulated genes in mouse embryonic fibroblast cells

summary: We used RNA-Seq assay to characterize AMPK-regulated gene expression patterns and then compared with EZH2-dependent transcriptional profile in MEF. We wanted to determine whether and how AMPK and EZH2 co-regulate a subset of genes.

overall_design: AMPKa WT and DKO MEFs were used for RNA-Seq assays in order to compare the transcriptional profiles that are regulated by either AMPK or EZH2.


title: KDM4 inhibition targets breast cancer stem cells [ChIP-Seq]

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

summary: We treated breast cancer stemm cells (BCSC) with a KDM4 inhibitor or performed knockdown of KDM4A

overall_design: BCSC1 cells were cultured in the presence and absence of KDM4(i) or infected with a shRNA KDM4A adenovirus

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: DamID for Lola-O

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: longitudinals lacking (lola) is among the most complex genes in Drosophila melanogaster, encoding up to 20 different protein isoforms and acting as a key transcription factor in axonal pathfinding and neural reprograming. To better characterize Lola function we have generated specific mutations in each isoform using the CRISPR/Cas9 system. Our targeted screen allows us to revisit the previously demonstrated roles for few isoforms, to assign known functions to specific isoforms and to reveal a critical role for a specific variant in the octopaminergic pathway. Thus, our comprehensive study expands the repertoire of Lola functions, and demonstrates that the CRISPR/Cas9 approach is a valuable tool to systematically address the role of complex loci in vivo.

overall_design: Embryos were collected for two hours at 25°C and subsequently developed for 20 hours, collected and frozen. Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors.Libraries were generated using the NebNext Ultra II DNA Library Kit. Libraries were sequenced on a NextSeq 500.

first: Nadja

last: Dinges

first: Nastasja

last: Kreim

first: Violeta

last: Morin

first: Tony

last: Southall


title: KDM4 inhibition targets breast cancer stem cells [RNA-Seq]

summary: We treated breast cancer stemm cells (BCSC) with a KDM4 inhibitor

overall_design: BCSC1 cells were cultured in the presence and absence of KDM4(i)


title: A small RNA pathway mediates allelic dosage in endosperm

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata

platform_organism:
Arabidopsis thaliana
Arabidopsis lyrata


title: A small RNA pathway mediates allelic dosage in endosperm [mRNA-seq]

summary: Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.

overall_design: Examination of parent-of-origin specific and total gene expression in wild type, nrpd1, and WT female x nrpd1 male endosperm 6-7 days after pollination - 11 samples.

first: Robert

last: Erdmann

first: P

last: Satyaki


title: Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function


title: Dynamic Profiles of transcriptome in porcine liver

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

country: China

institute: Huazhong Agricultural University

summary: To evaluate the roles of gene regulation in porcine liver, dynamic profiles of transcriptome were investigated  in swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same day-old(90d).

overall_design: Using high-throughput sequencing technology to reveal the characteristic of  transcriptome during porcine liver development.

first: Changchun

last: Li


title: KDM4 inhibition targets breast cancer stem cells


title: A small RNA pathway mediates allelic dosage in endosperm [sRNA-seq]

overall_design: Sequencing of 34 small RNA samples from A. thaliana dissected seed tissues (embryo, endosperm, and seed coat) 6 days after pollination and 15 small RNA samples from A. lyrata dissected seed tissues 15 days after pollination.

first: Maja

last: Klosinska


title: FOXO1 is an oncogenic mediator in AML1-ETO leukemia

city: Cincinnati

first: Shan

last: Lin

state: OH

address: 3333 Burnet Avenue, CCHMC

department: EHCB

institute: Cincinnati Children's Hospital Medical Center

summary: Transcriptome analysis by RNAseq of human CD34+ hematopoietic stem and progenitor cells transduced with empty vector control(MIT), AML1-ETO (AE), wildtype FOXO1 (F WT) or FOXO1 DNA binding deficient mutant (F DB). We find wildtype FOXO1 partially recapitulates gene signature of AML1-ETO

overall_design: Human CD34+ hematopoietic stem and progenitor cells from three donors were transduced with retrovirus expressing MIT, AE, F WT or F DB. Transduced cells were sorted at day 5 after transduction, RNA was collected for RNAseq.

first: James

middle: C

last: Mulloy


title: CD40 in thymic DC maturation and Treg cell development

status: Public on Dec 14 2017

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary:
The aim is to determine which genes are distinctively expressed in each of the subsets of DCs
Four subsets of dendritic cells in mouse thymus were sorted based on their expression of Sirpa and their maturation status: Sirpa+ immature DCs, Sirpa+ mature DCs, Sirpa- immature DCs, and Sirpa- mature DCs

overall_design: the four subset were compaired to each other, there were 2 samples per group

first: Jaekak

last: Oh

last: Wu

first: Rebecca

last: Barbeau

first: David

last: Erle

first: Jeooung-Sook

last: Shin


title: High intracellular c-di-GMP levels antagonize quorum sensing and virulence gene expression in Burkholderia cenocepacia H111

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

summary: In this study, we have analysed the transcriptional profile of B. cenocepacia H111 upon artificially altering the global cellular c-di-GMP levels. A total of 111 genes was found to be differentially expressed, of which 96 genes were down-regulated when c-di-GMP concentrations were increased. The BDSF, AHL and c-di-GMP regulons overlap for the regulation of 24 genes. Intriguingly, at a high intracellular c-di-GMP level expression of the AHL synthase cepI was found to be more than 10-fold down-regulated. Among the exclusively c-di-GMP regulated genes were genes of the phenylacetate catabolic pathway and of the type III secretion system.

overall_design: Altered c-di-GMP levels in B. cenocepacia

first: Nadine

last: Schmid

first: Angela

last: Suppiger

first: Elisabeth

last: Steiner

first: Volkhard

last: Kaever

first: Mustafa

last: Fazli

first: Tim

last: Tolker-Nielsen

first: Urs

last: Jenal

first: Leo

last: Eberl


title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

first: William

last: Mallard

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

summary: The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, bulk cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches. We further identify candidate RNAs localized to mitochondria-ER junctions and nuclear lamina, two compartments that are recalcitrant to classical biochemical purification. Since APEX-RIP is simple, versatile, and does not require special instrumentation, we envision its broad application in a variety of biological contexts.

overall_design: 27 samples total, from five experimental courses (negative controls, and mitochondrial, nuclear, cytosolic, and endoplasmic reticulum-targeted APEX-RIP). Negative controls: 4 samples (2 replicates, with paired inputs and mock RIPs);  Mitochondrial APEX-RIP: 6 samples (3 replicates, with paired inputs and RIPs);  Nuclear APEX-RIP: 6 samples (3 replicates, with paired inputs and RIPs); Cytosolic APEX-RIP: 6 samples (6 replicates, with paired inputs and RIPs);  ER-targeted APEX-RIP ("KDEL"): 4 samples (2 replicates, with paired inputs and RIPs).

first: Pornchai

last: Kaewsapsak

last: Shechner

first: John

middle: L

last: Rinn

first: Alice

last: Ting


title: Genome wide study of adult microglia in Specific-pathogen-free (SPF) mice treated or not during one week with antibiotics (ABX) in males and females.

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: RNAseq was performed on microglia from male and female, controls and ABX to elucidate the genetic differences implicates by microbiota and gender.

overall_design: Microglia from SPF and GF mice from embryonic and adult stages of both gender were sorted for sequencing. DEGs were obtained to observe if any significant genes were affected. Pathway analysis was performed with the set of DEGs. SPF mice were given ampicillin (1mg/ml), streptomycin (5mg/ml), colistin (1mg/ml) and amphotericin (0.1mg/ml) in sterile drinking water ad libitum for one week, between 7 and 8 weeks of age. Sterile drinking water devoid of antibiotics was provided to control mice ad libitum.

first: Morgane

last: Thion

first: Fanny

last: Coulpier

first: Sonia

last: Garel


title: The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

city: Stockholm

first: kun

last: wang

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholms Universitet

summary: This is ChIPseq result of FadR (Saci_1107), which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

overall_design: genome-scale binding site identification with output and mock samples as control

first: Kun

last: Wang


title: Global patterns of the methylome in porcine liver

first: Yuhua

last: Fu

type: Methylation profiling by high throughput sequencing

summary: To explore the methylome differences of swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same daya-old (90d).

overall_design: Using high-throughput sequencing technology to reveal the global patterns of the methylome in porcine liver.

first: Changchun

last: Li


title: Early NKT cell wave of IL-4 serves as an innate link to support initiation of B cell immunity during infection

first: Andrew

last: Navia

address: 77 Massachusetts Ave

department: IMES

institute: MIT

summary: IL-4/GFP- enhanced transcript (4Get) reporter mice were infected with 200 PFU of Influenza A virus PR8 strain. At day 3 of infection, mediastinal lymph nodes were harvested and GFP+ cells sorted and separated by their ability to bind a CD1d-tetramer (Tet+ n=133 , Tet- n=109 ). Single-cell RNA-Seq was used to identify subpopulations of IL-4 producing cells. Single-cell transcriptomes were clustered using Seurat and differentially expressed genes within each cluster were used to resolve IL-4+ subpopulations and aid in defining their role in initiating B cell immunity during influenza infection.

overall_design: Examine cells involved in accute viral response in the lymph node after influenza infection

first: Mauro

last: Gaya

first: Sanjay

last: Prakadan

first: Sam

last: Kazer

first: Alex

last: Shalek

first: Facundo

last: Batista


title: Transcriptional profile of TL1A transgenic mice

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary:
To assess the effect of different forms of TL1A within different organs of the mouse we generated 2 different transgenic mouse lines where TL1A was expressed under the control of the CD2 promoter. 2 forms of TL1A was used. Either WT TL1A, which led to over expression of both membrane bound and soluble forms of TL1A (Refered to as Mem+Sol) or TL1A Delta 69-93 which only overexpressed membrane restricted TL1A (Refered to as Mem).
Lungs and terminal ileums were taken from Either Mem, Mem+sol or WT litermate control mice at 12 weeks of age and the transcriptome assessed using RNAseq
Through this we demonstrated enrichment of different transcripts and pathways both dependent on and independent of the form of TL1A and the site of action. This study is also the first to use RNASeq to assess the resualt of overexpression of TL1A within the mouse.

overall_design: Poly-A purified mRNA profiles from the Ileum and Lung of Mem, Mem+Sol and WT mice generated using Illumina based RNASeq


title: Gcn5 regulates FGF signaling outputs through c-Myc during early differentiation of embryoid bodies [RNA-Seq]

city: Smithville

first: Li

state: TX

address: 1808 Park Rd 1C

department: Epigenetics and molecular carcinogenesis

institute: UT-MD Anderson Cancer Center

summary: Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers.  How particular chromatin modifying enzymes affect specific developmental processes is not well defined. Here we report that Gcn5, a HAT essential for embryonic development, is largely required for c-MYC target gene transcription downstream of FGF signaling in early embryoid bodies (EBs). Gcn5 null EBs display deficient activation of ERK and p38, disorganized cytoskeletal networks, and compromised capacity to differentiate toward mesodermal and endodermal lineages. These findings establish a regulatory role for Gcn5 in execution of a critical signaling pathway during early development.

overall_design: To determine changes in gene expression profile upon Gcn5 loss at early differentiation stages, RNA from day 3 and day 5 EBs differentiated from Gcn5 fx/fx (4_1) and Gcn5-/-(4_C2) ES cells were isolated for deep sequencing, in duplicates. Key genes identified from RNAseq were validated by qRT-PCR using a second biological pair of Gcn5fxf/x and Gcn5-/- cells.

first: Sharon

last: Dent

first: Yue

last: Lu


title: Microenvironmental-derived Regulation of HIF-Signaling Drives Transcriptional Heterogeneity in Glioblastoma Multiforme

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

institute: Medical Center Freiburg

summary: The evolving and highly heterogeneous nature of malignant brain tumors underlies their limited response to therapy and poor prognosis. In addition to genetic alterations, highly dynamic processes such as transcriptional and metabolic reprograming play an important role in the development of tumor heterogeneity. The present study reports an adaptive mechanism in which the metabolic environment of malignant glioma drives transcriptional reprogramming. Multi-regional analysis of a glioblastoma patient biopsy revealed a metabolic landscape marked by varying stages of hypoxia and creatine enrichment. Creatine treatment and metabolism was further shown to promote a synergistic effect through up-regulation of the glycine-cleavage system and chemical regulation of Prolyl-Hydroxylase Domain (PHD). Consequently, creatine maintained a reduction of reactive oxygen species and change of the a-ketoglutarate/succinate ratio leading to an inhibition of the HIF-signaling in primary tumor cell lines. These effects shifted the transcriptional pattern toward a proneural subtype and reduced the rate of cell migration and invasion in vitro.

overall_design: For metabolic treatment, different metabolites were supplemented into the medium. Creatine-enriched environment was simulated by 15 mMol creatine supplementation. Cells were cultured under normoxic (21% O2) or hypoxic (3% O2) conditions.


title: Epigenetic Therapy Increases Therapeutic Efficacy in Myeloproliferative Neoplasms  Through Inhibition of Aberrant Inflammatory Signaling

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

summary:
The mechanisms that mediate transformation in MPN are not fully delineated and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify Nfb signaling as a key pathway activated in malignant and non-malignant cells in MPN.

Genetic and functional studies underscore the central role of JAK/STAT signaling in myeloproliferative neoplasms (MPNs). However, the mechanisms that mediate transformation in MPNs are not fully delineated, and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify nuclear factor kB (NF-kB) signaling as a key pathway activated in malignant and non-malignant cells in MPN. Inhibition of BET bromodomain proteins attenuated NF-kB signaling and reduced cytokine production in vivo. Most importantly, combined JAK/BET inhibition resulted in a marked reduction in the serum levels of inflammatory cytokines, reduced disease burden, and reversed bone marrow fibrosis in vivo.

overall_design:
Mutant (GFP-positive) megakaryocytic-erythroid progenitors (MEP) were separated by fluorescent-activated cell sorting (FACS) using green fluorescent protein (GFP) to identify MPLW515L-expressing cells and specific cell surface marker; Epigenetic profiling using H3K27Ac and H3K4Me1 are performed. FASTQ reads are aligned to mouse reference genome (build mm9)

RNA-seq of human SET-2 cell line treated with vehicle, ruxolitinib, JQ1, or combination therapy (n=12)

RNA-seq of JAK2fl/WT Cre-negative and Cre-positive MEPs (n=6)

RNA-seq of MEP MPLW515L GFP+ cells treated with vehicle, ruxolitinib, JQ1, or combination therapy (n=9)

RNA-seq of control MIGR1 and MPLW515L-positive MEPs (n=6)

first: Maria

last: Kleppe

first: Lihua

last: Zou

first: Sofie

last: De Groote

first: Lauren

last: Dong

first: Efthymia

last: Papalexi

first: Corinne

last: Hill

first: Matthew

last: Keller

first: Jaime

last: Reyes

first: Justin

last: Roberts

first: Franck

last: Rapaport

first: Julie

last: Teruya-Feldstein

first: Jun

last: Qi

first: Raajit

last: Rampal

first: Richard

last: Koche

first: James

middle: E

last: Bradner


title: The anti-leukemic effect of R-2HG depends on its acting as an m6A mRNA modifier-M6A Seq

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: m6A-seq in NOMO-1, MA9.3RAS and MA9.3ITD cells with or without R-2HG treatment.

overall_design: In sensitive leukemia cells we identified, R-2HG dramatically increases global N6-methyladenosine (m6A) modification via directly targeting and inhibiting FTO. We performed m6A-seq in NOMO-1 (one of the most sensitive cells) with or without R-2HG treatment for 48 hours to confirm whether R-2HG can dramatically up-regulates m6A modification and to determine which transcripts are with enriched m6A abundance after R-2HG treatment. We also performed m6A-seq in R-2HG- and PBS-treated sensitive cells (MA9.3ITD) with or without FTO knockdown, as well as R-2HG- and PBS-treated resistant cells (MA9.3RAS) with or without FTO expression to further analyze the effects of R-2HG and FTO on m6A modification.

first: Rui

last: Su

first: Lei


title: Extreme heterogeneity of influenza virus infection in single cells

city: San Diego

first: Alistair

middle: Brian

last: Russell

address: 9500 Gilman Dr,

institute: University of California, San Diego

summary: Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in production of viral gene transcripts -- viral transcripts compose less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. Some infected cells fail to express at least one viral gene, and this gene absence partially explains variation in viral transcriptional load. Despite variation in total viral load, the relative abundances of viral mRNAs are fairly consistent across infected cells. Activation of innate immune pathways is rare, but some cellular genes co-vary in abundance with the amount of viral mRNA. Overall, our results highlight the complexity of viral infection at the level of single cells.

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

overall_design: Dataset consists of a total of five single-cell datasets generated using the 10x Genomics Chromium Single Cell 3' Solution platform. All samples were generated from a tissue culture infection model using A549 cells from ATCC and Influenza A/WSN/1933 virus. Uninfected control sample identically processed. Infected samples were generated from cells infected for 6, 8, and 10 hours with a single replicate at 8 hours.

middle: B

first: Cole

last: Trapnell

first: Jesse

last: Bloom


title: 5hmC and gene expression data in breast cancer cell lines treated with an antioxidant

status: Public on Dec 13 2017

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary: In this study, we identify genes with enriched 5-hydroxymethyl-cytosine (5hmC) modifications correlated with gene expression in breast cancer cell lines treated with an antioxidant. Results of our differential analysis showed that treatment with an antioxidant caused significant changes to gene-localized 5hmC enrichment patterns in MDA-MB-468 breast cancer cells. The 5hmC enrichment results were validated in a set of patient specimens when compared with adjacent non cancer tissue.

overall_design: PVU-Seq and RNA sequencing of the triple negative breast cancer cell line MDA-MB-468 in triplicate. PVU-Seq of 2 breast tumor patients (2 tumor samples and the 2 matched normal) by enzymatic digestion of PvuRts1l coupled with high-throughput sequencing (PVU-Seq).

first: Cristina

last: Mitrea


title: Transcriptional profiles reflect the mutational mechanism by which Wnt signaling is activated in mouse tumors and predict outcome in colorectal cancer patients

city: Columbus

first: Joanna

last: Groden

address: 986 BRT 460 West 12th Ave.

department: Department of Cancer Biology and Genetics

institute: The Ohio State University, College of Medicine

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

overall_design: Refer to individual Series


title: Investigation on the anaerobic propionate degradation by Escherichia coli K12

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

institute: Max Rubner-Institute

summary: Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the gamma-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. The typical downregulation of the citric acid cycle under anoxic conditions is only partially responsible for the inability to use propionate under anoxic conditions since an arcA mutant  shows very limited growth on propionate. RT-PCR and transcriptomic analysis revealed a post-transcriptional regulation of the prp-genecluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA was hydrolyzed in the 3`-5` direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R catalyzes the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli.

overall_design: RNA-seq of E. coli K12 wild type and delta-rnr mutant under aerobic and anaerobic growth with and without propionate. Duplicate samples for each condition.

first: Francesca

middle: M

last: Simonte

last: Dötsch

first: Johannes

last: Gescher


title: The anti-leukemic effect of R-2HG depends on its acting as an m6A mRNA modifier-RNA Seq-Resistant, sensitive and healthy control

summary: To identify the potential genes/signaling pathways related to R-2HG sensitivity in leukemia cells.

overall_design:
Via MTT assays, we determined the various sensitivities to R-2HG treatment in leukemia cells. We selected five resistant leukemia cells (NB4, TF-1, HEL, MA9.3RAS and K562), for sensitive leukemia cells (ML-2, NOMO-1, U937 and MA9.3ITD) and four healthy control samples (two CD34+ hematopoietic stem/progenitor cells (CD34+ HSPC) and two mononuclear cells (MNC)) for RNA-sequencing.

NOTE: The original processed data files were replaced with updated processed data files (containing 'cell line name' column headers, instead of 'sample id') on May 2019 to avoid confusion.

last: Dong


title: Whole genome DNA methylation profile of sperm cells in mammalian species

city: Los Angeles

first: Andrew

middle: D

last: Smith

state: California

address: 1050 Childs way

institute: University of Southern California

summary: DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. Our results point to an evolutionary expansion of the unmethylated portion of mammalian genomes. Within the mutually orthologous genome this trend is driven both by the birth of unmethylated regions and by widening of intervals that are unmethylated in ancestors. We find strikingly divergent global features in rodents. At the same time, we observe the evolutionary emergence of methylome features in mouse sperm bears association with similar pathways to those found in human. Together,these results revealed general principles in mammalian epigenome evolution.

sample_organism:
Gorilla gorilla
Canis lupus familiaris
Rattus norvegicus

overall_design: Genomic DNA form gorilla, rat and dog (1 gorilla individual; 2 rat individuals; 4 dog individuals; individuals sequenced separately) mature sperm was isolated, bisulfite converted and sequenced

first: Jianghan

last: Qu

first: Emily

last: Hodges

first: Antoine

last: Molaro

first: Brent

last: Young

first: Beckie

last: Williams

first: Matthew

last: Dean

first: Gregory

middle: J

last: Hannon


title: RNAseq of CD45+ cells excluding mast cells from the skin of K14HPV16 Mcpt5-Cre- and K14HPV16 Mcpt5-Cre+ mice

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: The experiment aimed at determing the influence of mast cell deficiency on the transcriptome of skin-infiltrating leukocytes in K14HPV16 mice at 2month and 6month of age.

overall_design: Skin-inflitrating leucocytes were FACS-purified from mast cell proficient (Mcpt5-Cre-) and mast cell deficient (Mcpt5-Cre+) K14HPV16 mice. Mast cells (CD117 high, FCeR1 high) were excluded from the sorting gate. In order to control for minimal mast cell contamination during sorting from K14HPV16 Mcpt5-Cre- skin, mast cell signature transcripts were identified by comparing transcriptomes of samples fromK14HPV16 Mcpt5-Cre- mice in which mast cells were flow cytometrically included vs excluded.

first: Shanawaz

last: Ghouse

first: Rayk

last: Behrendt


title: A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

city: Seattle

first: Pamela

middle: S.

last: Becker

state: WA

address: 1959 NE Pacific St

department: Medicine

institute: University of Washington


title: A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia [RNA-Seq]

summary:
We demonstrate a promising approach to identify robust molecular markers for targeted treatment of acute myeloid leukemia. We show that our method outperforms several state-of-the-art approaches in identifying molecular markers replicated in validation data and predicting drug sensitivity accurately.
Finally, we identify SMARCA4 as a marker and driver of sensitivity to topoisomerase II inhibitors, mitoxantrone and etoposide, in AML by showing that cell lines transduced to have high SMARCA4 expression reveal dramatically increased sensitivity to these agents.

overall_design:
We measured the gene expression of samples from 30 different AML patients with acute myeloid leukemia in order to identify reliable gene expression markers for drug sensitivity. We used this dataset for validation.
This Series represents 12 patient samples.

first: C

last: Blau


title: High capacity of the endoplasmic reticulum to prevent secretion and aggregation of amyloidgenic proteins

city: Freiburg

first: Ritwick

last: Sawarkar

address: 51 Stubeweg

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Protein aggregation is associated with neurodegeneration and various other pathologies. How specific cellular environments modulate the aggregation of disease proteins is not well understood. Here we investigated how the endoplasmic reticulum (ER) quality control system handles β-sheet proteins that were designed de novo to form amyloid-like fibrils. While these proteins undergo toxic aggregation in the cytosol, we find that targeting them to the ER (ER-β) strongly reduces their toxicity. ER-β is retained within the ER in a soluble polymeric state, despite reaching very high concentrations exceeding those of ER-resident molecular chaperones. ER-β is not removed by ER-associated degradation (ERAD) but interferes with ERAD of other proteins. These findings demonstrate a remarkable capacity of the ER to prevent the formation of insoluble β-aggregates and the secretion of potentially toxic protein species. Our results also suggest a generic mechanism by which proteins with exposed β-sheet  structure in the ER interfere with proteostasis.

overall_design: We have performed RNA-sequencing (RNA-seq) in HEK293 cells transfected with ER-β or empty vector (EV) control plasmids in triplicate.

first: Lisa

last: Vincenz-Donnelly

first: Roman

last: Körner

first: Jenny

last: Presto

first: Jan

last: Johansson

first: Erik

last: Hansen

first: F

middle: U

last: Hartl

first: Mark

last: Hipp


title: Effector and regulatory T cells roll at high shear stress by inducible tether and sling formation

first: Klaus

last: Ley

address: 9420 Athena Circle

department: Inflammation Biology

institute: La Jolla Institute for Allergy and Immunology

summary: The adaptive immune response involves T cell differentiation and migration to  sites of inflammation. T cell trafficking is initiated by tethering and rolling on  inflamed endothelium. Tethers and slings, discovered in neutrophils, facilitate  cell rolling at high shear stress. Here we demonstrate that PSGL-1 binding to  P- or E-selectins and the ability to form tethers and slings during rolling are  highly inducible in T-helper-1 (Th1), Th17 and regulatory (Treg), but less in  Th2 cells. In vivo, endogenous Tregs rolled stably in cremaster venules at  physiological shear stress. Quantitative dynamic footprinting nanoscopy of  Th1, Th17 and Tregs uncovered the formation of multiple tethers. Importantly,  human Th1 cells also showed tethers and slings. RNA-Seq revealed that  sling-forming cells induced genetic pathways related to cell motility. We  conclude that differentiated CD4 T cells stabilize rolling by inducible tether  and sling formation. These phenotypic changes approximate the adhesion  phenotype of neutrophils and support CD4 T cell access to sites of  inflammation in non-lymphoid tissues.

overall_design: Examination of mRNA expression profiles contributing to Tethers and Slings formation in CD4 T cell subsets by RNA-seq deep sequencing analysis by Hiseq 4000

first: Michael

last: Abadier

first: Akula

last: Pramod

first: Sara

last: McArdle

first: Alex

last: Marki

first: Zhichao

last: Fan

first: Edgar

last: Gutierrez

last: Groisman


title: Although abundant in tumor tissue, mast cells have no effect on immunological micro-milieu or growth of HPV-induced or transplanted tumors.

first: Axel

last: Roers


title: Genomic distribution of dBigH1 in whole testes and early embryos

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona


title: mRNA profiles of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E

city: Houston

first: Yugang

last: Wang

address: 6767 Bertner Avenue

institute: MD Anderson Cancer Center

summary:
Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E Transcriptomes. And quantitatively analyze the cell signaling pathways that regulated by the studied mutants.
Methods: total mRNA was extracted from U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E.llumina compatible libraries were prepared by using the KAPA Stranded mRNA-Seq Library Preparation Kit for Illumina® platforms (KAPA Biosystems). In brief, 250 ng of total RNA was enriched for poly-A-tailed mRNA by using Kapa’s mRNA Capture beads. Poly-A-enriched RNA was fragmented to a median size of 150 bp by using chemical fragmentation and converted into double-stranded cDNA with dUTP incorporated into the second cDNA strand. The ends of the double-stranded cDNA were polished, 5’-phosphorylated, and 3’-A-tailed for the ligation of indexed adapters. Adapter-ligated DNA fragments were amplified by 8 cycles of PCR. The strand with incorporated dUTP was not amplified. The resulting libraries were quantified by qPCR and assessed for size distribution by using the 4200 TapeStation (Agilent Technologies), and then multiplexed, 4 per pool, and sequenced on the Illumina’s NextSeq500 by using the mid-output, 75-bp paired-end read format.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the human genome and quantified the expression of protein coding genes in the U251 cells of WT Gcn5 and Gcn5 Y645A mutant/WT DLST and DLST R224A/K226E mutant.  Altered expression of 3 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed analysis of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E Transcriptomes. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that Gcn5 Y45A mutant and DLST R224A/K226E mutant, which reduce histone H3 K79 succinylation, can regulate several cell signaling pathways that important for cancer cell proliferation.

first: Zheng

last: Yin

first: Ke

last: Liu


title: Transcriptome analysis of single cells from the developing mouse dentate gyrus

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: RNA sequencing was performed on 24185 single cells from dentate gyrus of CD-1, C57Bl/6, or hGFAP-GFP reporter mice, sampled at ages ranging from embryonal day 16.5 to postnatal day 132, with the aim of comparing peri- and postnatal neurogenesis in the dentate gyrus

overall_design: 24185 single cells isolated from the dentate gyrus of mice

first: Hannah

last: Hochgerner

first: Amit

last: Zeisel


title: Genomic distribution of dBigH1 in whole testes [ChIP-Seq]

summary: This analysis largely reflected the genomic distribution of dBigH1 in spermatocytes since the vast majority of dBigH1-expressing cells in testes correspond to spermatocytes. In these studies, we observed that dBigH1 was not uniformely distributed across the genome.

overall_design: ChIP-Seq peak calling of dBigH1 against input sample in whole testes

first: Albert

last: Carbonell

first: Salvador

last: Pérez-Montero

first: Paula

last: Climent-Cantó

last: Reina

first: Fernando

last: Azorín


title: APC_ChIP-seq

first: Joanna

last: Groden

summary: Anti-APC ChIP-seq data were collected from HCT-116 cells and 44,771 genomic sequences were found to be enriched.

overall_design: Examination by ChIP-seq of chromatin binding profiles for APC in a colon cancer cell line expressing wild-type APC and a degradation-resistant β-catenin that constitutively activates canonical WNT signaling

first: William

last: Hankey

first: Baris

last: Hancioglu


title: mRNA data from extracellular vesicles secreted by Trichuris muris

city: Smithfield

first: Javier

last: Sotillo

address: 14-88 McGregor rd

department: AITHM

country: Australia

institute: James Cook University

summary: RNA-Seq analysis of the mRNA present in the extracellular vesicles secreted by the nematode Trichuris muris

overall_design: Analyis of the mRNA extracted from the extracellular vesicles secreted by the nematode Trichuris muris

first: Ramon

last: Eichenberger

first: Matt

last: Field

first: Alex

last: Loukas


title: RNAseq of MB49 inoculated tumor-assotiated macrophages from MC-proficient and MC-deficient animals

first: Axel

last: Roers

summary: RNA seq was used to compare the expression profile of macrophages in presence and absense of mast cells. MB49 cells were injected i.d. into Mcpt5-Cre+ R26DTA animals and cre-negative littermates. Macrophages were sorted at 20 d.p.i.

overall_design: Macrophage RNA profiles of MB49 TAMs (tumor-associated macrophages), harvested at 20 d.p.i. in MC-Proficient and MC-deficient animals

first: Anastasia

last: Polikaprova

first: Rayk

last: Behrendt


title: Genomic distribution of dBigH1 in early embryos [ChIP-Seq]

first: Oscar

last: Reina Garcia

summary: This analysis largely reflected the genomic distribution of dBigH1 in 0-2hpf early embryos. In these studies, we observed that dBigH1 was uniformely distributed across the genome.

overall_design: ChIP-Seq peak calling of dBigH1 against input sample in early embryos


title: RNAseq of B16 inoculated tumor-assotiated macrophages from MC-proficient and MC-deficient animals

summary: RNA seq was used to compare the expression profile of macrophages in presence and absense of mast cells. B16 cells were injected i.d. into Mcpt5-Cre+ R26DTA animals and cre-negative littermates. Macrophages were sorted at 16 d.p.i.

overall_design: Macrophage RNA profiles of B16F10 TAMs (tumor-associated macrophages), harvested at 20 d.p.i. in MC-Proficient and MC-deficient animals


title: The anti-leukemic effect of R-2HG depends on its acting as an m6A mRNA modifier-RNA Seq-PBS / R-2HG treatment

first: Jianjun

last: Chen

summary: RNA-seq from R-2HG sensitive leukemia cells treated with R-2HG or PBS.

overall_design: With MTT assays, we identified R-2HG exhibits an anti-leukemia function. We conducted RNA-Seq in the two sensitive cells (NOMO-1 and MA9.3ITD) with R-2HG or without R-2HG treatment for 48 hours to investigate which genes/α-ketoglutarate-dependent dioxygenases/signaling pathways are responsible for the anti-leukemia function of R-2HG. For each group, there are three duplicates.

first: Rui

last: Su

first: Lei

last: Dong


title: RNA-seq analysis of YFV-17D specific and total naive CD8 T cells in humans

city: Atlanta

first: Rama

last: Akondy

address: 1462 CLifton Rd

department: Emory Vaccine Center

institute: Emory University

summary: These 14 samples originate from peripheral blood mononuclear cells (PBMC) from donors at different times after they were vaccinated with the YF-17D vaccine.

overall_design: 10,000 to 100,000 tetramer+ CD8 T cells specific for the NS4B-214 epitope in YFV-17D were purified by flow cytometry based sorting, from 8 vaccinees. Total Naive (CD45RA+ CD8+) CD8 t cells were also sorted from these donors.  Subsets were defined based on the time after vaccination. The subsets (cell types) include: Naive CD8 T cells (n=6); YFV-specific Effector CD8 T cells (day 14 after vaccination, n =3) and YFV-specific long term memory CD8 T cells (4 to 12 years after vaccination, n=5).

first: Rafi

last: Ahmed


title: mRNA-seq data from murine colon adenomas and non-adenoma tissues

summary: We report that colon adenomas from ApcMin/+ mice not only exhibit similarities in gene expression profile to colon adenomas from azoxymethane / dextran sulfate sodium-treated mice (with activating Ctnnb1 mutations) due to the activation of canonical WNT signaling, but also unique transcriptional changes in the pathways regulating cell cycle progression / proliferation, chromosome segregation / cytoskeletal organization and apoptosis.  Subsequent experiments characterized changes in gene expression unique to colon adenomas from ApcMin/+ mice including increases in the H2afv, Map6 and Nsmf transcripts.

overall_design: Examination of gene expression profiles in 2 different colon adenoma types with activated canonical WNT signaling, relative to their respective non-adenoma controls


title: Genome-wide maps of histone H3 K79 succinylation in U251 cells.

first: Yugang

last: Wang

summary: We report the nuclear Gcn5/α-KGDH complex plays vital role in histone H3 K79 succinylation. By obtaining over 731 million reads from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of histone H3 K79 succinylation, Gcn5, and α-KGDH in U251 cells.

overall_design: Examination of histone H3 K79 succinylation, Gcn5 occupancy on chromatin, and α-KGDH occupany on chromatin in U251 cells.

first: Ke

last: Liu

first: Zheng

last: Yin


title: Dietary interventions modulate global non-coding RNA expression: a role for microRNA-chromatin-mRNA crosstalk [Chd1KD_mRNA]

city: Shanghai

first: Jing-Dong

middle: Jackie

last: Han

address: 320 Yue Yang Road

institute: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Using high-throughput deep sequencing we profiled coding and non-coding RNA expression in Hepa1-6 cells after knockdown of Chd1.

overall_design: Mouse Hepa1-6 cells were treated with lentiviruses containing either scrambled or Chd1 shRNA and used for RNA-sequencing.


title: Genome wide study of microglia in Specific-pathogen-free (SPF) and Germ-free (GF) mice at different stages in males and females (RNA-Seq)

status: Public on Dec 12 2017

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: RNAseq was performed on microglia from male and female, SPF or GF mice to elucidate the genetic differences implicated by microbiota and gender. DEGs between the various groups gave some ideas on what different pathways or functions might be affected due to the different factors.

overall_design: Microglia from SPF and GF mice from embryonic and adult stages of both gender were sorted for sequencing. DEGs were obtained to observe if any signicant genes were affected. Pathway analysis was performed with the set of DEGs.

first: Donovan

last: Low

first: Guillaume

last: Hoeffel

first: Florent

last: Ginhoux


title: Gene expression profile homology between  in vitro induced neuron and in vivo induced neuron using GeneChip microarray analysis

first: Sashwati

last: Roy

department: Surgery

institute: Ohio State University

summary: in vitro induced neuron and in vivo induced neuron using GeneChip microaraay analysis

overall_design: Induced neuron generated in vitro or laser-capture microdissected from mice skin were subjected to murine transcriptome array (MTA 1.0)


title: Massively parallel reporter assay of 3’UTR sequences identifies in vivo rules for mRNA degradation

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

summary: The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here, we introduce UTR-Seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens-of-thousands of 3’UTR sequences during early zebrafish embryogenesis. UTR-Seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation. Three signals regulated early-onset rates: stabilizing poly-U and UUAG sequences, and destabilizing GC-rich signals. Three signals explained late-onset degradation: miR-430 seeds, AU-rich sequences and Pumilio recognition sites. Sequence based regression models translated 3’UTRs into their unique decay patterns, and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial 3’UTRs that conferred specific mRNA dynamics. UTR-Seq provides a general strategy to uncover the rules of RNA cis-regulation.

overall_design: temporal expression profiles of reporter mRNAs from zebrafish embryos (7 replicates total) or oocytes (2 replicates total). A total of five embryo replicates were collected using pre-adenylated (A+) reporters in three separate experiments. In the first experiment, a sample was collected every hour between 1h to 8h, and at 10h. In the second experiment, a single sample was collected every hour between 1h to 10h, and split into two after RNA extraction to produce two technical replicates (techrep). In the third experiment, two separate samples were collected every two hours between 2h to 10h to produce two same-day biological replicates (biorep). A total of two replicates were collected using non-adenylated (A-) reporters in two separate experiments. In the first experiment, a sample was collected every hour between 1h to 8h, and at 10h. In the second experiment (rep), samples were collected at 1h, 2h, 3h, 4h (3 samples), 6h, 8h and 10h.

first: Alexander

middle: F

last: Schier


title: Transcriptomic profiling of human pluripotent stem cell derived ROR1+ cells

city: Darlinghurst

first: Andrian

last: Yang

state: NSW

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

summary: RNA-seq profiling of gene expression of ROR1+ cells differentiated from human pluripotent stem cells.

first: Michael

last: O'Connor

first: Joshua

middle: W

last: Ho


title: Arid1a promotes tumor initiation but restrains progression and metastasis in liver cancer [ATAC-seq]

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university

summary: ARID1A is hypothesized to be one of the most common tumor suppressors in human cancer.  However, the functional consequences of ARID1A gain and loss are not clear. We report that  mice with complete liver-specific Arid1a deficiency were resistant to MYC induced  liver carcinogenesis, indicating a requirement during tumor initiation. Mechanistically, Arid1a loss  constrained tumor formation by reducing Cytochrome P450 expression, which in turn mitigated  oxidative stress. We also examined the heterozygous state and found it potentiated metastasis formation and heterozygous has similar gene accessibility pattern with homozygous compared to WT.

overall_design: Liver tumor tissues were collected from LAP-MYC; Arid1a WT,Arid1a Het and Arid1a Homo knockout mice, then nuclears are extracted and genomic DNA were tagged for ATAC-seq.

first: Sam

first: Luo

last: Xin

first: Hao

last: Zhu


title: RNA-seq analysis of the role of HBO1 (KAT7/MYST2) in the ovarian cancer cell line UWB1.289.

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary: Analysis of change in transcriptosome after stable lentiviral HBO1 knockdown in UWB1.289 ovarian cancer cell line.

overall_design: Total RNA was obtained from UWB1.289 cells transduced with shCtrl and shHBO1. shHBO1 samples were compared to shCtrl samples.

first: Marcos

last: Quintela


title: RNA-sequencing analysis of Douglas-fir transcriptome responses to diesel emissions generated with CeO2 nanoparticle additive

city: Corvallis

first: Jay

middle: R

last: Reichman

state: OR

address: 200 SW 35th St.

department: Office of Research and Development

institute: US Environmental Protection Agency

summary: Transcriptome changes of Douglas-fir seedlings were analyzed to investigate molecular impacts of exposure to airborne emissions released from combustion of diesel fuel containing engineered cerium dioxide (CeO2) nanoparticle catalysts (DECe). We analyzed mRNA-sequencing data from exposed one-year-old needles.  Our hypothesis is that 2-week chamber exposure to DECe would induce certain distinct transcriptome changes in the needles compared with responses to conventional diesel exhaust (DE) or filtered DECe Gas Phase. Blast2GO gene ontologies (GOs) enriched by significantly up-regulated DECe transcripts were nested within the GOs for DE, however, 93.5% of enriched GOs for significantly down-regulated DECe transcripts were unique.  DECe attenuated expression of genes that affect functions of transferases, kinases, transmembrane transporters, transcription factors, diester hydrolases and RNA polymerase III; processes of protein phosphorylation, responses to stimuli, hormones and chemicals, carbohydrate transport, RNA polymerase III transcription, and cellular anion homeostasis; plus, components of the plasma membrane.  MapMan analysis also identified RNA regulation of transcription, protein degradation, and lipid metabolism pathways that were enriched with DECe down-regulated transcripts. Divergent DECe treatment effects were associated with significantly elevated needle uptake of cerium. DE affected expression of more genes than DECe. Nevertheless, unique transcriptome profile changes suggest that chronic DECe exposure may adversely affect plant growth and development.

overall_design: mRNA profiles for needles grown in the previous year from Douglas-fir seedlings; Charcoal / Purafil HEPA filtered air (Air Control) N=6; Emissions released from combustion of diesel fuel containing engineered CeO2 nanoparticle catalysts (DECe) N=7; Emissions released from combustion of diesel fuel (DE) N=7; HEPA filtered DECe (DECe Gas Phase) N=6; Illumina sequencing. Chamber conditions measured included particulate matter concentration, particle size distribution, concentrations of gas components (O2, CO, NO, NO2 and NOX), as well as temperature and relative humidity.  Cerium deposition in an on needles was quantified by ICP-MS.

middle: T

last: Rygiewicz

first: Mark

middle: G

last: Johnson

middle: A

last: Bollman

first: Bonnie

last: Smith

first: Q

last: Krantz

first: Charly

last: King

first: Christian

middle: P

last: Andersen


title: ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [RNA-Seq]

city: Rochester

first: Patrick

last: Murphy

address: 601 Elmwood Ave

institute: University of Rochester

summary: The function and retention/reprogramming of epigenetic marks during the germline-to-embryo transition is a key issue in developmental and cellular biology, with relevance to stem cell programming and trans-generational inheritance.  In zebrafish, DNAme patterns are programmed in transcriptionally-quiescent early cleavage embryos; paternally-inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a ‘placeholder’ nucleosome, containing the histone H2A variant H2A.Z(FV) and H3K4me1, occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors.  Upon genome-wide transcriptional onset, genes with the Placeholder become either active H3K4me3-marked or silent H3K4me3/K27me3-marked (bivalent).  Importantly, functional perturbation causing Placeholder loss confers DNAme acquisition, whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation.  Thus, during transcriptionally quiescent stages (gamete-zygote-cleavage), an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNAme, poising parental genes for either gene-specific activation or facultative repression.

overall_design: Transcript abundance was analyzed for zebrafish sperm, and cleavage stage embryos that were either wild type or mutant for the anp32e gene.

first: ShanFu

last: Wu

first: Cody

last: James

first: Candice

middle: L

last: Wike

first: Bradley

last: Cairns


title: Arid1a promotes tumor initiation but restrains progression and metastasis in liver cancer [RNA-seq]

first: Xuxu

last: Sun

summary: ARID1A is hypothesized to be one of the most common tumor suppressors in human cancer.  However, the functional consequences of ARID1A gain and loss are not clear. We report that  mice with complete liver-specific Arid1a deficiency were resistant to MYC induced  liver carcinogenesis, indicating a requirement during tumor initiation. Mechanistically, Arid1a loss  constrained tumor formation by reducing Cytochrome P450 expression, which in turn mitigated  oxidative stress. We also examined the heterozygous state and found it potentiated metastasis formation and heterozygous has similar gene expression pattern with homozygous compared to WT.

overall_design: Liver tumor tissues were collected from LAP-MYC; Arid1a WT,Arid1a Het and Arid1a Homo knockout mice, then transcriptional profiling were generated by RNA-seq analysis.Liver tissues were collected from Rag1-/-; LAP-MYC; Arid1a WT with ad-cre or ad-ARID1A overexpression mice, then transcriptional profiling were generated by RNA-seq analysis.

middle: C

last: Wang

last: Xin


title: Dietary interventions modulate global non-coding RNA expression: a role for microRNA-chromatin-mRNA crosstalk [Diet_miRNA]

first: Jing-Dong

last: Han

summary: Using high-throughput deep sequencing, microRNA expression was profiled across six dietary intervention groups, including low fat (LF) or high fat (HF) with or without calorie restriction (LF+CR, HF+CR) or exercise (LF+Ex, HF+Ex).

overall_design: Mice were treated starting at 5 weeks of age with LF or HF diet with or without CR or Ex. Liver RNA was extracted and used for small RNA-sequencing at midlife (62 weeks of age).


title: ETV2 cooperates with SCL for timely gene activation during hemogenic endothelium specification

first: Dan

last: Duan

state: CA

address: 615 Charles E. Young Dr, Los Angeles, 90095

institute: UCLA

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

overall_design: Refer to individual Series


title: Dietary interventions modulate global non-coding RNA expression: a role for microRNA-chromatin-mRNA crosstalk


title: IL-11 is a crucial determinant of cardiovascular fibrosis (mouse single cell)

status: Public on Dec 11 2017

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

summary: Fibrosis is a common pathology in cardiovascular disease. In the heart, fibrosis causes mechanical and electrical dysfunction and in the kidney, it predicts the onset of renal failure. Transforming growth factor β1 (TGFβ1) is the principal pro-fibrotic factor, but its inhibition is associated with side effects due to its pleiotropic roles. We hypothesized that downstream effectors of TGFβ1 in fibroblasts could be attractive therapeutic targets and lack upstream toxicity. Here we show, using integrated imaging–genomics analyses of primary human fibroblasts, that upregulation of interleukin-11 (IL-11) is the dominant transcriptional response to TGFβ1 exposure and required for its pro-fibrotic effect. IL-11 and its receptor (IL11RA) are expressed specifically in fibroblasts, in which they drive non-canonical, ERK-dependent autocrine signaling that is required for fibrogenic protein synthesis. In mice, fibroblast-specific Il11 transgene expression or Il-11 injection causes heart and kidney fibrosis and organ failure, whereas genetic deletion of Il11ra1 protects against disease. Therefore, inhibition of IL-11 prevents fibroblast activation across organs and species in response to a range of important pro-fibrotic stimuli. These results reveal a central role of IL-11 in fibrosis and we propose that inhibition of IL-11 is a potential therapeutic strategy to treat fibrotic diseases.

overall_design: Murnine cardiac cells isolated from a transgenic PlnR9C/+ animal with confirmed dilated cardiomyopathy or a wild type littermate were captured and processed for single-cell RNA-seq using the Chromium Single Cell 3' system (10x Genomics).

first: Hiroko

last: Wakimoto

first: Jonathan

last: Seidman

first: Christine

middle: E


title: ETV2 cooperates with SCL for timely gene activation during hemogenic endothelium specification [ATAC-Seq]

summary: By performing ATAC sequencing in WT, Etv2KoiSCL and Etv2KOiETV2 ES cell derived day 4.75 endothelial cells, we report here ETV2 increases chromatin accessiblity at its binding sites.

overall_design: Examination of ATAC seq signal in day 4.75 EB (embryoid body) Tie2+CD31+CD41- endothelial cells derived from WT, Etv2KOiSCL and Etv2KOiETV2 ES cells

first: Tonis

last: Org

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud

first: Hanna

middle: K

last: Mikkola


title: Sexual Regeneration RNAseq

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Sexual Schmidtea mediterranea Trunk Regeneration. Sexual biotype Schmidtea mediterranea trunk fragments were sequenced at 0 day, 3 day, 5 day and 7 day post amputation along with whole worm juvenile animals in order identify sexual specific transcripts. Juvenile worms lack sex organs, testes and ovaries present in D0 trunk fragments. Days 3-7 represent time points of degeneration and regeneration of the sexual organs, testes and ovaries.

overall_design: Day 0 trunk fragments, Day3, Day 5 and Day 7 regenerations and intact juvenile animals

first: Y

last: Xiang

first: D

last: Miller

first: E

last: Ross

first: R

middle: S

last: Hawley

first: S

last: Zhang

first: A

last: Alvarado


title: Dietary interventions modulate global non-coding RNA expression: a role for microRNA-chromatin-mRNA crosstalk [Diet_mRNA]

first: Jing-Dong

summary: Using high-throughput deep sequencing, both coding and long non-coding RNA expression was profiled across six dietary intervention groups, including low fat (LF) or high fat (HF) with or without calorie restriction (LF+CR, HF+CR) or exercise (LF+Ex, HF+Ex).

overall_design: Mice were treated starting at 5 weeks of age with LF or HF diet with or without CR or Ex. Liver RNA was extracted and used for polyA+ RNA-sequencing at midlife (62 weeks of age).


title: Time-resolved transcriptome analysis with genetic perturbations reveals a critical time window for effective plant immunity

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

summary: Pathogen invasion in plants is associated with transcriptional reprogramming. Enigmatically, plants induce similar transcriptome responses upon infection by virulent or avirulent pathogens. This renders the importance of transcriptional reprogramming for immunity obscure. Here, using RNA-seq, we generate time-series transcriptome data coupled with genetic perturbations to reveal temporal dynamics upon infection by virulent or avirulent strains of a bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana. Fast and sustained transcriptional reprogramming occurs upon infection with avirulent strains while virulent strain infection leads to a slower response with comparable gene expression patterns and magnitudes. Importantly, transcriptome analysis of resistant and susceptible mutants responding to avirulent strains links delayed transcriptional reprogramming to compromised immunity. Taken together, our results pinpoint the early critical time window of transcriptional reprogramming for establishing effective immunity against the bacterial pathogen.

overall_design: Leaves of Col-0 and all the single, double, triple and quadruple mutants of dde2-2, ein2-1, pad4-1, sid2-2 were syringe-infiltrated with mock (water) or suspensions of Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) carrying an empty vector (pLAFR), Pto DC3000 carrying AvrRpt2, or Pto DC3000 carrying AvrRpm1 at the OD600 of 0.001. Similarly, leaves of the rpm1-3 rps2-101C mutant plants were inoculated with mock, Pto DC3000 carrying AvrRpt2 or Pto DC3000 carrying AvrRpm1. Three fully-expanded leaves (leaves 7-9) from three different plants were harvested as a single biological replicate at 1, 2, 3, 4, 6, 9, 12, 16, 20, 24, 36, 48 hours post inoculation (hpi). To generate three biological replicates, three independent experimental trials were carried out, in which plant positions within pots and growth chambers were randomized in order to avoid undesirable systematic effects. For the statistcal analysis, 348 samples (M001-M348) were used.

first: Carilin

last: Seyfferth

first: Barbara

last: Kracher

first: Kenichi

last: Tsuda


title: Time course RNA-seq analysis of barley MLA1 immune receptor-mediated response to barley powdery mildew fungus Bgh in defense phytohormone signaling-depleted Arabidopsis thaliana mutant.

city: Cologne

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary: RNA-seq experiments in Arabidopsis detected MLA1-dependent gene regulation which does not require defence phytohormones signalling.

overall_design: Three biological replicates were obtained per condition.  Arabidopsis plants expressing an MLA1-HA construct in pen2 pad4 sag101 dde2 ein2 sid2 (ppsdes) background were challenged with either Bgh isolate K1 expressing the cognate AVRA1 effector for MLA1 or Bgh isolate A6 expressing other AVRA effectors. Samples were collected at 12, 18, 24 hours post inoculation (hpi) of Bgh.

first: Takaki

last: Maekawa

first: Florence

last: Jacob

first: Paul

last: Schulze-Lefert


title: Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

institute: École Polytechnique Fédérale de Lausanne

summary: Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here we dissected temporal and tissue-specific regulation at multiple layers of gene regulation by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: (1) tissue-specific rhythmically active transcription factors that notably regulated feeding-fasting related rhythms in liver and sodium homeostasis in kidney; (2) co-localized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-Seq) in liver and kidney identified liver-specific chromatin loops that recruited clock transcription factors to promoters in a tissue-specific manner. Furthermore, this looping was remarkably promoter-specific, nearby alternative promoters with differential temporal outputs formed distinct chromatin loops. These findings suggest that precise chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.

overall_design: RNA-Seq from total RNA of mouse kidney during the dirunal cycle. Time-series mRNA profiles of wild type (WT) and Bmal -/- mice under ad libitum and night restriced feeding regimen were generated by deep sequencing. Chromosome conformation capture (4C-Seq) in liver and kidney was also performed.

first: Jake

last: Yeung

first: Jerome

last: Mermet

first: Celine

last: Jouffe

first: Julien

last: Marquis

first: Aline

last: Charpagne

first: Frederic

last: Gachon


title: Study of expression changes during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system which mirrors NLR activation II

summary: Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance and defence gene reprogramming through the stress response regulator, EDS1. Using RNA-seq, we analyzed the early RPS4-mediated transcriptional changes over time in a temperature-conditioned and pathogen-independent system.

overall_design: We used transgenic Arabidopsis plants over-expressing RPS4, a genetic background in which an immune response can be turned on rapidly and synchronously in leaf cells after a switch from high to moderate temperature. In order to substract defense-unrelated artifacts due to the temperature stimulus, we used Col-0 WT plants in parallel as negative control. Three replicates were obtained per condition.

first: Servane

last: Blanvillain-Baufumé

first: Bruno

last: Huettel

first: Jane

last: Parker


title: Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia using Next-Generation Sequencing and Bioinformatics

city: Kaohsiung

first: Po-Lin

last: Kuo

address: 100, Shih-Chuan 1st Road

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

summary: Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia, and long-term hypoxia were analyzed using next-generation sequencing. The results showed that long-term hypoxia promoted the ability of colony formation and transwell migration compared to normoxia. In addition, the differentially expressed genes induced by long-term hypoxia were involved in various biological processes including cell proliferation, the tumor necrosis factor signaling pathway, basal cell carcinoma, and cancer pathways. The upregulated (L1CAM and FBN1) and downregulated (AUTS2, MAPT, AGT, and USH1C) genes in 786-O under long-term hypoxia were also observed in clinical ccRCC samples along with malignant grade. The expressions of these genes were significantly correlated with survival outcomes in patients with renal cancer. We also found that long-term hypoxia in 786-O resulted in decreased expressions of hsa-miR-100 and has-miR-378, and this effect was also observed in samples of metastatic ccRCC compared to samples of non-metastatic ccRCC. These findings may provide a new direction for the study of potential molecular mechanisms associated with the progression of ccRCC.

first: Szu-Chia

last: Chen

first: Feng-Wei

first: Ya-Ling

last: Hsu


title: ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming

first: Patrick

last: Murphy


title: Recruitment of the EMSY/KDM5A/SIN3B complex to target genes is regulated by ZNF131

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: Recent work from others and us revealed interactions between the Sin3/HDAC complex, the H3K4me3 demethylase KDM5A, GATAD1 and EMSY. Here, we characterize the EMSY/KDM5A/SIN3B complex in detail by quantitative interaction proteomics and ChIP-sequencing. We identify a novel substoichiometric interactor of the complex, ZNF131, which recruits EMSY to a large number of active, H3K4me3 marked promoters. Interestingly, using an EMSY knock-out line and subsequent rescue experiments, we show that EMSY is in most cases positively correlated with transcriptional activity of its target genes and stimulates cell proliferation. Finally, by immunohistochemical staining of primary breast tissue microarrays we find that EMSY/KDM5A/SIN3B complex subunits are frequently overexpressed in primary breast cancer cases in a correlative manner. Taken together, these data open venues for exploring the possibility that sporadic breast cancer patients with EMSY amplification might benefit from epigenetic combination therapy targeting both the KDM5A demethylase and histone deacetylases.

overall_design: ChIP-Seq for EMSY in HeLa GFP cell line with and without ZNF131 knockdown

first: Radhika

last: Varier

first: Filomena

last: Matarese

first: Hendrik

last: Stunnenberg

first: Michiel

last: Vermeulen


title: ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [RRBS]

overall_design: DNA methylation was analyzed for Sperm and Sphere stage embryos that were either mutant for the anp32e gene, or were injected with either an SRCAP morpholino or recombinant Anp32e protein.

first: ShanFu

last: Wu

first: Cody

last: James

first: Candice

last: Wike

first: Bradley

last: Cairns


title: ETV2 cooperates with SCL for timely gene activation during hemogenic endothelium specification [ChIP-Seq]

city: Los Angeles

first: Dan

last: Duan

summary: By comparing SCL binding in day 4 Etv2KOiSCL and  Etv2KOiETV2 mesodermal cells to WT, we showed delayed gene activation or repression could not be simly explained by loss of SCL binding in Etv2KOiSCL mesodermal cells

overall_design: Examination of genome wide chromatin occupancy of Scl in ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

first: Tonis

last: Org

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud

first: Hanna

last: Mikkola


title: MethlyC-Seq of met18 mutant

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in  met18 mutant

overall_design: MethylC-Seq: 1 mutant examined, met18

first: Cheng-Guo

first: Kai

last: Tang


title: Identification and expression of salinity-regulated genes in marbled eel (Anguilla marmorata) based on transcriptome analysis

status: Public on Dec 10 2017

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

summary: we used next-generation sequencing technology to characterise mRNA-seq of brackish water (BW, 10‰), fresh water (FW, 0‰), and sea water (SW, 25‰)-treated Anguilla marmorata's gill, kidney and intestine to elucidate the molecular mechanisms of salinity adaptation.

overall_design: Examination of 3 different salinity-treated in Anguilla marmorata.

first: Quanquan

last: Cao


title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

institute: John Innes Centre

summary: We report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.

overall_design: Whole genome bisulfite sequencing and RNA-seq of wild type and RdDM mutant arabidopsis male sex cells and somatic tissues

first: James

last: Walker

first: Hongbo

last: Gao

first: Jingyi

last: Zhang

first: Billy

last: Aldridge

first: Martin

last: Vickers

last: Higgins


title: Study of expression changes during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system which mirrors NLR activation

first: Barbara

last: Kracher

first: Florence

last: Jacob

first: Takaki

last: Maekawa

first: Paul

last: Schulze-Lefert


title: Whole genome DNA methylation analysis of human CD8 T cell specific for the Yellow fever virus vaccine

city: Atlanta

first: Rama

last: Akondy

state: GA

address: 1462 CLifton Rd

institute: Emory University

summary: Central questions regarding the origin of memory CD8 T cells, their turnover and longevity in vivo are not well-defined in humans. Here, we have used the highly efficacious live yellow fever virus vaccine (YFV-17D) to address these issues in the context of a primary acute viral infection. We interrogated genome-wide CpG methylation of YFV tetramer-specific CD8 T cells. These findings provide a better understanding of how memory CD8 T cells are formed and maintained in humans.

overall_design: A2-NS4B214 tetramer+ CD8 T cells were isolated by FACS from one donor vaccinated with YFV-17D 14 days previously (effector) and a different donor vaccinated 166 days previously (memory). To obtain the required cell numbers from the memory donor, a leukapheresis procedure was performed. Total naive CD8 T cells from the memory donor were used as a control. Methylation profiling was performed using the Me-DIP sequencing services from Active motif. Briefly, genomic DNA was fragmented, denatured and a 5-methyl cytosine specific antibody was used for immunoprecipitation based enrichment of methylated DNA regions, the enriched DNA samples were amplified and Next-gen sequencing performed.

first: Haydn

last: Kissick

first: Rafi

last: Ahmed


title: ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [ChIP-Seq]

first: Patrick

last: Murphy

summary: The function and retention/reprogramming of epigenetic marks during the germline-to-embryo transition is a key issue in developmental and cellular biology, with relevance to stem cell programming and trans-generational inheritance.  In zebrafish, DNAme patterns are programmed in transcriptionally-quiescent early cleavage embryos; paternally-inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a ‘placeholder’ nucleosome, containing the histone H2A variant H2A.Z(FV) and H3K4me1, occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors.  Upon genome-wide transcriptional onset, genes with the Placeholder become either active H3K4me3-marked or silent H3K4me3/K27me3-marked (bivalent).  Importantly, functional perturbation causing Placeholder loss confers DNAme acquisition, whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation.  Thus, during transcriptionally quiescent stages (gamete-zygote-cleavage), an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNAme, poising parental genes for either gene-specific activation or facultative repression.

overall_design: Enrichment for chromatin features was determined using ChIP-Seq for various zebrafish stages (Sperm, preZGA, postZGA) in wild type and mutant anp32e embryos

first: ShanFu

last: Wu

first: Cody

last: James

first: Candice

last: Wike

first: Bradley

last: Cairns


title: circRNA-sequencing

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

institute: changzheng hospital

summary: circRNA sequencing for 10 samples.

overall_design: Examing 2 conditions, each with 5 replicates