title: The extent of ribosome queuing in budding yeast

city: Tel Aviv-Yafo

first: Tamir

last: Tuller

address: 30 Levanon st.

department: Biomedical Engineering Dept.

country: Israel

institute: Tel Aviv University

summary: Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution, synthetic biology, gene expression regulation, intracellular biophysics, and more. However, this phenomenon hasn't been quantified yet at a genomic level. Nevertheless, methodologies for studying translation (e.g. ribosome footprints) are usually calibrated to capture only single ribosome protected footprints (mRPFs) and thus limited in their ability to detect ribosome queuing. On the other hand, most of the models in the field assume and analyze a certain level of queuing.     Here we present an experimental-computational approach for studying ribosome queuing based on sequencing of RNA footprints extracted from pairs of ribosomes (dRPFs) using a modified ribosome profiling protocol. We combine our approach with traditional ribosome profiling to generate a detailed profile of ribosome traffic. The data are analyzed using computational models of translation dynamics.    The approach was implemented on the Saccharomyces cerevisiae transcriptome. Our data shows that ribosome queuing is more frequent than previously thought: the measured ratio of ribosomes within dRPFs to mRPFs is 0.2-0.35, suggesting that at least one to five translating ribosomes is in a traffic jam; these queued ribosomes cannot be captured by traditional methods.     We found that specific regions are enriched with queued ribosomes, such as the 5’-end of ORFs, and regions upstream to mRPF peaks, among others. While queuing is related to higher density of ribosomes on the transcript (characteristic of highly translated genes), we report cases where traffic jams are relatively more severe in lowly expressed genes and possibly even selected for. In addition, our analysis demonstrates that higher adaptation of the coding region to the intracellular tRNA levels is associated with lower queuing levels. Our analysis also suggests that the Saccharomyces cerevisiae transcriptome undergoes selection for eliminating traffic jams. Thus, our proposed approach is an essential tool for high resolution analysis of ribosome traffic during mRNA translation and understanding its evolution.

overall_design: We present an experimental-computational approach for studying ribosome queuing based on sequencing of RNA footprints extracted from pairs of ribosomes (dRPFs) using a modified ribosome profiling protocol. We combine our approach with traditional ribosome profiling to generate a detailed profile of ribosome traffic. The data are analyzed using computational models of translation dynamics.

first: Alon

last: Diament

first: Anna

last: Feldman

first: Elisheva

last: Schochet

first: Yoav

last: Arava

first: Martin

last: Kupiec


title: single-cell-RNA-sequencing analysis of naive and Listeria monocytogenes-specific CD8+ T cells

status: Public on Jan 17 2018

city: Paris

first: Luigia

last: Pace

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type: Expression profiling by high throughput sequencing

summary:
The histone methyltransferase Suv39h1 silences transcriptional programs during CD8+-T cell differentiation
The study explores the role of gene silencing by Suv39h1, a histone methyltransferase, that plays a critical role in heterochromatin dynamics.

overall_design: Naïve littermate and Suv39h1-KO CD8+ T cells, and day 7 p.i. Kb-OVA+ CD8+ T cells (from Listeria m.-OVA infected mice), were isolated by FACS. scRNA-seq was performed according to 10X Genomics technology. Both biological (Rep) and technical (tech) replicates were processed.

first: Paul

last: Gueguen

first: Mylène

last: Bohec

first: Sylvain

last: Baulande

first: Christel

last: Goudot

first: Sebastian

last: Amigorena


title: Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System

city: Philadelphia

first: Guo-li

last: Ming

state: PA

address: Clinical Research Building  Suite 105, 415 Curie Boulevard

department: Neuroscience

country: USA

institute: University of Pennsylvania

summary: N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury. Loss of either m6A methyltransferase complex component Mettl14 or m6A-binding protein Ythdf1 globally attenuates injury induced protein translation in adult DRGs and reduces functional axon regeneration in the peripheral nervous system in vivo. Furthermore, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult central nervous system is attenuated upon Mettl14 knockdown. Our study reveals a critical epitranscriptomic mechanism in promoting injury-induced protein synthesis and axon regeneration in the adult mammalian nervous system.

overall_design: The distribution and levels of m6A in DRG transcripts was analyzed by m6Aseq. RNA sequencing was used to identify transcript abundance differences between Mettl14 mutant and wt DRGs at naïve and sciatic nerve injury day1 (SNLD1) conditions.

first: Yi-Lan

last: Weng

first: Hongjun

last: Song


title: H3K9me3 native ChIP-seq analysis of in vitro cultured wild-type CD8+ T cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: H3K9me3 mark dynamic changes during CD8+-T cell differentiation in vitro

overall_design: Naïve (day 0) and in vitro cultured mouse CD8+ T cells on day 3 were analyzed for H3K9me3  mark enrichment by native ChIP sequencing.

first: Elina

last: Zueva

first: Alban

last: Lermine

first: Vivien

last: Deshaies


title: H3K9me3 ChIP-seq analysis of in vitro cultured littermate and Suv39h1-KO CD8+ T cells

overall_design: H3K9me3 mark deposition by the histone methyltransferase Suv39h1 during CD8+-T cell differentiation in vitro in wildtype and Suv39h1-KO cells.


title: Ultraconserved Enhancers Are Required for Normal Development [RNA-seq]

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Analysis of the transcriptional changes in the forebrain resulting from the loss of ultraconserved enhancers near Arx gene.

overall_design: Forebrain was dissected from wild-type and enhancer-null embryonic mice (e11.5) and processed for deep RNA-seq analysis.

first: Yoko

last: Yuzawa

first: Diane

last: Dickel


title: RNA-Seq of Kaposi’s sarcoma reveal alterations in glucose and lipid metabolism

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma (KS). In sub-Saharan Africa, the high prevalence of both HIV-1 and KSHV has made KS a leading cancer in the region, associated with poor prognosis and high mortality due to late medical presentation and advanced disease stages. A better understanding of the cellular and viral transcriptome profiles during neoplastic growth will aid in the definition of biomarkers and cellular functions associated with KS tumorigenesis and progression. Our approach is to examine the transcriptome profile in actual KS lesions versus non-cancer tissues from the same individual for a total of four male African epidemic KS patients. These patients have undetectable HIV-1 plasma viral load after successful anti-retroviral therapy. Our results capture the cellular complexity of in vivo lesion environment and provide a marked contrast to those derived from in vitro monoculture models.  The findings demonstrate that latency and immune modulation related functions dominate the viral gene expression pattern. Moreover, KSHV significantly affected the cellular transcriptome profile with genes involved in lipid and glucose metabolism disorder pathways being the most substantially dysregulated. Despite the implied infiltration of immune cells into the lesions as predicted by CIBERSORT, KS tumor continued to progress, suggesting immunological dysfunction in these KS patients despite control of HIV-1 viremia. Lastly, there is limited overlap of our in vivo dataset with in vitro studies, suggesting a limitation of in vitro KS models.

overall_design: RNA-seq of Kaposi’s sarcoma lesions and control tissues

first: Charles

last: Wood

first: For-Yue

last: Tso


title: microRNA-sequencing of inbred mouse strain hippocampus and frontal cortex

status: Public on Jan 18 2018

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: We carried out small RNA sequencing to determine miRNA expression patterns of hippocampus and frontal cortex in six inbred mouse strains. We analyzed miRNA expression levels, isomiR distribution and miRNA editing events.
Methods: We constructed small RNA libraries starting from the total RNA extracted from the hippocampus and frontal cortex of three animals per strain. The sequencing was carried out using Illumina HiSeq2000 (single-end). The sequence reads that passed quality filters were mapped to the mouse genome (mm10) and to known miRNAs (miRBase v21) using miRDeep2, SeqBuster, and sRNAbench, to obtain miRNA and isomiR expression levels and to predict novel miRNAs. Genome alignments were analysed for miRNA editing using FreeBayes.
Results: We detected significant miRNA and isomiR expression level differences between the strains and brain regions. Most of the miRNA loci produced a number of isomiRs. Some miRNAs were consistently edited with a pattern that matches the activity of known RNA editing enzymes.

overall_design: Small RNA sequencing of hippocampus and frontal cortex of 6 inbred mouse strains using Illumina HiSeq2000

first: Juho

last: Väänänen

first: Kalevi

last: Trontti


title: single-cell-RNA-sequencing and H3K9me3 occupancy of CD8+ T cells

first: Luigia

last: Pace

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

overall_design: Refer to individual Series


title: Regional heterogeneity in response of airway epithelial cells to cigarette smoke

status: Public on Jan 16 2018

city: Tokyo

first: Tadashi

last: Sato

address: 3-1-3 Hongo, Bunkyo-ku

department: Department of Respiratory Medicine

country: Japan

institute: Juntendo University Graduate School of Medicine

summary: To investigate the biochemical and genetic alterations that occur in response to cigarette smoke exposure among airway epithelial cells from different sites in the lungs, we performed microarray-based analysis using small airway epithelial cells (SAEC) and normal human bronchial epithelial cells (NHBE) following 24 h of cigarette smoke extract (CSE). In microarray-based analysis, the small airway showed higher susceptibility to CS compared to the large airway, such as enhanced expression of inflammatory-related pathways including the TNF signaling pathway. Among the TNF-related genes, PTGS2, also known as COX-2, showed the greatest difference in expression levels, with higher CSE-induced increments of both mRNA and protein expression in SAEC compared to NHBE.

overall_design: SAEC and NHBE were subjected to 2.5% CSE for 24h. Microarray-based analysis was used to identify gene and protein expression profiles that are altered by CSE exposure in both cell types.

first: Hario

last: Baskoro

first: Keiko

last: Karasutani

first: Yohei

last: Suzuki

first: Aki

last: Mitsui

first: Naoko

last: Arano

first: Fariz

last: Nurwidya

first: Motoyasu

last: Kato

first: Fumiyuki

last: Takahashi

first: Yuzo

last: Kodama

first: Kuniaki

last: Seyama

first: Kazuhisa


title: Ultraconserved Enhancers Are Required for Normal Development [Drop-seq]

first: Iros

last: Barozzi

summary: Non-coding ultraconserved regions showing hundreds of consecutive bases of perfect evolutionary sequence conservation across mammalian genomes have intrigued biologists in the decade since they were first described. While many of these sequences are known to represent distant-acting enhancers, initial deletion studies in mice showed that their loss had no obvious impact on viability or fertility. To explore the discrepancy between extraordinary evolutionary constraint and an apparent lack of phenotypes when deleted in vivo, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved brain enhancers near the essential neuronal transcription factor Arx. While the loss of any single or pair of ultraconserved enhancers resulted in viable and fertile mice, detailed phenotyping revealed neurological or growth abnormalities in nearly all cases, including substantial alterations of neuron populations and abnormalities of the dentate gyrus. Our results demonstrate the functional importance of ultraconserved enhancers and highlight that extreme sequence conservation may result from evolutionary selection against fitness deficits that appear subtle in a laboratory setting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cell suspensions were prepared from E12.5 mouse forebrains, and single-cell mRNAseq libraries were generated with Drop-Seq. Experiments were performed on transgenics embryos in which a validated forebrain enhancer (hs119, hs121, hs122, hs123, http://enhancer.lbl.gov/) controlled the expression of a reporter gene (either GFP or mCherry).

first: Diane

middle: E

last: Dickel

first: Athena

middle: R

last: Ypsilanti

first: Ramon

last: Pla

first: Yiwen

last: Zhu

first: Brandon

last: Mannion

first: Yupar

last: Khin

first: Yoko

last: Fukuda-Yuzawa

first: Ingrid

last: Plajzer-Frick

first: Catherine

middle: S

last: Pickle

first: Elizabeth

last: Lee

first: Anne

middle: N

last: Harrington

first: Quan

middle: T

last: Pham

first: Tyler

middle: H

last: Garvin

first: Momoe

first: Jennifer

middle: A

last: Akiyama

first: Veena

last: Afzal

first: John

middle: L

last: Rubenstein

first: Axel

last: Visel

first: Len

last: Pennacchio


title: Changes in relative transcript amounts caused by heat in Streptococcus pneumoniae

city: Oxford

first: Angela

middle: B

last: Brueggemann

address: Peter Medawar Building for Pathogen Research

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: RNA sequencing was used to explore the expression of all genes in Streptococcus pneumoniae under heat stress. The pneumococcal strain 2/2 was grown in broth culture under control (37°C) and high temperature (40°C) conditions. 2/2 culture samples were taken at sequential time points and RNA was extracted and sequenced.

overall_design: Streptococcus pneumoniae isolate 2/2 was cultured in seven 10 ml tubes of brain-heart infusion broth and incubated at 40°C + 5% CO2 for 6 h to mimic heat shock. The experimental control was the same isolate 2/2, also cultured in seven 10 ml tubes of brain-heart infusion broth but incubated at standard conditions of 37°C + 5% CO2. Broth cultures at five time points (2, 3, 4, 5 and 6 h of incubation) were removed and 19 ml of RNAprotect Bacteria Reagent (Qiagen) was added to stabilise the RNA. RNA was extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol. Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc) and sequencing was performed on the MiSeq (Illumina, Inc). The sequenced forward and reverse reads were paired and mapped to the S. pneumoniae strain 2/2 genome using Bowtie2 with the highest sensitivity option. Differential gene expression was analysed in Geneious version 9.1 (Biomatters Ltd) using the DESeq method. Genes with an adjusted p value <0.05 were considered to be differentially expressed.

first: Reza

last: Rezaei Javan

first: Andries

last: van Tonder

first: Caroline

last: Harrold


title: Transcriptional and cistromic profiling of mouse nephron progenitor cells

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California


title: Function of three homologs of RNase III in Synechococcus sp. PCC 7002

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

summary: RNase III is a ribonucleases that recognizes and cleaves double-stranded RNA. RNase III has been known be involved in rRNA processing, but has many additional roles controlling both expression and RNA turnover of specific messages. Many organisms have just one RNase III while some have both a full length RNase III and a mini-III that lacks the double-stranded RNA binding domain. The cyanobacteria Synechococcus sp. PCC 7002 has three homologs of RNase III that are unessential even when deleted in combination. We were interested what coding regions these RNase III enzymes were influencing and if they had redundant or distinct specificities.  To address these questions we collected samples for RNA-sequencing from WT, the single, double, and triple RNase III mutants in triplicate. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. We describe the role of two RNase III’s in 23S rRNA maturation, and show how the third is involved in copy number regulation of one of the six plasmids (pAQ3). Purified enzymes were capable of cleaving some E. coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.

overall_design: Samples were taken from WT and all single, double, and triple RNase III mutants at an OD ~0.1 in biological triplicate.

middle: C

first: Jeffrey

last: Carmeron

first: Brian

middle: F

last: Pfleger


title: Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation (APCA and ADCA lines RNASeq)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary:
Analysis of transcriptome from AR-deleted CARN-derived lines (ADCA) and controls, AR-positive CARN-derived lines (APCA)
ADCA and APCA lines at passage 5 or 6 were grown to approximately 70-80% confluency in the presence of DHT, lysed in Trizol and frozen for subsequent molecular analysis

overall_design: Total RNA obtained from ADCA and APCA cell lines. Frozen cells in Trizol were processed for RNA isolation and transcriptome analysis using the MagMAX-96 for Microarray kit (Ambion).

first: Chee

middle: W

last: Chua

first: Bo

last: Li

first: Michael

middle: M

last: Shen


title: Comparative profiling of the heterochromatin landscape in different life cycle stages, strains and species of malaria parasites

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

summary: Heterochromatin is a tightly packaged form of DNA that leads to permanent or temporal gene silencing. In P. falciparum heterochromatin is formed after trimethylation of lysine 9 on histone H3 and consequent binding of heterochromatin protein 1 (HP1). Genome-wide profiling studies established that in P. falciparum blood stage schizonts heterochromatin is formed at subtelomeres and some intra-chromosomal islands. Reversible silencing of genes located in these regions has been shown to be key to, among others, antigenic variation, invasion pathway selection or commitment to gametocytogenesis. However, heterochromatic gene silencing has not been investigated in many other Plasmodium species, strains or life cycle stages, yet. Here, we used ChIP-seq to profile HP1 occupancy in asexual parasites of six different species (P. falciparum, P. knowlesi, P. vivax, P. berghei, P. yoelii, and P. chabaudi) and of four different P. falciparum strains (3D7, PF2004, NF54, NF135) as well as two different P. knowlesi clones (A1C1, A1H1). Additionally, we performed HP1 ChIP-seq on three asexual stages (ring, trophozoite and schizont stage) and two sexual stages of P. falciparum parasites. Collectively, the generated HP1 profiles provide a detailed catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control at different life cycle stages, strains and species across the genus Plasmodium.

sample_organism:
Plasmodium berghei
Plasmodium chabaudi
Plasmodium falciparum
Plasmodium knowlesi
Plasmodium vivax
Plasmodium yoelii

overall_design: In total, we sequenced 26 samples (14 HP1-ChIP-seq samples and 12 inputs) generated from chromatin from six different Plasmodium species (P. chabaudi, P. berghei, P. yoelii, P. knowlesi, P. vivax and P. falciparum), four different strains of P. falciparum (3D7, NF54, NF135 and Pf2004) and two different strains of P. knowlesi (A1.C1 and A1.H1) as well as three different intraerythrocytic stages of the P. falciparum 3D7 strain (ring, trophozoite and schizont stages) and three different stages of the P. falciparum Pf2004 strain (schizont stages, stage II/III gametocytes and stage IV/V gametocytes).

last: Filarsky

first: Regina

last: Hoo

first: Igor

last: Niederwieser

first: Xue

last: Yan Yam

first: Nicolas

last: Brancucci

first: Franziska

last: Mohring

first: Annals

last: Mushunje

first: Ximei

last: Huang

first: Peter

last: Christensen

first: Francois

last: Nosten

first: Bruce

last: Russell

first: Rob

last: Moon

first: Matthias

last: Marti

last: Preiser

first: Richard

last: Bartfai

first: Till

last: Voss


title: Sorted Mouse Phagocytes RNAseq

status: Public on Jan 15 2018

city: Zurich

first: Irina

last: Leonardi

address: Sternwartst. 14

department: Gastroenterology and Hepathology

country: Switzerland

institute: USZ

summary: RNAseq of murine CD11b+ CD103+ DCs and CD11b+ CX3CR1+ Mononuclear Phagocyes

overall_design: Cells were sorted from the colonic lamina propria of CX3CR1-GFP/+ mice

first: Iliyan

last: Iliev


title: Genome-wide determinants of sequence-specific DNA binding

city: University Park

first: Bongsoo

last: Park

address: 453 North Frear Building

institute: Penn State University

summary: DNA binding protein are generally thought to bind specific DNA sequences through selective interactions with DNA bases. However, it is now becoming more widely appreciated that DNA shape, which may not be specified by a unique base sequence, also contributes to site-specific binding. Here we elucidate how DNA sequence and shape confer site specificity on a genomic scale, and relate this to specificity imparted indirectly through occlusion of sequences by the in vivo environment. For simplicity, we focus on the set of General Regulatory Factors (GRFs) that do not rely on other factors for binding. They also serve a related function in organizing chromatin. Remarkably, we find that GRFs will not bind to their cognate motif if the DNA surrounding that sequence lacks a specific shape. While proper DNA sequence/shape properties tend to be restricted to promoter regions, weaker sites that are still binding-competent reside in gene bodies, but are prevented from binding by resident chromatin. Thus, site-specificity is achieved across a genome in vivo by the combined action of favorable DNA sequence and shape interactions, and occlusion by chromatin.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Genome-wide analysis of yeast general regulatory factors using an in vitro version of ChIP-exo

first: Matthew

last: Rossi

first: William

last: Lai

first: B

last: Pugh


title: Expression levels of genes of LCMV.GP66-77 specific CD4 T cells isolated from bone marrow (BM) and spleen, 3 days after antigenic re-challenge

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: We performed RNA-Seq and compared expression levels of genes of reactivated LCMV.GP66-77 specific CD4 T cells isolated from bone marrow (BM) and spleen of LCMV.GP61-80 primed C57BL/6 mice. Cells were isolated 3 days after antigenic re-challenge

overall_design: C57BL/6 mice were primed at day 0 with LCMV.GP61-80-NP-MSA + poly(I:C) and immunized again at day 14 with LCMV.GP61-80 + poly(I:C). 60 days later, C57BL/6 mice were boosted with LCMV.GP61-80-NP-MSA + poly(I:C) and 3 days after the boost, LCMV specific CD4 T cells were isolated from BM and spleen

first: Francesco

last: Siracusa

first: Mairi

last: McGrath

first: Patrick

last: Maschmeyer

first: Markus

last: Bardua

first: Katrin

last: Lehmann

first: Gitta

last: Heinz

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi

first: Hyun-Dong

last: Chang

first: Koji

last: Tokoyda

first: Andreas

last: Radbruch


title: Oryza sativa Argonaute 18 is a regulator of male sterility (sRNA-Seq)

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

summary: Artificial miRNA mediated knock-down ago18 transgenic lines [ago18(1), ago18(2)] showed developmentally compromised phenotype in both vegetative and reproductive tissues compared to wild-type control. We have performed small RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO18 in rice.

overall_design: We have performed small RNA seq analysis using vegetative and reproductive tissues of both WT and knock-down tansgenic lines. Four weeks old seedlings were considered as vegetative tissues and two different stage of panicle were examined as reprodictive tissues. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

middle: V

last: Shivaprasad

first: Swetha

last: Chenna

first: Soumita

last: Das


title: Transcript-indexed ATAC-seq reveals paired single-cell T cell receptor identity and chromatin accessibility for precision immune profiling [Ensembl]

city: Stanford

first: Ansuman

last: Satpathy

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford University

summary: T cells create vast amounts of diversity in their T cell receptor (TCR) genes, enabling individual clones to recognize particular peptide-MHC ligands. Here we combine transposase accessible chromatin analysis and TCR sequencing (T-ATAC-seq) at the single-cell level. Using this approach, we identify epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers, and primary leukemic T cells from clinical patient samples. In healthy peripheral blood CD4+ T cells, we identify cis and trans regulators of naive and memory T cell states and find significant heterogeneity in surface marker-defined populations. In patients with cutaneous T cell lymphoma, we identify leukemic and non-leukemic regulatory pathways in cells from the same individual, which has been previously challenging. Thus, T-ATAC-seq is a new tool enabling analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity, and immunotherapy.

overall_design: CD4+ T cell subsets were sorted form peripheral blood of healthy human volunteers. 50-60,000 cells from each subset were subject to open chromatin ATAC-seq profiling. Samples include 2 or 3 biological replicates from Naïve CD4+ T cells, CD4+ T helper 1 (TH1) cells, CD4+ T helper 2 (TH2) cells, CD4+ T helper 17 (TH17) cells, CD4+ T helper 1-17 (TH1-17) cells, and T regulatory cells (TREG).

first: Naresha

last: Saligrama

first: Jason

middle: D

last: Buenrostro

first: Yuning

last: Wei

first: Beijing

last: Wu

first: Adam

last: Rubin

first: Jeffrey

last: Granja

first: Caleb

last: Lareau

first: Rui

last: Li

first: Yanyan

last: Qi

first: Kevin

last: Parker

first: Maxwell

last: Mumbach

first: William

last: Serratelli

first: David

middle: G

last: Gennert

first: Alicia

last: Schep

first: M

last: Corces

first: Youn

last: Kim

first: Paul

last: Khavari

last: Greenleaf

first: Mark

last: Davis

first: Howard

middle: Y


title: RNA sequencing analyisis to identify genes regulated by GW9662 in human cord blood hematopoietic stem and progenitor cells

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

summary: PPARγ antagonist GW9662 treatment could enhance ex vivo expansion of human cord blood hematopoietic stem and progenitor cells (HSCs/HPCs). To gain mechanistical insights into how antagonizing PPARγ promotes expansion of HSCs/HPCs, we performed RNA sequencing (RNA seq) analysis to identify genes involved in this process. Loss of function of PPARγ in CB CD34+ cells resulted in downregulation of a number of differentiation associated genes, including CD38, CD1d, HIC1, FAM20C, DUSP4, DHRS3 and ALDH1A2, suggesting that PPARγ antagonist may maintain stemness of CB CD34+ cells, at least in part by preventing differentiation. We also observed that FBP1, encoding fructose 1, 6-bisphosphatase, a negative regulator of glycolytic flux, was significantly downregulated by treating CB CD34+ cells with GW9662. Our study demonstrates that antagonizing PPARγ signaling drives ex vivo expansion of human CB HSCs/HPCs by switching on FBP1 repressed glycolysis and preventing differentiation.

overall_design: Total RNA was extracted from Vehicle or GW9662 treated cord blood CD34+ cells, and then RNA sequencing analysis was performed.

first: Xinxin

last: Huang

first: Hal

middle: E

last: Broxmeyer


title: Transcript-indexed ATAC-seq reveals paired single-cell T cell receptor identity and chromatin accessibility for precision immune profiling [single cell]

first: Ansuman

last: Satpathy

overall_design: CD4+ Jurkat cells, primary CD4+ T cell subsets sorted from peripheral blood of healthy human volunteers, or primary CD4+ T cells sorted from peripheral blood of patients with Sezary syndrome. Single cells from each cell population were subjected to open chromatin single-cell ATAC-seq profiling. Single-cell samples include Jurkat cells, CD4+ Naive T cells, CD4+CD45RA- Memory T cells, CD4+ TH17 cells, and CD26+ and CD26- CD4+ cells from Sezary patients. Single cell experiments were performed in cell samples from 2-3 biological replicates (each replicate is indicated by it's J or C plate number).

first: Naresha

last: Saligrama

first: Jason

last: Buenrostro

first: Yuning

last: Wei

first: Beijing

last: Wu

first: Adam

middle: J

last: Rubin

first: Jeffrey

last: Granja

middle: R

middle: S

last: Chang


title: Transcript-indexed ATAC-seq reveals paired single-cell T cell receptor identity and chromatin accessibility for precision immune profiling


title: A single master regulatory gene optix underlies both color and iridescence in butterflies

city: ithaca

first: Linlin

last: Zhang

state: NY

address: 215 TOWER RD

department: Ecology and Evolutionary Department

institute: Cornell University

summary: It is debated to what extent individual regulatory genes might underlie non-gradualistic evolution of complex morphological traits. We have shown that a single regulatory gene, optix, is required for development of all color and iridescence in nymphalid butterfly wings by CRISPR/Cas9 genome editing. To investigate how wing features are controlled by optix, we used mRNA-seq to compare transcript abundance in wild type and optix knockout wings of V. cardui and J. coenia. We generated an average of 269 million reads 36 bp paired-end Nexseq 500 reads from 16 libraries and identified numerous candidate genes including known genes involved in the insect melanin and ommochrome biosynthetic pathways and suspected components potential involved in scale structure.

sample_organism:
Junonia coenia
Vanessa cardui

platform_organism:
Junonia coenia
Vanessa cardui

overall_design: Butterfly forewings and hindwings were sampled separately at a late stage of pupal development when ommochrome and melanin pigments are both becoming visible, with two biological replicates each of both wild type and knockout phenotypes, using Illumina Nextseq 500 for 36 bp paired end sequencing.

first: Robert

last: Reed


title: Genome-wide analysis of HDAC9 and BRG1 protein-RNA interactions in TAA by CLIP-seq

status: Public on Jan 13 2018

city: Boston

first: christian

middle: lacks

last: lino cardenas

state: Massachusetts

address: 185 Cambridge st Room 3224

department: division of cardiovascular

institute: Massachusetts general hospital-Harvard medical school

summary: We analyze the protein-RNA interactions of HDAC9 and BRG1 in human aortic smooth muscle cells overexpressing mutant aneurysm alleles (TGFBR2G357W and ACTA2R179H) and wild-type cells using CLIP-seq.

overall_design: Determination of HDAC9 and BRG1 interaction with RNAs during the aneurysm state in vitro.

first: Christian

last: Lino Cardenas

last: Lindsay


title: RNA-seq of pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into transcriptional landscape

status: Public on Jan 12 2018

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

summary:
Background: The human pathogen Corynebacterium diphtheriae is the causative agent of the disease diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced several years ago, not much is known about the transcriptome. Our aim was to use RNA Sequencing to close this knowledge gap and gain insights into the transcriptional landscape of C. diphtheriae.
Results: We applied two different RNA Sequencing techniques, one to retrieve 5' ends of primary transcripts and one to obtain full length transcripts, to gain insights into various features of the C. diphtheriae NCTC 13129 transcriptome. By examining the data we identified 1,657 transcription start sites (TSS) of which 1,229 were assigned to genes and 428 to putative novel transcripts. By using the TSS data SigA promotor regions and their motifs could be analyzed in detail, revealing a well conserved –10 but unconserved –35 motif, respectively. Furthermore with the TSS data in hand 5' UTR lengths were explored. The observed 5' UTRs range from leaderless, which make up 20 % of all genes, up to over 450 bp long leaders, which may harbor regulatory functions. The C. diphtheriae transcriptome consists of 470 operons which are further divided into 167 sub-operon structures. In addition we discovered that the deletion of the iron sensing transcription regulator DtxR, which also controls expression of diphtheria toxin (DT), has a strong influence on general gene expression. Nearly 15 % of the genome is differentially expressed, indicating that DtxR might have other functions next to regulation of iron metabolism and DT. Furthermore we shed light on the transcriptional landscape of the DT encoding gene tox and present evidence for an additional TSS and three tox antisense RNAs, which might reveal new ways of transcriptional regulation.
Conclusions: This study presents extensive insights into the transcriptome of C. diphtheriae and provides a basis for future studies regarding transcriptional regulators, gene characterization and the tox gene in particular.

overall_design: RNA-Seq of primary transcripts of wild type cells and whole transcriptome of wild type and dtxR mutant in triplicates.

first: Tobias

last: Busche


title: PRKCI regulates tumor microenvironment through YAP1

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

overall_design: Refer to individual Series


title: Frequent derepression of the Iroquois homeobox gene IRX3 in human acute leukemia

city: Manchester

first: Tim

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: The Iroquois homeodomain transcription factor gene IRX3 is highly expressed in the developing nervous system, limb buds and heart. In adults, expression levels specify risk of obesity. We now report a significant functional role for IRX3 in human acute leukemia. While transcript levels are very low in normal human bone marrow cell populations, high level IRX3 expression is observed in ~30% of patients with acute myeloid leukemia (AML), ~50% of patients with T-acute lymphoblastic leukemia and ~20% of patients with B-acute lymphoblastic leukemia, typically in association with high levels of HOXA9. Expression of IRX3 alone was sufficient to immortalise murine bone marrow stem and progenitor cells, and induce T- and B-lineage leukemias in vivo with incomplete penetrance. IRX3 knockdown induced terminal differentiation of AML cells. Combined IRX3 and Hoxa9 expression in murine bone marrow stem and progenitor cells substantially enhanced the morphologic and phenotypic differentiation block of the resulting AMLs by comparison with Hoxa9-only leukemias, through suppression of a myelomonocytic program. Likewise, in cases of primary human AML, high IRX3 expression is associated with reduced myelomonocytic differentiation. Thus, tissue-inappropriate derepression of IRX3 modulates the cellular consequences of HOX gene expression to enhance differentiation block in human AML.

overall_design: Murine acute myeloid leukemias - 3 samples from separate mice with AML initiated by HOXA9 and 3 samples from separate mice with AML initiated by HOXA9 and IRX3 coexpression


title: Isolation and Functional Interrogation of Adult Human Prostate Epithelial Stem Cells at Single Cell Resolution

city: CHICAGO

first: WENYANG

last: HU

state: IL

address: 909 S WOLCOTT

department: UROLOGY

institute: UNIVERSITY OF ILLINOIS AT CHICAGO

summary: Using primary cultures of normal human prostate epithelial cells, we developed a novel prostasphere-based, label-retention assay that permits identification and isolation of stem cells at a single cell level. Their bona fide stem cell nature was confirmed using in vitro and in vivo regenerative assays and documentation of symmetric/asymmetric division. Robust WNT10B and KRT13 expression without E-cadherin or KRT14 staining distinguished individual stem cells from daughter progenitors in spheroids. Following FACS to separate stem and progenitor cells, RNA-seq identified unique gene signatures for the separate populations which may serve as biomarkers. Pathways enrichment in stem cells identified ribosome biogenesis and membrane estrogen-receptor signaling with NFĸB signaling enriched in progenitors and these were biologically confirmed. Further, bioassays identified heightened autophagy flux and reduced metabolism in stem cells relative to progenitors. These approaches similarly identified cancer stem-like cells from prostate cancer specimens and prostate, breast and colon cancer cell lines suggesting wide applicability. Together, the present studies isolate and identify unique characteristics of normal human prostate stem cells and uncover processes that maintain stem cell homeostasis in the prostate gland.

overall_design: Comparing RNA-seq gene profiles in label-retaining prostate stem cells and non-retaining progenitor cells

first: Wen-Yang

last: Hu

first: Hong

first: Gail

last: Prins


title: Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [RNA-Seq]

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

institute: Institute of Cancer Research

summary: We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and SUM44 ESR1-positive cell-lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR).

overall_design: RNAseq examination of gene expression changes due to long term estrogen deprivation in two breast cancer cell lines with and without ESR1 mutations

first: Lesley-Ann

last: Martin


title: PRKCI regulates tumor microenvironment through YAP1 [ChIP-Seq]

summary: A key feature of serous ovarian cancer is frequent amplification in the 3q26 locus, which harbors the PRKCI gene. Here we show that PRKCI is amplified and overexpressed in a 78% of high-grade serous ovarian carcinoma. Our in vivo studies with orthotopic mouse models establish it as an ovarian cancer oncogene. This oncogenic property of PRKCI is mediated by regulation of YAP1 activity. Accordingly YAP1 knockdown partially rescues PRKCI mediated tumorigenesis. Integrated gene expression profiling and YAP1 promoter occupancy analyses reveal that PRKCI and YAP1 cooperate to transcriptionally regulate genes affecting the tumor immune microenvironment. Consistently, CD11b+Gr1+Ly6G+ MDSCs are increased in the tumor microenvironment of PRKCI over-expressing tumors. Importantly, we show that elevated PRKCI expression in high-grade serous ovarian carcinomas strongly correlated with assignment to immunoreactive subtype.  In summary, we identify PRKCI and YAP1 as key mediators of a tumor-promoting immunosuppressive microenvironment in ovarian cancers.

overall_design: OVCAR5 cell chromatin isolated and YAP1 binding to DNA determined by chromatin IP and the DNA isolated is sequenced to determine genomewide occupancy

first: Sharmistha

last: Sarkar

first: Lynda

last: Chin


title: Chromosomal instability promotes metastasis through a cytosolic DNA response

city: New York

first: Charles

last: Murphy

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Chromosomal instability (CIN) is a hallmark of cancer, and it results from ongoing errors in chromosome segregation during mitosis. While CIN is a major driver of tumor evolution, its role in metastasis has not been established. Here we show that CIN promotes metastasis by sustaining a tumor-cell autonomous inflammatory response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose envelopes frequently rupture exposing their DNA content to the cytosol. This leads to the activation of the cGAS-STING cytosolic DNA-sensing pathway and downstream noncanonical NF-kB signaling.  Genetic suppression of CIN significantly delays metastasis in transplantable tumor models, whereas inducing chromosome segregation errors promotes cellular invasion and metastasis in a STING-dependent manner. In contrast to primary tumors, human and mouse metastases strongly select for CIN, in part, due to its ability to enrich for metastasis-initiating mesenchymal subpopulations, offering an opportunity to target chromosome segregation errors for therapeutic benefit.

overall_design:
To determine whether CIN is causally involved in metastasis, we devised a genetic approach to alter the rate of chromosome missegregation in transplantable tumor models of human TNBC (MDA-MB-231);
cont: Control sample. Part of the CIN-medium group.
Ka; Overexpression of Kif2a, which does not affect the number of chromosome segregation errors during anaphase and serves as an additional control. Part of the CIN-medium group.
Kb; Overexpression of Kif2b, which leads to suppressed chromosome segregation errors during anaphase. Part of the CIN-low group.
MK; Overexpression of MCAK which leads to suppressed chromosome segregation errors during anaphase. Part of the CIN-low group.
MKH; Overexpression of dominant-negative form of MCAK, leading to increased number of chromosome segregation errors during anaphase. Part of the CIN-high group.

first: Samuel

last: Bakhoum

first: Bryan

last: Ngo


title: Oncogenic roles of ARID5B in T-ALL

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

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


title: Precise genome-wide mapping of single nucleosomes and linkers in vivo

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: We develop a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in budding yeast. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, histone H1 and H2A.Z in defining the chromatin landscape. A biophysical model that neglects DNA sequence is presented and shows that steric occlusion suffices to explain the salient features of nucleosome positioning. Our study indicates that steric occlusion, and not DNA sequence, is the most important determinant of genome-wide nucleosome positioning.

overall_design: Permeabilized S. cerevisiae cells with cysteine substituted for histone H3Q85C were labeled on cysteines with orthophenantroline complex, which chelates a copper ion. In an oxidizing environment the derivatized residue contacts a deoxyribose CIH and cleaves DNA, and the fragments that are released are purified and subjected to paired-end Illumina sequencing.

first: Srinivas

last: Ramachandran

first: Terri

last: Bryson

first: Steven

last: Henikoff


city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

country: South Korea

institute: Korea University

summary: The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome. In multi-species in-vitro biofilms PA partially inhibited SA growth. However, no significant inhibition of MRSA was detected during in-vivo colonization of multi-species in rat bullae. A total of 1797 genes were significantly (p < 0.05) differentially expressed in MRSA or PA or MRSA+PA colonized rat middle ear mucosa with respect to the control. The poly-microbial colonization of MRSA and PA induced the differential expression of a significant number of genes that are involved in immune response, inflammation, signaling, development, and defense; these were not expressed with single species colonization by either MRSA or PA. Genes involved in defense, immune response, inflammatory response, and developmental process were exclusively up-regulated, and genes that are involved in nervous system signaling, development and transmission, regulation of cell growth and development, anatomical and system development, and cell differentiation were down-regulated after multi-species inoculation.

overall_design: S. aureus (MRSA), Pseudomonas aeruginosa (PA) or mixed culture (MRSA +PA) were inoculated in rat middle ear and incubated for 1 week. Vehicle control animals were inoculated with media only. Rats were sacrificed and middle ear mucosa were removed. Total RNA was isolated and sequenced for gene expression study. Differential gene expression in SA colonization, PA colonization or mixed species colonization were evaluated with respect to media only (vehicle control).

first: Jae-Jun

last: Song

middle: K


title: Targeted inhibition of TET1 transcription as a potent therapeutic strategy for acute myeloid leukemia

city: Chicago

first: Xiaolong

last: Cui

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary: Effective therapy of acute myeloid leukemia (AML) remains an unmet need. DNA methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is a potent oncogene in AML. Through a series of data analysis and drug screening, we identified two compounds (i.e., NSC-311068 and NSC-370284) that selectively suppress TET1 transcription and 5-hydroxymethylcytosine (5hmC) modification, and effectively inhibit cell viability in AML with high level expression of TET1 (i.e., TET1-high AML), including AML carrying t(11q23)/MLL-rearrangements and t(8;21) AML. NSC-311068 and especially NSC-370284 significantly repressed TET1-high AML progression in vivo. UC-514321, an optimized derivative of NSC-370284, exhibited an even more potent therapeutic effect and prolonged the median survival of TET1-high AML mice over three folds. NSC-370284 and its derivative showed strong synergistic effects with standard chemotherapy. NSC-370284 directly targeted STAT3/5, transcriptional activators of TET1, and thus repressed TET1 expression. Our results highlight the therapeutic potential of targeting the STAT/TET1 axis by selective inhibitors in AML treatment.

overall_design: Selective 5hmC chemical labeling approach to profile genome-wide 5hmC distributions across different samples

first: Xi

last: Jiang

first: Ji

last: Nie

first: Chuan

last: He

first: Jianjun

last: Chen


title: Targeted inhibition of STAT/TET1 axis as a potent therapeutic strategy for acute myeloid leukemia

city: wuhan

first: linjian

last: xia

address: wuhan

country: China

institute: wuhan University

summary: Effective therapy of acute myeloid leukemia (AML) remains an unmet need. DNA methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Through a series of data analysis and drug screening, we identified two compounds (i.e., NSC-311068 and NSC-370284) that selectively suppress TET1 transcription and 5-hydroxymethylcytosine (5hmC) modification, and effectively inhibit cell viability in AML with high level expression of TET1 (i.e., TET1-high AML), including AML carrying t(11q23)/MLL-rearrangements and t(8;21) AML. NSC-311068 and especially NSC-370284 significantly repressed TET1-high AML progression in vivo. UC-514321, a structural analog of NSC-370284, exhibited a more potent therapeutic effect and prolonged the median survival of TET1-high AML mice over three folds. NSC-370284 and UC-514321 both directly target STAT3/5, transcriptional activators of TET1, and thus repress TET1 expression. They also exhibit strong synergistic effects with standard chemotherapy. Our results highlight the therapeutic potential of targeting the STAT/TET1 axis by selective inhibitors in AML treatment.

overall_design: To assess the influence of NSC-370284 on gene expression pattern, we treated THP-1 cells with 50 nM NSC-370284 or DMSO control. RNA samples were collected after 24 hours of treatment. RNA sequencing was performed.

first: Kyle

last: Ferchen

first: Chunjiang


title: miRNA profiling of A549 cell line

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: miRNA profiling of A549 cell line

overall_design: A549 cell line under hypoxia and Normoxia condition (no replicate)

first: R

last: Rezzonico

first: B

last: Marcet

first: O

last: Mercey

first: K

first: P

last: Barbry


title: RNA-seq profiling of LPS-treated vs un-treated primary monocytes derived from rhesus macaques and sooty mangabeys

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: To characterize more broadly the effect of attenuated TLR4 signaling responses in sooty mangabeys, we performed a comparative RNA-seq profiling of LPS-treated primary monocytes from rhesus macaques and sooty mangabeys. Production of TNF- and IL6 mRNA was significantly lower in sooty mangabeys. Moreover, we observed that induction of NF-κB -regulated inflammatory genes was broadly and significantly reduced in sooty mangabeys, for TNF-a and IL-6 signaling pathways, compared to rhesus macaques. Overall, these data indicate that LPS stimulation of SM blood cells results in a significantly blunted production of pro-inflammatory cytokines as compared to rhesus macaque macrophages.

sample_organism:
Cercocebus atys
Macaca mulatta

platform_organism:
Cercocebus atys
Macaca mulatta

overall_design: Examination of LPS-treated and un-treated primary monocytes derived from 6 rhesus macaques and 6 sooty mangabeys for a total of 24 samples.

first: David

last: Palesch

first: Steven

last: Bosinger

first: Thomas

middle: H

last: Vanderford

first: Mirko

last: Paiardini

first: Ann

last: Chahroudi

first: Zachary

middle: P

last: Johnson

first: Frank

last: Kirchhoff

first: Beatrice

last: Hahn

first: Robert

middle: B

last: Norgren Jr

first: Nirav

last: Patel

first: Donald

middle: L

last: Sodora

first: Reem

last: Dawoud

middle: A

last: Harris

first: Yue

last: Liu

first: Muthuswamy

last: Raveendran

first: Yi

last: Han

first: Adam

last: English

first: Gregg

last: Thomas

first: Matthew

first: Lenore

last: Pipes

first: Christopher

last: Mason

first: Donna

last: Muzny

first: Richard

last: Gibbs

first: Kim

last: Worley

first: Daniel

last: Sauter

first: Jeffrey

last: Rogers

first: Guido

last: Silvestri


title: Coordinate regulation of ammonium transporters and components of the mating and pathogenic programs in Ustilago maydis

city: Louisville

first: Michael

last: Perlin

state: KY

address: Biology, Belknap-LS 139

department: Biology

institute: University of Louisville

summary: Next generation sequencing was used to assess transcriptome changes in haploid U. maydis wild type and mutant strains grown under nitrogen-replete and low ammonium media.

overall_design: Wild type and mutant strains were grown for 48 hours at 26 C,  in microarray media ((6.25% Holliday Salt Solution (Holliday, 1974), 1% glucose,  and 2% agar)  with either 30 mM Glutamine/50 mM Ammonium sulfate (Hi) or 50 uM Ammonium sulfate (Lo)

first: R

middle: M

last: Wallen


title: Placenta-derived exosomes as early biomarker of preeclampsia - Potential role of exosomal miRNAs across gestation.

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

summary: Preeclampsia (PE) and its related diseases is one of the most significant pregnancy complications, occurring at an incidence of 3-5% and is responsible for nearly 40% of premature births delivered before 35 weeks. There is a need to develop strategies for early prediction of patients who will develop PE, in order to establish preventive strategies to reduce the prevalence and severity of the disease and their associated aftereffects. Therefore, a prospective cohort of patients were recruited at three time points during pregnancy for each patient (i.e. 11-14 (early gestational age), 22-24 (middle gestational age) and 32-36 (late gestational age) weeks gestation). A retrospective stratified study design was used to characterize miRNAs in exosomes derived from maternal plasma of normal (n=32 per time point) and PE (n=15 per time point) pregnancies.

overall_design: miRNAs were profiled from exosomes using next generation seqeuencing, utilizing the Illumina NextSeq 500 platform

first: Carlos

last: Salomon

first: Gregory

last: Rice


title: Integrative proteogenomic characterization of colorectal cancer cell lines and primary tumors

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Insitute of Medical Reseach

summary: Integrative analysis of global RNASeq and proteomic data comparing human colorectal cancer (CRC) cell lines to primary tumors and normal tissues.

overall_design: Examination of mRNA expression levels across 44 colorectal cell lines.

first: Jing

last: Wang

first: Dmitri

last: Mouradov

first: Xiaojing

first: Robert

middle: N

last: Jorissen

middle: C

last: Chambers

first: Lisa

last: Zimmerman

first: Suhas

last: Vasaikar

middle: G

last: Love

first: Shan

last: Li

first: Kym

last: Lowes

first: Karl

last: Leuchowius

first: Helene

last: Jousset

first: Janet

last: Weinstock

last: Yau

first: John

last: Mariadason

last: Coffey

last: Slebos

first: Antony

middle: W

last: Burgess

last: Liebler

first: Bing

last: Zhang


title: RNA-Sequencing Analysis of Abscission-related Transcriptome in Citrus Calyx Abscission Zone Reveals Distinguishing Profile of Phytohormone Expression Associated with Abscission of HLB-affected Sweet Orange

city: FORT PIERCE

first: JINHE

last: BAI

state: FLORIDA

address: 2001 SOUTH ROCK RD

department: HORTICULTURAL RESEARCH LABORATORY

institute: USDA-ARS

summary: Citrus greening or huanglongbing (HLB) disease is caused by Candidatus liberibacter asiaticus (CLas) and associated with an increase in pre-harvest fruit drop, for which the molecular mechanisms remain unknown. In order to understand the molecular basis of the HLB-associated fruit abscission, by means of RNA-Sequencing analysis (RNA-Seq), transcriptomes in citrus calyx abscission zones were analyzed and compared among fruit dropped (D) or retained (R) from healthy (h) or HLB-diseased (d) trees upon shaking the trees. Cluster analysis based on the transcript reads indicates that dropped fruit from HLB-diseased trees (Dd) have largest distances from all other groups. Differentially expressed genes (DEGs) were identified between Dd and Rd, Dh and Rh, Rd and Rh, Dd and Dh. Wilcoxon test of the whole dataset of DEGs revealed that consistently up-regulated genes in Dd versus Rd and Dd versus Dh are in the functional categories of “secondary metabolism, lipid metabolism and hormone-ethylene and –jasmonate”; while those down-regulated genes didn’t show clear pattern of regulation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the significant biological processes or pathways involved in HLB-related fruit abscission were those related to defense response, secondary metabolism and hormone signaling. Among them, “response to chitin” was the most significant (p= 9.95E-13) biological process, and “jasmonic acid biosynthesis” was the most significant (p= 4.6E-5) pathway. Genes related to synthesis and signaling of ethylene (ET) and jasmonate (JA) were consistently up-regulated, while abscisic acid, auxin, brassinosteroid, cytokinin, and gibberellin were generally down-regulated in Dd; but not in Dh. Consistent with the transcriptomic data, fruit ethylene production was detected in two third of the Dd fruit, but none of Rd, Dh or Rh fruit. And, in agreement with the hormone expression profiles, substantial numbers of downstream JA/ET-responsive defense related genes were up-regulated in Dd, but not in Dh. Thirty representative DEGs covering categories of hormone, secondary metabolism, and JA/ET responsive defense responses were verified by qRT-PCR. The results indicate that HLB-associated pre-harvest fruit abscission is mediated by JA/ET signaling, which has been known to be triggered by infection of necrotrophic pathogens.

overall_design: Six-year old ‘Hamlin’ orange trees (Citrus sinensis (L.) Osbeck), about 2.5-3.0 m tall, on 'Swingle' citrumelo (C. paradisi Macf. × Poncirus trifoliata (L) Raf.) rootstock, in a commercial grove located in Southern Florida. Thirty six trees were selected for the experiment, of which eighteen were CLas negative (healthy) and the other eighteen were CLas positive (HLB), as tested by qPCR using the method of Li et al. (2006). The selected trees were similar in size, and all were grown under similar agro-climatic conditions and received common cultural practices and the grower’s standard pest and disease management. Fruit were harvested on 1 Dec. 2014 (during commercial harvest season). The ground under the trees was cleaned just before shaking the trees, and trees were shaken manually. For HLB-diseased trees (d), many of the fruit dropped (Dd) upon shaking the trees. For healthy trees (h), the forces of shaking were strong enough to get enough number of dropped fruit (Dh) from the trees. The dropped fruit (Dd or Dh) were collected, and the retained fruit on HLB-diseased (Rd) or healthy trees (Rh) were hand-picked off the trees (Fig. 1A). The fruit from nine trees were pooled together as a group. There were two groups (biological replicates) for each of the Dd, Rd, Dh and Rh. Thirty fruit were randomly picked from each of the Dd, Rd, Dh and Rh groups, and the AZ-C were excised (Fig.1B) and immediately frozen in liquid nitrogen and stored at –80 ºC for RNA isolation. Another thirty fruit from each of the groups were transported to the laboratory where fruit ethylene production was measured.

first: Wei

last: Zhao

first: Elizabeth

last: Baldwin

first: Jinhe

last: Bai

first: Anne

last: Plotto

first: Mike

last: Irey


title: TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal information about the sequenced RNA. Here we report TimeLapse-seq, which uses oxidative-nucleophilic-aromatic substitution to convert 4-thiouridine into cytidine analogs, yielding apparent U-to-C mutations that mark new transcripts upon sequencing. TimeLapse-seq is a single-molecule approach that is adaptable to many applications and reveals RNA dynamics and induced differential expression concealed in traditional RNA-seq.

overall_design: RNA isolated from cells +/- s4U feed was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced. All sequencing was performed in duplicate per condition assessed.

first: Jeremy

last: Schofield

first: Erin

middle: E

last: Duffy

first: Lea

last: Kiefer

first: Meaghan

last: Sullivan


title: ARID5B ChIP-seq in Jurkat

first: Phuong

last: Cao Thi Ngoc

summary: ChIP-seq analysis was performed in Jurkat cells (T-cell acute lymphoblastic leukemia cell line)

overall_design: ARID5B ChIP-seq

middle: Z

last: Leong

first: Shi

last: Tan

middle: Y

last: Yam

first: Takaomi

last: Sanda


title: Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis.

status: Public on Jan 11 2018

city: St. Andrews

first: David

last: Shuker

address: Greenside Place

department: School of Biology

institute: University of St Andrews

summary: Female Nasonia facultatively vary their offspring sex ratio in line with Hamilton’s theory of Local Mate Competition (LMC). A single female or “foundress” laying eggs on a patch will lay just enough sons to fertilise her daughters. As the number of “foundresses” laying eggs on a patch increases (and LMC declines) females produce increasingly male-biased sex ratios. Phenotypic studies have revealed the cues females use to estimate the level of LMC their sons will experience but our understanding of the genetics underlying sex allocation is limited. Here, we exposed females to three foundress number conditions, i.e. three LMC conditions, and allowed them to oviposit. mRNA was extracted from only the heads of these females to target the brain tissue. The subsequent RNA-seq experiment confirmed that differential gene expression is not associated with the response to sex allocation cues and that we must instead turn to the underlying neuroscience to reveal the underpinnings of this impressive behavioural plasticity.

overall_design: Examination of gene expression in female parasiotids exposed to one of three "foundress number" treatments; single-, five- or ten-foundress. There are n=8, n=7 and n=8 biological replicates per condition respectively.

first: Nicola

last: Cook

first: Rebecca

last: Boulton

first: Jade

last: Green

first: Urmi

last: Trivedi

first: Eran

last: Tauber

first: Bart

last: Pannebakker

first: Michael

last: Ritchie


title: RNA-seq analysis in knockdown Jurkat samples for each factor of TAL1 complex

summary: RNA-seq of control, shTAL1, shGATA3, shRUNX1, shMYB, shHEB, shE2A, shLMO1 and shARID5B Jurkat cells

first: Wei


title: RNA-Seq expression profiling of mouse DEN-initiated hepatocytes with or without Tgfbr2 inactivation

status: Public on Jan 10 2018

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

institute: Tulane University

summary: Initiated hepatocytes (IHCs), isolated from DEN exposed Tgfbr2 flox/flox mouse, were infected with GFP or Cre-expressed adenovirus, followed by 1ng/ml TGFβ × 48 hours incubation. Then total RNAs were isolated and processed to routine sequencing on Illumina platform. RNA-Seq libraries were prepared from total RNA using polyA enrichment.

overall_design: Examination of transcriptome differences between initiated hepatocytes with or without Tgfbr2 inactivation.

first: Chang

last: Han

first: Tong

last: Wu


title: NK cell regulation of T cells following LCMV infection of vaccinated and unvaccinated mice

city: Boston

first: MALIKA

last: AID

state: MA

address: 3 blackfan street

institute: BIDMC

summary: NK cells may provide a “rheostat” function and have been shown to reduce the magnitude of antigen-specific T cell responses following infection. It remains unknown whether NK cells similarly modulate vaccine-elicited T cell responses following viral challenge. We used the LCMV clone 13 infection model to address whether NK cells regulate T cell responses in Adenovirus vector vaccinated mice following challenge. As expected, NK cell depletion in unvaccinated mice resulted in increased virus-specific CD4+ and CD8+ T cell responses and immunopathology following LCMV challenge. In contrast, NK cell depletion had minimal to no impact on antigen-specific T cell responses in mice that were vaccinated with an Ad5-GP vector prior to LCMV challenge. Moreover, NK cell depletion in vaccinated mice prior to challenge did not result in immunopathology and did not compromise protective efficacy. These data suggest that Adenovirus vaccine-elicited T cells may be less sensitive to NK cell-rheostat regulation than are T cells primed by LCMV infection.

overall_design: Splenic GP33-specific CD8+ T cells were isolated via FACS cell sorting at 8 days post-infection from LCMV Cl-13 infected mice. Depending on the experimental group (specifics in sample information), they may have received a prior Ad5-GP vaccine, NK-depleting antibody or isotype control antibody prior to challenge.

first: Eryn

last: Blass

first: Malika

last: Aid

first: Dan

last: Barouch


title: RNA-sequencing in A549 cells transfected with TUFT1 siRNA

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

institute: University of Tokyo

summary: We searched for roles of TUFT1 by RNA-seq in lung cancer cells.

overall_design: Expression of mRNA in a lung adenocarcinoma cancer cell line A549 transfected with TUFT1 siRNA.

first: Natsumi

last: Kawasaki

first: Kazunobu

last: Isogaya

first: Masato

last: Morikawa

first: Kohei

last: Miyazono


title: Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression [ATAC-seq]

city: New York

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Tissue regeneration relies on resident stem cells (SCs), whose activity and lineage choices are influenced by microenvironment. Exploiting the synchronized, cyclical bouts of tissue regeneration in hair follicles (HFs), we investigate how microenvironment dynamics shape the emergence of SC lineages. Employing epigenetic and ChIP-seq profiling, we uncover how signal-dependent transcription factors couple spatio-temporal cues to chromatin dynamics, thereby choreographing SC lineages. Using enhancer-driven reporters, mutagenesis and genetics, we show that simultaneous BMP-inhibitory and WNT signals set the stage for lineage choices by establishing chromatin platforms permissive for diversification. Mechanistically, when binding of BMP-effector pSMAD1 is relieved, super-enhancers driving HF-SC master regulators become silenced. Concomitantly, multipotent, lineage-fated super-enhancers silent in HF-SCs become activated by exchanging WNT-effectors TCF3/4 for LEF1. Throughout regeneration, lineage super-enhancers continue reliance upon LEF1, but then achieve specificity by accommodating additional incoming signaling effectors. Barriers to progenitor plasticity mount as diverse, signal-sensitive transcription factors shape LEF1-regulated super-enhancer dynamics.

overall_design: Mouse bulge hair follicle stem cell and hair germ cells at telogen stage and basal transient amplifying cells (TACs) and suprabasal TACs at anagen were FACS-purified and analyzed by ATAC-seq

first: Rene

last: Adam

first: Elaine

last: Fuchs


title: Expression data from purified mouse CD4+ T cells

city: Columbia

first: William

middle: James

last: Becker

state: South Carolina

address: 6439 Garners Ferry Rd.

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary:
T cells are the main responding arm of the immune system to allografts. One mechanism that may be encouraging tolerance to allografts is T regulatory cells, a CD4+ T cell phenotype that displays antigen-directed immune suppression. T regulatory cells are reduced after allografting in the graft draining lymph node compared to the syngeneic graft draining lymph node, and miRNAs may be responsible for this decrease in suppressive cells.
We used microarrays to detail what miRNAs are dysregulated after allografting in purified CD4+ T cells to identify what miRNAs are hindering the expansion of pro-tolerogenic T regulatory cells.

overall_design: Female C57BL/6 mice were given either tail-skin syngeneic grafts (C57BL/6 --> C57BL/6) or allogenic grafts (C3H --> C57BL/6) on the dorsal lateral surface of the recipient mouse. Allograft directed inflammation or syngeneic graft acceptance proceeded for 10 days. Mice were sacrificed and their draining lymph nodes (axillary and brachial) were harvested. CD4+ T cells were purified from single cell suspensions of this population via magnetic bead isolation. Purity was verified to be > 90% CD4+ by flow cytometry before the purified cells were subjected to total RNA extraction before hybridization on Affymetrix arrays. Naive CD4+ T cells from axillary and brachial lymph nodes were extracted and purified as well for a non-surgery control. Thus, samples were from three groups: Naive CD4+ T cells (N4), allograft-responding CD4+ cells (Al4) or syngeneic graft-responding CD4+ cells (Au4).

first: Mitzi

last: Nagarkatti

first: Prakash


title: Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The adult mouse subependymal zone (SEZ) provides a niche for mammalian neural stem cells (NSCs). However, the molecular signature, self-renewal potential and fate behavior of NSCs remain poorly defined. Here we propose a model in which the fate of active NSCs is coupled to the total number of neighboring NSCs in a shared niche. Using knock-in reporter alleles and single-cell RNA sequencing, we show that the Wnt target Tnfrsf19/Troy identifies both active and quiescent NSCs. Quantitative analysis of genetic lineage tracing of individual NSCs under homeostasis or in response to injury reveals rapid expansion of stem cell number before some return to quiescence. This behavior is best explained by stochastic fate decisions, where stem cell number within a shared niche fluctuates over time. Fate-mapping proliferating cells using a novel Ki67iresCreER allele confirms that active NSCs reversibly return to quiescence, achieving long-term self-renewal. Our findings suggest a novel niche-based mechanism for the regulation of NSC fate and number.

overall_design: We analysed the adult mouse subependymal zone (SEZ), the largest neruogenic niche in the brain, at a single cell level. For this, we used SORT-seq, a combination of FACS and single cell RNA-sequencing that resulted in high quality transcriptome data from ~1500 single cells (out of ~2500 cells sequenced). To identify different cell types, we used knock-in mouse models, surface labeling using antibdoies as well as lineage tracing. Troy-GFPiresCreER +/ki mice were used to identify NSCs. Ki67-tagRFP ki/ki mice were used to identify dividing cells. Ki67-iresCreER +/ki Rosa-tdTomato +/ki mice were administered a single injection of 5mg of Tamoxifen to label dividing cells (day2 - d2) and follow their progeny (day60 - d60) in the SEZ as well as the olfactory bulb (for d60 only). We also included published markers; combinations of anti-GLAST antibody (to identify NSCs) and EGF binding ability using alexa647-conjugated EGF (to identify dividing cells), combinations of anti-Prom1 (Cell contacting the ventricles) and anti-CD24 antibodies (high in neuroblasts), as well as anti-O4 antibody (oligodendrocytes) to create an atlas of NSCs.

last: Basak

first: Teresa

last: Krieger

first: Mauro

middle: J

last: Muraro

first: Kay

last: Wiebrands

first: Daniel

last: Stange

first: Javier

middle: F

last: Aldeguer

first: Nicolas

last: Rivron

first: Marc

last: van de Wetering

first: Johan

last: van Es

first: Alexander

last: van Oudenaarden

first: Benjamin

last: Simons

first: Hans

last: Clevers


title: Circuitry rewiring directly couples competence to predation in the gut-dweller Streptococcus salivarius

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

institute: UNIL

summary: Small distortions in transcriptional networks might lead to drastic phenotypical changes, especially in cellular developmental programs such as competence for natural transformation. Here, we report a pervasive circuitry rewiring for competence and predation interplay in commensal streptococci. Canonically, in model species of streptococci such as Streptococcus pneumoniae and Streptococcus mutans, the pheromone-based two-component system BlpRH is a central node that orchestrates the production of antimicrobial compounds (bacteriocins) and incorporates signal from the competence activation cascade. However, the human commensal Streptococcus salivarius does not contain a functional BlpRH pair and in this species, the competence signaling system ComRS directly couples bacteriocin production and competence commitment. This network shortcut might account for an optimal reaction against microbial competitors and could explain the high prevalence of S. salivarius in the human digestive tract. Moreover, the broad spectrum of bacteriocin activity against pathogenic bacteria showcases the commensal and genetically tractable S. salivarius species as a user-friendly model for natural transformation and bacterial predation.

overall_design: Examination of mRNA transcriptional profiles in WT and 2 mutant strains activated with a pheromone  + Examination of small RNA transcriptional profiles in WT with or without pheromone induction

first: Laetitia

last: Fontaine

first: Andrea

last: Sass

first: Catherine

last: Nannan

first: Jacques

last: Mahillon

first: Tom

last: Coenye

first: Pascal

last: Hols


title: Transcriptomic data of B-cell lymphoma bearing mice treated with anti-CD20/-CD27 mAb therapy

city: Southampton

first: Sean

last: Lim

address: Southampton CRUK Cancer Research Centre, Tremona Road

institute: University of Southampton

summary: We report the single-cell RNA sequencing data obtained from BCL1 lymphoma-bearing mice treated with either isotype control, anti-CD20 mAb, anti-CD27 mAb or anti-CD20+anti-CD27 mAb together

overall_design: Examination of transcriptomic changes in BCL1 lymphoma bearing mice treated under four different conditions

middle: H

first: Matthew

last: Rose-Zerilli


title: CRAC of yeast RNA polymerase II in various thermosensitive strains at permissive and non-permissive temperature and anchor-away strains with the addition of rapamycin.

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

summary: We obtained  RNA polymerase II occupancy profile across the genome of S.cerevisiae in several strains, Wild type  at 25 and 37 degrees C,  RNA15-1 at 25 and 37 degrees C, anchor-away parental strain plus rapamycin, Reb1 anchor-away plus rapamycin, Rap1 anchor-away plus rapamycin, Nrd1-AID plus auxin, and nrd1-AID without auxin.  This allowed us to compare polymerase profiles when these proteins are depleted from the nucleus.

overall_design: investigation of RNA polymerase II profile in various strains depleted for Rap1, Reb1, Rna15, and Nrd1.

first: Jean-Baptiste

last: Briand

first: Tito

last: Candelli

first: Drice

last: Challal

first: Jocelyne

last: Boulay

first: Odil

last: Porrua

first: Jessie

last: Colin


title: Inference of transcription regulatory network in low phytic acid soybean seeds

city: Blacksburg

first: M.A. Saghai

last: Maroof

state: VA

address: 220 Ag Quad Ln

department: Crop & Soil Environmental Sciences

institute: Virginia Tech

summary: A dominant loss of function mutation in myo-inositol phosphate synthase gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified several transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling and seed dormancy. We validated the predicted regulatory network by comparing it with published regulatory interactions in Arabidopsis. Some regulatory interactions were found in the low phytic acid mutants but not in non-mutant plants. These findings provide important hypotheses on expression regulation of myo-inositol metabolism, and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.

overall_design:
Four soybean experimental lines designated as: (i) 3mlpa, (ii) 3MWT, (iii) 1mlpa, and (iv) 1MWT were used in this study. The lpa mutant line, ‘3mlpa’, carrying three mutations mips1/mrp-l/mrp-n, and its non-mutant sibling line with normal phytic acid, ‘3MWT’, were derived from crossing of ‘CX-1834’ (lpa line with two mpr-l/mrp-n mutations on soybean chromosomes 19 and 3, respectively) with ‘V99-5089’ (lpa line with single mips1 mutation) (Saghai Maroof et al., 2009). Another lpa line, ‘1mlpa’, carrying a single mips1 mutation on soybean chromosome 11, and its isogenic sibling line with normal phytic acid, ‘1MWT’, were derived from crossing of ‘Essex’ (a normal phytic acid line with no mutations) with V99-5089 (Saghai Maroof and Buss, 2008; Glover, 2011). Developing seeds were sampled in triplicates for each experimental soybean line based on seed lengths corresponding to 2-4 mm (stage1), 4-6 mm (stage2), 6-8 mm (stage3), 8-10 mm (stage4), and 10-12 mm (stage5), respectively. Samples were flash frozen using liquid nitrogen and stored at -70°C. High-quality total RNA (RIN 9-10) was extracted from frozen samples using RNeasy Plant Mini Kit, with on-column DNase digestion (QIAGEN). Total of 60 mRNA libraries were prepared from total RNA samples and sequenced as 100SE using HiSeq2000.

This study includes the re-analysis of all samples in GSE75575

first: M

last: Saghai Maroof

first: Neelam

middle: R

last: Redekar

first: Song

last: Li


title: RNA-seq of total RNA in various anchor away strains with and without the addition of rapamycin.

summary: we obtained RNA-seq profiles for Reb1 and Rap1-AA in presence and absence of rapamycin and in the absence of Rrp6. Additionally, we obtained RNA-seq profiles in a strain depleted for the protein Rap1 but expressing its DNA binding domain alone.

overall_design: investigation of RNA-seq profiles in Reb1- and Rap1-AA in the absence of Rrp6 and in the context of Rap1-DBD (dna binding domain) alone.


title: Histone deacetylase SRT2 mediates ethylene-induced transcriptional repression through interaction with ENAP1

city: Austin

first: FAN

last: ZHANG

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin

summary: We report that SRT2 can regulate plant growth in ethylene. We examined the RNA expression in srt1srt2 mutant (in Col background).

overall_design: RNA profiles of 3-day old srt1srt2 mutant (in Col background) were generated by sequencing, in 2 replications, using Illumina HiSeq 4000

first: Hong

last: Qiao

first: Fan

last: Zhang

first: Likai

last: Wang


title: Ozone-Induced Vascular Contractility and Pulmonary Injury are Differentially Impacted by Diets Enriched with Coconut Oil, Fish Oil, and Olive Oil

city: Research Triangle Park

first: Brian

middle: Norris

last: Chorley

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US Environmental Protection Agency

summary: Fish oil, olive oil, and coconut oil dietary supplementation have several cardioprotective benefits, but it is not established if they can protect against air pollution-induced adverse effects.  We hypothesized that these dietary supplements would attenuate ozone-induced systemic and pulmonary effects.  Male Wistar Kyoto rats were fed either a normal diet, or a diet enriched with fish, olive, or coconut oil starting at 4 weeks of age for 8 weeks.  Animals were then exposed to air or ozone (0.8 ppm), 4h/day for 2 consecutive days.  The fish oil diet completely abolished phenylephrine-induced vasoconstriction that was increased following ozone exposure in the animals fed all other diets. Only the fish oil diet increased baseline levels of bronchoalveolar lavage fluid (BALF) markers of lung injury and inflammation.  Ozone-induced pulmonary injury/inflammation were comparable in rats on normal, coconut oil, and olive oil diets with altered expression of markers in animals fed the fish oil diet. Fish oil, regardless of exposure, led to enlarged, foamy macrophages in the BALF that coincided with decreased mRNA expression of cholesterol transporters, cholesterol receptors, and nuclear receptors in the lung.  Serum miRNA profile was assessed using small RNA-sequencing in normal and fish oil groups and demonstrated marked depletion of a variety of miRNAs, several of which were of splenic origin. No ozone-specific changes were noted. Collectively, these data indicate that while fish oil offered protection from ozone-induced aortic vasoconstriction, it increased pulmonary injury/inflammation and impaired lipid transport mechanisms resulting in foamy macrophage accumulation, demonstrating the need to be cognizant of potential off-target pulmonary effects that might offset the overall benefit of this vasoprotective dietary supplement.

overall_design: Using an Illumina NextSeq sequencer, 24 samples were analyzed by small RNA-sequencing from the serum of 4 wk old male Wistar Kyoto rats. 4 conditions were assessed: control (normal diet), 6% by weight fish oil supplemented diet for 8 weeks, control diet plus 0.8 ppm ozone for 4h/day for 2 consecutive days, or fish oil diet plus 0.8 ppm ozone for 4h/day for 2 consecutive days. n=6 for each treatment group.

first: Gleta

last: Carswell

first: Gail

last: Nelson

first: Wan-Yun

last: Cheng

first: Andres

last: Henriquez

first: Myles

last: Hodge

first: Virginia

last: Bass

first: Judy

last: Richards

first: Mette

last: Schladweiler

first: Allen

last: Ledbetter

first: Haiyan

last: Tong

first: Kymberly

last: Gowdy

first: Urmila

middle: P

last: Kodavanti

first: Samantha

last: Snow


title: Mechanisms of tolerance and resistance to EGFR inhibition in lung cancer [RNA-seq]

first: Wen Cai

state: MASSACHUSETTS

address: 330 BROOKLINE AVENUE, CLS417

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary:
Purpose: Multiple mechanims have been proposed that lead to reduced effectiveness of EGFR tyrosine kinase inhibitors (TKIs) in lung cancer and yet resistance to osimertinib and gefitinib still remains a challenge in the clinic. The goals of this study are to identify key genes contributing to tolerance and resistance to EGFR inhibition.
Methods: mRNA profiles of gefitinib and osimertinib tolerant cells in PC9 and HCC827 cells were generated by deep sequencing using Illumina. In addition, mRNA profiles of cells (AALE, PC9 and HCC827) overexpressing with miR-147b or miR-21 and mRNA profiles of cells (H1975 and PC9ER) with miR-147b and miR-21 knocking down were generated by deep sequencing. The mappable reads were aligned to the human transcripts using Bowtie2 and gene abundance was estimated using RSEM.
Results: Upregulation of miR-147b and miR-21 expression is related to tolerance and resistance to gefitinib and osimertinib in lung cancer. The signaling pathways of transcripts by knocking down miR-147b or miR-21 in resistant cells (H1975 and PC9ER) and by overexpressing miR-147b or miR-21 in both sensistive cells (HCC827 and PC9) and immortalized lung epithelial cells (AALE) are consistent with the key signaling pathways shown in tolerant cells to gefitinib and osimertinib in HCC827 and PC9 cells (HCC827GTR/OTR vs HCC827 and PC9GTR/OTR vs PC9).
Conclusions: Our work identifies key signaling pathways that mediate EGFR-TKI tolerance and resistance in lung cancer. Our study provides potential targets to improve the efficacy of EGFR-TKIs therapy in cancer pagtients.

overall_design: mRNA profiles of gefitinib and osimertinib tolerant cells in PC9 and HCC827 cells were generated by deep sequencing using Illumina. In addition, mRNA profiles of cells (AALE, PC9 and HCC827) overexpressing miR-147b or miR-21 as well as cells (H1975 and PC9ER) with miR-147b and miR-21 knocking down were generated by deep sequencing.

first: Wencai

first: Frank

last: Slack


title: Identification of trancripts regulated by the Listeria monocytogenes two-component system regulator VirR by RNA-seq

first: Daniel

last: Grubaugh

address: 77 Ave Louis Pasteur

department: MBIB

institute: Harvard Medical School

summary: Here we use RNA sequencing to identify the regulon of the two-component system regulator VirR under normal growth conditions. We generated an in-frame deletion of the virR gene and extracted RNA from this strain grown to mid-log phase in LB as well as the 10403S parental strain. We then analyzed differential expression of transcripts between these two strains using RNA-seq

overall_design: Differential gene expression analysis of the Listeria monocytogenes virR deletion mutant relative to parental 10403S strain

first: Darren

last: Higgins


title: Human muscle miRNA sequencing at rest and after protein feeding and the relationship with muscle phenotype

city: Auckland

first: Cameron

last: Mitchell

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: The loss of muscle size, strength and quality with ageing, is a major determinant of morbidity and mortality in the elderly. The regulatory pathways that impact on the muscle phenotype include the translational regulation maintained by microRNAs (miRNA). Yet the miRNAs that are expressed in human skeletal muscle and whose expression levels correlate to muscle size, strength and quality are unknown. Here we used next-generation sequencing to characterise the expression profile of miRNAs in the m. vastus lateralis obtained by biopsy from middle-aged males (n=48; 50.0±4.3 years). Isokinetic strength testing and mid-thigh computed tomography was undertaken for muscle phenotype analysis. miR-486-5p accounted for 21% of the total miR sequence reads, with  miR-10b-5p, miR-133a-3p, and miR-22-3p accounting for a further 15%, 12% and 10% respectively. Isokinetic knee extension strength and muscle cross-sectional area were positively correlated with miR-100-5p, miR-99b-5p and miR-191-5p expression. Whilst muscle attenuation, reflective of myofiber lipid content was negatively correlated to let-7f-5p, miR-30d-5p and miR-125b-5p expression. In-silico analysis implicates miRNAs related to strength and muscle size in the regulation of mammalian target of rapamycin, whist miRNAs related to muscle attenuation may have potential roles controlling the transforming growth factor- β/SMAD3 pathway which regulated fibrosis, adipogenesis and lipid accumulation.

overall_design: Fasted muscle biopsies were collected from 49 healthy middle aged men from the vastus lateralis muscle. The men also underwent an isokinetic strength test of knee extension as 60degrees/s. Computed tomography imaging was also performed at 50% of femur length to identify muscle cross sectional area and attenuation. A subset of men ingested 20g of dairy protein and an additional biopsy was collected at 90 minutes (n=9) or 210 minutes afterwards (n=16).Musclel mRNA profiles  were generated by next generation sequencing using Illumina HiSeq 2500.

first: David

last: Cameron-Smith


title: Gene expression in a Streptomyces coelicolor strain defective in sco1423 encoding a polyprenol phosphate mannose synthase (Ppm1) compared to the complemented mutant and the wild type parent

city: York

first: Katherine

last: Newling

address: Wentworth Way

institute: University of York

summary: Polyprenol phosphate mannose (PPM) is a lipid linked sugar donor used by extra-cytoplasmic glycosyl tranferases in bacteria. PPM is synthesised by polyprenol phosphate mannose synthase, Ppm1, and in most Actinobacteria is used as the sugar donor for protein O-mannosyl transferase, Pmt, in protein glycosylation.  Ppm1 and Pmt have homologues in yeasts and humans, where they are required for protein O-mannosylation.  Actinobacteria also use PPM for lipoglycan biosynthesis. Here we show that ppm1 mutants of Streptomyces coelicolor have increased susceptibility to a number of antibiotics that target cell wall biosynthesis. The pmt mutants also have mildly increased antibiotic susceptibilities, in particular to -lactams and vancomycin. Despite normal induction of the vancomycin gene cluster, vanSRJKHAX, the pmt and ppm1 mutants remained highly vancomycin sensitive indicating that the mechanism of resistance is blocked post-transcriptionally. Differential RNA expression analysis indicated that catabolic pathways were downregulated and anabolic ones upregulated in the ppm1 mutant compared to the parent or complemented strains. Of note was the increase in expression of fatty acid biosynthetic genes in the ppm1- mutant. A change in lipid composition was confirmed using Raman spectroscopy, which showed that the ppm1- mutant had a greater relative proportion of unsaturated fatty acids compared to the parent or the complemented mutant. Taken together these data suggest that an inability to synthesise PPM (ppm1-) and loss of the glycoproteome (pmt- mutant) can detrimentally affect membrane or cell envelope functions leading to loss of intrinsic and, in the case of vancomycin, acquired antibiotic resistance.

overall_design: Three strains of Streptomyces coelicolor were used; J1929 (the parent strain), DT3017 (a ppm1- mutant derivative of J1929) and DT3017pDT16 (DT3017 containing a plasmid that expressed the wild type allele of ppm1). All three strains were grown in a fermenter and mRNA extracted for RNA sequencing. The  biomass from three biological replicates(r1, r2 and r3) of each strain grown in a fermenter was harvested at 6 hours post-inoculation and therefore during rapid vegetative growth.

first: Robert

last: Howlett

first: Nicholas

last: Read

first: Margaret

last: Smith


title: Astrocyte-specific transcriptome responses to chronic ethanol consumption

first: Emma

last: Erickson

address: 2500 Speedway MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

summary:
Purpose: Traditional whole-tissue sequencing approaches do not fully capture brain cell-type specific effects of chronic alcohol. Therefore, the purpose of this study was to identify the specific transcriptome alterations in astrocytes due to chronic alcohol.
Methods: We performed RNA-sequencing on astrocytes isolated from the prefrontal cortex (PFC) of C57BL/6J mice following chronic every-other-day alcohol consumption.
Results: Differential expression analysis revealed alcohol-induced gene expression changes unique to astrocytes that could not be identified using whole tissue homogenate analysis. Enrichment analysis revealed involvement of calcium-related signaling and regulation of extracellular matrix genes in the astrocyte response to alcohol abuse.
Conclusion: Our study presents the first focused analysis on the astrocyte transcriptome following chronic alcohol consumption, provides a framework for studying the functional response of astrocytes to alcohol and the possible astrocyte-specific effects of alcohol. In addition, our data represents a novel resource for groups interested in biological functions of astrocytes in the adult mouse PFC.

overall_design: Illumina RNA-sequencing of isolated astrocytes and total homogenate from PFC of mice following chronic alcohol consumption

middle: K

first: R

last: Mayfield

middle: A

last: Harris


title: Transcriptome analysis of HGC-27 after infection with Sendai virus

status: Public on Jan 09 2018

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

summary: To better understand the interactions between Hippo signaling and antiviral signaling at transcription level, a high-throughput RNA-seq technology was utilized in gastric cancer cells HGC-27  at 48 hours after Sendai virus (SeV) infection.

overall_design: The SeV-infected and non-infected cells were collected at 48 hours.  Each group had 2 biological replicates.

first: Jingmin

last: Guan

first: Zhaocai

last: Zhou


title: RNA-seq analysis of human expandable arterial endothelial precursors (eAEPs), expandable mesenchymal precursors (eMPs), and controls

city: Madison

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

summary: The following is an excerpt from the abstract of Miller et al. In this study, we find that two transcription factors, MYCN and SOX17, enable the indefinite propagation of human endothelial arterial precursors in vitro (“expandable arterial endothelial precursors,” eAEPs). Independent eAEP lines differ in their proclivity to undergo an endothelial-to-mesenchymal transition (EndoMT), a hallmark event in a broad array of vascular diseases and disorders. Some lines spontaneously become mesenchymal over time in culture, an effect exacerbated by inhibition of the fibroblast growth factor (FGF) receptor, while others do not readily convert. These distinctions were exploited to identify genes that correlate with resistance to an EndoMT and to elucidate transcriptional changes that underpin the transition. We believe the eAEPs may be useful not only as tractable tools for biological or pathological studies, but also as platforms for drug discovery.

overall_design: Examination of eAEPs and eMPs, their mature progeny, and control vascular cells by RNA-seq.


title: Protein expression landscape of mouse embryos during pre-implantation development

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

summary: Pre-implantation embryo development is an intricate and precisely regulated process orchestrated by maternally inherited proteins and newly synthesized proteins following zygotic genome activation. Although genomic and transcriptomic studies have enriched our understanding of genetic programs underlying this process, the protein expression landscape remains unexplored. Using quantitative mass spectrometry, we identified nearly 5000 proteins from 8000 mouse embryos of each stage (zygote, 2-cell, 4-cell, 8-cell, morula, blastocyst). We found that protein expression of zygote, morula and blastocyst show apparent difference from 2- to 8-cell embryos. Analysis of protein phosphorylation led to extraction of critical kinases and signal transduction pathways. We identified novel factors and proved that they play important roles in early embryo development. Combined analysis of transcriptomic and proteomic data reveals coordinated control of RNA degradation, transcription and translation, and identifies novel exon junction-derived peptides. Our study provides an invaluable resource for further mechanistic studies and suggests novel players governing pre-implantation embryo development.

overall_design: We performed RNA-sequencing of Rrp9 knock-down embryos in morula stage

first: Yawei

first: Xiaoyu

last: Liu

first: Bin

last: Tang

first: Chong

last: Li

first: Zhaohui

last: Kou

first: Lin

first: Wenqiang

first: You

last: Wu

first: Xiaochen

first: Jingyi

first: Yanhong

last: Zhao

first: Jiqing

last: Yin

first: Hong

last: Wang

first: She

last: Chen

first: Lujian

last: Liao