title: Crohn’s Disease Differentially Affects Region Specific Composition and Aerotolerance Profiles of Mucosally-Adherent Bacteria

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina, Chapel Hill

summary:
BACKGROUND: The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn’s disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen has been proposed as a contributor to CD dybiosis.
METHODS: 16S rRNA data was generated using colonic and ileal mucosal from patients with CD and without inflammatory bowel diseases (nonIBD). We developed profiles reflecting bacterial abundance within defined aerotolerance categories.  Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes.
RESULTS: Bacterial diversity decreased in CD in both ileum and colon. Aerotolerance profiles significantly differed between intestinal segments in nonIBD, though both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundance of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, though specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected pre-operative tissues of patients that developed disease recurrence across two independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera.
CONCLUSIONS: Mucosally adherent bacteria in colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.

overall_design: V1V2 regions of bacterial 16S rRNA was sequenced with the 27F-YM and 338R primers  from mucosal biopsies from the colon and terminal ileum of IBD patients from University of North Carolina at Chapel Hill (UNC) and Washingston University in St. Louis and from nonIBD patients from UNC.

first: Nur

middle: M

last: Shahir

first: Jeremy

middle: R

last: Wang

first: Elizabeth

last: Wolber

last: Schaner

first: Daniel

middle: N

last: Frank

first: Diana

last: Ir

first: Charles

middle: E

last: Robertson

last: Chaumont

first: Timothy

last: Sadiq

first: Mark

last: Koruda

first: Reza

last: Rahbar

first: Billy

last: Nix

first: Rodney

last: Newberry

first: Ryan

last: Sartor

first: Shehzad

last: Sheikh

first: Terrence


title: Regulatory constraint and selection during human knee evolution drive modern osteoarthritis risk

status: Public on Apr 16 2020

city: Cambridge

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

country: USA

institute: Harvard Univserity

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The evolution of human bipedalism exposed the knee to unique biomechanical challenges, requiring changes in knee anatomy giving rise to the modern-day configuration. In order to better understand the relationship between derived knee morphology and the genetic factors associated with osteoarthritis risk, we performed epigenetic profiling of murine forelimb/hindlimb growth plates to identify regulatory elements shaping formation of specific knee structures, identifying signals of ancient positive selection upon which more recent genetic drift overlaps risk-associated loci. Our functional analyses of an osteoarthritis-risk variant within a reproducibly-associated locus establishes a novel model for studying this degenerative disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of open chromatin regions in multiple different growth plates (proximal vs distal femur, tibia, humerus, radius) at E15.5

last: Richard

first: Zun

last: Liu

first: Jessica

last: Willen


title: MicroRNA Clustering Assists Processing  of Suboptimal MicroRNA Hairpins  Through the Action of the ERH Protein

first: Wenwen

last: Fang

state: Massachusetts

address: Room 625, 455 Main Street

institute: Whitehead Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Microprocessor initiates processing of microRNAs (miRNAs) from hairpin regions of primary transcripts (pri-miRNAs). Pri-miRNAs often contain multiple miRNA hairpins, and this clustered arrangement can assist processing of otherwise defective hairpins. We find that miR-451, which derives from a hairpin with a suboptimal terminal loop and a suboptimal stem length, accumulates to 40-fold higher levels when clustered with a helper hairpin. This phenomenon tolerates changes in hairpin order, linker lengths, and the identities of the helper hairpin, the recipient hairpin, the linker-sequence, and the RNA polymerase that transcribes the hairpins. It can act reciprocally and need not occur co-transcriptionally. It requires Microprocessor recognition of the helper hairpin and linkage of the two hairpins, yet predominantly manifests after helper-hairpin processing. It also requires Enhancer of Rudimentary Homology (ERH), which copurifies with Microprocessor and can dimerize and interact with other proteins that can dimerize, suggesting a model in which Microprocessor recruits another Microprocessor.

overall_design: In this study, ERH was knocked down using inducible CRISPR interference (CRISPRi) in K562-dCas9-KRAB cells; small-RNA sequencing was performed on both ERH knockdown and contorl (no doxycycline induction) cells.

first: David

last: Bartel


title: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [mouse RNAseq]

status: Public on Apr 15 2020

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

type: Expression profiling by high throughput sequencing

summary: Better understanding the progression of neural stem cells (NSCs) in the developing cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of neuropsychiat-ric disorders. Here we used RNA-sequencing, cell imaging and lineage tracing of mouse and human in vitro NSCs to model the generation of cortical neuronal fates. We show that con-served signaling mechanisms regulate the acute transition from proliferative NSCs to commit-ted glutamatergic excitatory neurons.  As human telencephalic NSCs developed from pluripo-tentcy in vitro, they first transitioned through organizer states that spatially pattern the cortex before generating glutamatergic precursor fates. NSCs derived from multiple human pluripotent lines varied in these early states leading differentially to dorsal or ventral telencephalic fates. This work furthers systematic analysis of the earliest patterning events that generate the major neuronal trajectories of the human telencephalon. The gene amplitudes for the GWCoGAPS patterns in this data can be found in the supplemental files.

overall_design: Of the 3 series in this super series, this covers the in vitro proliferation and differentiation of primary murine cortical neural precursor cells (NPCs) with varying exposure to FGF2 following passage (used in Figure 1).

first: N

last: Micali

first: S

middle: K

last: Kim

first: M

last: Diaz-Bustamante

first: G

last: Stein-O'Brien

last: Seo

first: J

middle: H

last: Shin

first: B

middle: G

last: Rash

last: Ma

first: Y

last: Wang

middle: A

last: Olivares

last: Arellano

first: K

last: Maynard

first: E

last: Fertig

first: A

middle: J

last: Cross

first: R

last: Burli

last: Brandon

first: D

last: Weinberger

last: Chenoweth

last: Hoeppner

last: Sestan

first: P

last: Rakic

first: C

last: McKay


title: RNA-seq of murine breast cancer cell line AT3 infected with F. nucleatum

status: Public on Apr 20 2020

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: Fusobacterium nucleatum (F. nucleatum) is implicated to exacerbate colorectal cancer. However, there is also evidence that the bacterium accumulates on other cancer types such as breast cancer. In order to better understand the transcriptional response of breast cancer cells to infection with F. nucleatum, we performed RNA-seq of the murine breast cancer cell AT3 with F. nucleatum.

overall_design: Cells were seeded 2 days prior to infection and from this point on kept in an oxygen-controlled incubator (1% oxygen). The DMEM media was exchanged after 24h not containing otherwise used antibiotic mix. On the second day, AT3 cells were infected with F. nucleatum (m.o.i. of 10). Three biological replicates of infected and mock control samples were taken 24h after infection.

first: Lishay

last: Parhi

first: Tamar

last: Alon

first: Asaf

last: Sol

first: Deborah

last: Nejman

first: Amjad

last: Shhadeh

first: Tanya

last: Fainsod-Levi

first: Olga

last: Yajuk

first: Batya

last: Isaacson

first: Jawad

last: Abed

first: Naseem

last: Maalouf

first: Aviram

last: Nissan

first: Judith

last: Sandbank

first: Einav

last: Yehuda-Shnaidman

first: Jörg

last: Vogel

first: Ofer

last: Mandelboim

first: Zvi

last: Granot

first: Ravid

last: Straussman

first: Gilad

last: Bachrach


title: Defining the design principles of postnatal tissue growth

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

summary: SMARTseq2 scRNAseq of interfollicular epidermis basal cells at P20

overall_design: Examination of transcriptional heterogeneity and differentiation

first: Sophie

last: Dekoninck

first: Alejandro

last: Sifrim

first: Milan

last: Malfait

first: Thierry

last: Voet


title: RNA-seq and Ribo-seq of WT and METTL5 KO mECS.

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

summary: Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalysing these modifications, their substrates and biological functions remains vague. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyses m6A in 18S rRNA at position A1832. We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a changes gene expression, decrease in translation rate, spontaneous loss of pluripotency and compromised differentiation potential. Mice lacking METTL5 recapitulate symptoms of patients with METTL5 mutations, thereby providing a new mouse disease model. Overall, our work  highlights the importance of m6A in rRNA in stemness, differentiation, development and diseases.

overall_design: RNA and Riob-seq of WT and METTL5 KO mESC in biological replicates.

first: Valentina

middle: V

last: Ignatova

first: Paul

last: Stolz

first: Steffen

last: Kaiser

first: Tobias

last: Gustafsson

first: Palma

last: Lastres

first: Adrián

last: Sanz-Moreno

first: Yi-Li

last: Cho

first: Oana

last: Amarie

first: Antonio

last: Aguilar-Pimentel

first: Tanja

last: Klein-Rodewald

first: Julia

last: Calzada-Wack

first: Lore

last: Becker

first: Susan

last: Marschall

first: Markus

last: Kraiger

first: Lillian

last: Garrett

first: Claudia

last: Seisenberger

first: Sabine

last: Hölter

first: Kayla

last: Borland

first: Erik

last: De Logt

first: Pascal

middle: W

last: Jansen

first: Marijke

middle: P

last: Baltissen

first: Magdalena

last: Valenta

first: Michiel

last: Vermeulen

first: Wolfgang

last: Wurst

first: Valerie

last: Gailus-Durner

first: Helmut

last: Fuchs

first: Martin

last: de Angelis

first: Stefanie

last: Kellner

first: Sebastian

last: Bultmann

first: Robert

last: Schneider


title: A mechanism for microRNA arm switching regulated by uridylation [AQ-seq]

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Strand selection is a critical step in microRNA (miRNA) biogenesis. Although the dominant strand may alter depending on cellular contexts, the molecular mechanism and physiological significance of such alternative strand selection (or “arm switching”) remain elusive. Here we find miR-324 as one of the strongly regulated miRNAs by arm switching, and identify terminal uridylyl transferases TUT4 and TUT7 as the key regulators. Uridylation of pre-miR-324 by TUT4/7 re-positions DICER on the pre-miRNA and shifts the cleavage site. This alternative processing produces a duplex with a different terminus, from which the 3′ strand (3p) is selected instead of the 5′ strand (5p). In glioblastoma, the TUT4/7 and 3p levels are upregulated while the 5p level is reduced. Manipulation of the strand ratio is sufficient to impair glioblastoma cell proliferation. This study uncovers a role of uridylation as a molecular switch in alternative strand selection and implicates its therapeutic potential.

overall_design: AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs from fifteen mouse tissues (Mouse Total RNA Master Panel; Takara) as described in our previous study (Kim et al., 2019).

first: Jimi

first: Sha

last: Yu

first: Y

middle: Y

last: Lee

first: Junseong

last: Park

first: R

last: Choi

first: S

last: Yoon

last: Kang

first: V


title: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [human RNAseq #2]

first: Carlo

last: Colantuoni

overall_design: Of the 3 series in this super series, this covers RNAseq of 2 replicate iPSC lines from each of 3 new donors during 8, 17, 30 and 32 days of neural differentiation (used in Figure 5)

first: N

last: Micali

first: M

last: Diaz-Bustamante

first: G

last: Stein-O'Brien

last: Seo

first: J

last: Shin

first: B

last: Rash

last: Ma

last: Wang

last: Olivares

last: Arellano

first: K

last: Maynard

first: E

last: Fertig

first: A

last: Cross

last: Burli

last: Brandon

first: D

last: Weinberger

last: Chenoweth

last: Hoeppner

last: Sestan

first: P

last: Rakic

first: C

last: McKay


title: A mechanism for microRNA arm switching regulated by uridylation [RNA-seq]

first: Haedong

last: Kim

overall_design: RNA-seq libraries for DNA nanoball sequencing were generated using total RNAs isolated from cells transfected with control miRNA or miR-324 duplexes.

first: Jimi

first: Sha

last: Yu

first: Y

last: Lee

last: Park

last: Choi

last: Yoon

last: Kang


title: Expression data from treatment-induced senescence in mouse Emu-myc B-cell lymphoma model.

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

summary:
Treatment induced senescence (TIS) is a terminal cell cycle arrest program, increasingly recognized as a tumor suppressor mechanism complementing apoptosis in response to standard chemotherapy regimens. In particular cells with blocked apoptotic pathways rely on senescence as the only remaining failsafe mechanism to keep the neoplastic growth in check. However, little is known about biological properties, long-term fate of senescent tumor cells and their impact on the microenvironment.
We used global gene expression profiling by microarrays to gain insight in the molecular programme underlying the treatment-induced senescence in Emu-myc transgenic B-cell lymphomas (apoptosis protected by Bcl2 overexpression), which robustly enter senescence in response to DNA-damaging anticancer agents such as Adriamycin (ADR).

overall_design: Primary lymphoma cells isolated from lymph nodes of Emu-Myc transgenic mice were used. In this model the the c-Myc oncogene is constitutively expressed in the cells of B-cell lineage, leading to spontaneous development of aggressive B-cell lymphomas, resembling Burkitt lymphoma in humans. In order to bring up the senescence as the main failsafe mechanism, primary lymphoma cells are protected from apoptosis by retroviral over-expression of a strong antiapoptotic protein Bcl2. These cells (Myc;Bcl2) massively undergo senescence upon DNA-damaging treatment. Adriamycin (ADR) is a cytostatic drug, used as a standard part of several lymphoma treatment regimens. In this study, transcriptional profiles of matched pairs of untreated vs. 5 days ADR treated Myc;Bcl2 lymphomas were analysed.

first: Clemens

last: Schmitt

first: Kolja

last: Schleich

first: Michael

last: Hummel

first: Dido

last: Lenze

first: Jan

last: Dörr

first: Yong


title: KSHV Requires vCyc to Overcome Replicative Senescence in Primary Human Lymphatic Endothelial Cells

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: We performed high throughput RNA-sequencing on KSHV-infected blood and lymphatic HMVECs at 48hpi as well as WTKSHV- or KSHVDvcyc-infected lymphatic HMVECS at 1wpi to identify differences in gene expression induced by KSHV in these two cell types and gene expression changes that require the KSHV latent gene vcyclin.

overall_design: RNA was isolated from 2 blood-specific HMVEC cell lines and 2 lymphatic-specific HMVEC cell lines 3 separate times each

last: Lagunoff


title: Sodium chloride generates anti-inflammatory Th17 cell responses but amplifies Th17 cell pathogenicity in pro-inflammatory cytokine microenvironments

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: T helper cells integrate signals from their microenvironment to acquire distinct specialization programs for efficient clearance of diverse pathogens or for immunotolerance. Ionic signals have recently been demonstrated to affect T cell polarization and function. Sodium chloride (NaCl) was proposed to accumulate in peripheral tissues upon dietary intake and to promote autoimmunity via the Th17 cell axis. Here we demonstrate that high NaCl conditions induced a stable, pathogen-specific, anti-inflammatory Th17 cell fate in human T cells in vitro. The p38/MAPK pathway, involving NFAT5 and SGK1, regulated FoxP3 and interleukin (IL)-17-expression in high-NaCl conditions. The NaCl-induced acquisition of an anti-inflammatory Th17 cell fate was confirmed in vivo in an experimental autoimmune encephalomyelitis (EAE) mouse model, which demonstrated strongly reduced disease symptoms upon transfer of T cells polarized in high NaCl conditions. However, NaCl was coopted to promote murine and human Th17 cell pathogenicity, if T cell stimulation occurred in a pro-inflammatory and TGF--low cytokine microenvironment. Taken together, our findings reveal a context-dependent, dichotomous role for NaCl in shaping Th17 cell pathogenicity. NaCl might therefore prove beneficial for the treatment of chronic inflammatory diseases in combination with cytokine-blocking drugs.

overall_design: Th17 cells were isolated ex vivo and stimulated for 48 hours with CD3 and CD28 mAbs for a total culture time of 5 days in the presence of low and high NaCl concentrations.

first: Julia

last: Matthias

first: Sylvia

last: Heink

first: Felix

last: Picard

last: Zeiträg

first: Anna

last: Kolz

first: Ying-Yin

last: Chao

first: Dominik

last: Soll

first: Elke

last: Glasmacher

first: Ilse

last: Jacobsen

first: Thomas

last: Riedel

first: Anneli

last: Peters

first: Dirk

last: Baumjohann

first: Magdalena

last: Huber

last: Korn

first: Christina

last: Zielinski


title: A mechanism for microRNA arm switching regulated by uridylation

first: Haedong

last: Kim

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

overall_design: Refer to individual Series


title: Effect of cannabinoids on microRNA regulation of acute lung injury

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

summary: We used microRNA microarrays to identify dysregulated microRNAs in mononuclear cells isolated from SEB-injured mice treated with Vehicle or THC

overall_design: Mononuclear cells were isolatef by ficoll from inflammed lungs 72 hours post SEB injury from SEB+THC mice or SEB+Veh

first: Amira

last: Mohammed

first: Hasan

last: Alghetaa

first: Prakash

middle: S


title: ClpV3 affects pathogenicity in Pseudomonas aeruginosa

city: Winnipeg

first: Kangmin

last: Duan

state: MB

address: 66 Chancellors Cir

country: Canada

institute: University of Manitoba

summary: ClpV3 is a cytoplasmic AAA+ ATPase protein and is an essential component of H3-T6SS in Pseudomonas aeruginosa. Here, we report that an H3-T6SS deletion mutant PAO1(ΔclpV3) significantly affected the virulence-related phenotypes including pyocyanin production, biofilm formation, proteolytic activity and motilities. Most interestingly, the expression of T3SS genes was markedly affected, indicating a strong link between H3-T6SS and T3SS. RNA-Sequencing was performed to globally identify the genes differentially expressed when H3-T6SS was inactivated and the results obtained could be well correlated to the observed phenotypes.

overall_design: Gene expression was compared between wild-type P. aeruginosa PAO1 and clpV3 deletion mutant.

first: K


title: Photoperiodic spectral tuning of carbon metabolism in heterotrophic marine flavobacteria

city: Taichung

first: Asif

last: Hameed

state: Taichung

address: Kuo Kuang Rd.

department: Soil and Environmental Sciences

country: Taiwan

institute: National Chung Hsing University

summary: Influence of the constant full-spectrum light and short-to-long wavelengths of the visible spectrum (red, green and blue lights) and the significance of 12 h photoperiod was tested on heterotrophic marine flavobacteria Siansivirga zeaxanthinifaciens CC-SAMT-1T. RNA-seq analysis revealed remarkable qualitative and quantitative variations in terms of gene expression in CC-SAMT-1T with respect to incident lights. While blue light illumination stimulated expression of genes involved in inorganic carbon metabolism, green˗red lights largely upregulated the genes participating in high-molecular-weight (HMW) organic carbon metabolism. Constant full-spectrum light also displayed the upregulation of genes involved in the metabolism of HMW organic carbon. Thus, the short-to-long wavelengths of visible light and the 12 h photoperiod most likely to play a key role in the marine carbon cycle by tuning heterotrophic bacterial metabolism.

overall_design: Philips MASTER TL-D De Luxe 18W/965 fluorescent lamps were used as a source of full-spectrum light. Red (620–630 nm), green (520–535 nm) and blue (465–485 nm) light emitting diodes (Cree XLamp XP-E2) were used to assess the impact of short-to-long wavelengths. Lamps were installed inside the temperature-controlled orbital shaker incubator. Genome-wide expression was investigated in cell samples cultured under 36 h full-spectrum light (L36.1 and L36.2) illumination. Cell samples cultured under 36 h constant darkness (D36.1 and D36.2) served as controls. Bacterial cells cultured under darkness for 24 h were exposed to 12 h of red, green and blue light illuminations (D24R12, D24G12 and D24B12, respectively) and subjected to genome-wide expression analysis with reference to 36 h dark-incubated cell sample (D36). Analysis were done in duplicates for each sample.

first: Wei-An

last: Lai

first: Mariyam

last: Shahina

first: Paul

last: Stothard

first: Li-Sen

last: Young

first: Shih-Yao

last: Lin

first: Kandikere

last: Sridhar

first: Chiu-Chung


title: The role of CIC in brain development and neuronal differentiation

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College


title: ZAKα Recognizes Stalled Ribosomes through Partially Redundant Sensor Domains

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Impairment of ribosome function activates the MAPKKK ZAK, leading to activation of mitogen-activated protein (MAP) kinases p38 and JNK and inflammatory signaling. The mechanistic basis for activation of this ribotoxic stress response (RSR) re-mains completely obscure. We show that the long isoform of ZAK (ZAKα) directly associates with ribosomes by inserting its flexible C terminus into the ribosomal intersubunit space. Here, ZAKα binds helix14 of 18S ribosomal RNA (rRNA). An adjacent domainin ZAKa also probes the ribosome, and together, these sensor domains are critically required for RSR activation after inhibition of both the E-site, the peptidyl transferase center (PTC), and ribotoxinaction. Finally, we show that ablation of the RSR response leads to organismal phenotypes and decreased lifespan in the nematode Caenorhabditis elegans (C. elegans). Our findings yield mechanistic insight into how cells detect ribotoxic stress and provide experimental in vivo evidence for its physiological importance.

overall_design: 2 samples from Zakα pull-down experiments.

first: Anna

last: Constance Vind

first: Goda

last: Snieckute

first: Melanie

last: Blasius

first: Christopher

last: Tiedje

first: Dorte

last: Breinholdt Bekker-Jensen

first: Kasper

last: Langebjerg Andersen

first: Cathrine

last: Nordgaard

first: Maxim

last: Tollenaere

first: Anders

last: Henrik Lund

first: Jesper

last: Velgaard Olsen

first: Henrik

last: Nielsen

first: Simon

last: Bekker-Jensen


title: Integrative analysis of reference epigenomes in rice [BiSulfite-seq]

status: Public on Apr 25 2020

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

overall_design: Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues

first: Lun

last: Zhao

first: Qing

last: Zhang


title: RNA-Seq of CD8+ T cell subsets in B16-GP33 tumor

city: San diego

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

summary: Tissue-resident memory CD8+ T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. While the relevance of Trm in diverse diseases ranging from infection to cancer is appreciated, the development and functional heterogeneity of Trm remain poorly understood. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8+ T cells, including a Blimp1hiId3lo tissue-resident effector cell population most prominent in the early phase of acute viral and bacterial infections, and a molecularly distinct Blimp1loId3hi tissue-resident memory population that subsequently accumulated at later infection timepoints. These distinct Trm populations where characterized by unique transcriptional programs including differential roles for transcriptional regulators Blimp1, T-bet, Id2, and Id3 in supporting and maintaining intestinal Trm heterogeneity during infection. Extending our analysis to malignant tissue, we also identified discrete populations of effector-like and memory-like CD8+ T cell populations with tissue-resident gene-expression signatures within tumors that shared features of terminally-exhausted and progenitor-exhausted T cells, respectively. Clarification of CD8+ T cell ontogeny and heterogeneity in non-lymphoid tissues holds broad implications for enhancing vaccination and immunotherapy approaches.

overall_design: 10 samples, 2 replicates each, Spleen and TIL CD8+ T cell subsets

first: K

last: Omilusik

first: J

last: Milner

first: A


title: Single Cell RNA-Seq of CD8+ T cell subsets responding to tumor

overall_design: 16 samples, 2 replicates each, Single cell RNA sequencing was performed on CD8 T cells isolated from the spleen or B16 tumors at 1 timepoint


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

overall_design: 14 samples, 1-2 replicates each, Day 7 or Day 35 LCMV infection CD8+ T cell subsets


title: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [human RNAseq #1]

first: Carlo

last: Colantuoni

overall_design: Of the 3 series in this super series, this covers the passaging of human H9 ESC-derived neural stem cells (hNSCs) in vitro with varying exposure to FGF2 during final passage (all time points are 6 days after final passage - used in Figures 3 & 4).

first: N

last: Micali

first: S

last: Kim

first: M

last: Diaz-Bustamante

first: G

last: Stein-O'Brien

last: Seo

last: Shin

first: B

last: Rash

last: Ma

first: Y

last: Wang

last: Olivares

last: Arellano

last: Maynard

first: E

last: Fertig

last: Cross

first: R

last: Burli

last: Brandon

first: D

last: Weinberger

last: Chenoweth

last: Hoeppner

last: Sestan

first: P

last: Rakic

first: C

last: McKay


title: Type 1 dendritic cells are dysregulated systemically early in preinvasive carcinogenesis.

city: Philadelphia

first: Jeffrey

middle: Howard

last: Lin

state: PA

address: 3400 Civic Center Blvd

department: Immunology Graduate Group

institute: University of Pennsylvania


title: The role of CIC in brain development and neuronal differentiation (RNA-Seq)

first: Jihye

last: Paik

summary: RNA_seq analysis for Nes Cre;CIC+/+ vs.Nes Cre;CICflox/flox mouse brain

overall_design: Brain mRNA profiles of postnatal 1 day of CIC WT and CIC KO brains

first: Inah

last: Hwang


title: mTOR Inhibition Enables Long-Term Expansion of Human Neonatal Tracheal Aspirate-Derived Airway Basal Stem Cells

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Bronchopulmonary dysplasia remains one of the most common complication of prematurity, despite significant improvements in perinatal care.  Functional modeling of human lung development and disease, like BPD, is limited by our ability to access the lung and to maintain relevant stem cell populations in culture. Single cell RNA-sequencing confirmed the presence of epithelial cells in tracheal aspirates obtained from intubated neonates.  Using combined SMAD signaling inhibition and mTOR inhibition neonatal tracheal-aspirate derived (nTAD) basal stem cells can be expanded long-term and retain the ability to differentiate into pseudo-stratified airway epithelium.  Conclusions: Our data demonstrate that neonatal tracheal aspirate-derived epithelial cells can provide a novel ex vivo human cellular model to study neonatal lung development and disease.

overall_design: Basal Stem Cells cultured with or without Rapamycin were sequenced in duplicates to compare the effects of mTOR inhibition

first: Paul

last: Lerou

first: Jujie

last: Lu


title: Inguinal LN CD11c SubQ KPC

summary: Bulk RNA sequencing of sorted inguinal LN CD11c+ cells from healthy mice and mice subcutaneously implanted with KPC tumor both untreated and treated with CD40 agonist.

overall_design: n=4 per group. Groups: Healthy, Tumor-Draining LN, Tumor-Draining LN CD40 agonist

first: Robert

last: Vonderheide


title: Pathogenic Stem Cell Variation in Chronic Lung Disease

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Chronic obstructive lung disease is the third leading cause of death in the United States. We have identified and cloned the stem cell variants from patients lung samples using our cloning method. These stem cells functions are explored using combinations of microarray, single cell RNA-seq, ChIP-seq and in vivo assays.

overall_design: We have cultured distal lung stem cells colony on 3T3 feeder layer. The stem cells are injected into mouse for the in vivo differentiation and mouse xenograft is used to examine the functional aspect of the stem cells. Microarray is performed for the stem cells and cells from the xenograft (Xeno) samples using Affymetrix human exon 1.0 st array chip.

first: Wei

last: Rao

first: Shan

last: Wang

first: Rajasekaran

last: Mahalingam

first: Wa

last: Xian


title: Inguinal LN cDC1 SubQ KPC

summary: Bulk RNA sequencing of sorted inguinal LN cDC1s from healthy mice and mice subcutaneously implanted with KPC tumor both untreated and treated with CD40 agonist.

overall_design: n=3 per group. Groups: NoTumorNoCD40, NoTumorCD40, TumorNoCD40, TumorCD40


title: The histone-like protein AlgP regulon is distinct in nonmucoid and mucoid Pseudomonas aeruginosa and does not include alginate biosynthesis genes

status: Public on Apr 14 2020

city: Atlanta

first: Joanna

middle: B

last: Goldberg

state: Georgia

address: O. Wayne Rollins Research Center, Room 3009 1510 Clifton Road NE

institute: Emory University

summary: Here we show that deletion of AlgP in mucoid P. aeruginosa strain does not result in nonmucoid phenotype or reduced alginate production. We also show that there is no significant overlap in the AlgP regulon between mucoid and nonmucoid P. aeruginosa strains.

overall_design: The transcriptome of AlgP+/-mucoid and AlgP+/- nonmucoid P. aeruginosa was analyzed using RNA-seq with two biological replicates each.

first: Ashley

last: Cross

first: Erika

last: Csatary

first: Vishnu

last: Raghuram

first: Frances

middle: L

last: Diggle

first: Marvin

last: Whiteley

first: William

middle: M

last: Wuest


title: miRNA Microarray of cholesterol loaded and cholesterol depleted THP-1 macrophages

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

summary:
THP-1 macrophages were treated with acLDL to load with cholesterol
THP-1 macrophages were treated with statin to deplete cholesterol

overall_design: SABiosciences miRNA PCR Assay for THP-1 macrophages treated with acLDL or statin.

first: Katey

last: Rayner

first: Kathryn

last: Moore


title: 5-methylcytosine modification and the ALYREF reader protein promote retrovirus replication

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: The 5-methylcytosine (m5C) modification is present at appreciable amounts in the mammalian transcriptome, but its precise location and function is still poorly understood. Here, we identify high m5C levels and map their locations in a model retrovirus, the murine leukemia virus, and show that the ALYREF m5C reader protein regulates viral replication. Our results reveal a single-nucleotide m5C profile in a virus and its function in a eukaryotic mRNA.

sample_organism:
Mus musculus
Murine leukemia virus

platform_organism:
Mus musculus
Murine leukemia virus

overall_design: RNA bisulfite sequencing of murine leukemia virus (MLV) virions and infected mouse fibroblast, two biological replicate samples for each.

first: Matthew

last: Eckwahl

first: Ruyi

last: Xu

first: Julia

last: Michalkiewicz

first: Wen

last: Zhang

first: Pooja

last: Patel

first: Zhen

last: Cai


title: METTL3 and N6-methyladenosine Promotes Homologous Recombination Mediated Repair of DSBs by Facilitating R-loop Formation [other]

city: GuangZhou

first: Zhang

middle: Can

last: Feng

address: Graduate school, building 493, 135 xingang west road

institute: Sun Yat-sen University

summary: Examination of R-loop formation at I-PpoI cutting site (28S rDNA and DAB1) and other uncut genome in NC or siMETTL3 transferred HEK293T with or without I-PpoI cutting

overall_design: R-loop were isolated form NC or siMETTL3 transferred HEK293T with or without I-PpoI cutting using S9.6 antibody for paired-end sequening on HiseqXten

middle: C

first: Chen

last: Ping

first: Jiang

last: Ao

first: Peng

last: Di


title: METTL3 and N6-methyladenosine Promotes Homologous Recombination Mediated Repair of DSBs by Facilitating R-loop Formation

overall_design: Refer to individual Series


title: The role of CIC in brain development and neuronal differentiation (ChIP-Seq)

first: Jihye

last: Paik

summary: ChIP-seq analysis of CIC and H3K27Ac in the developing mouse brain

overall_design: ChIP of CIC in the mouse brain and ChIP of H3K27Ac in the CIC WT and CIC KO brain

first: Inah

last: Hwang


title: Culturing of Daoy cells in astrocyte conditioned media

city: Milwaukee

first: Ramani

last: Ramchandran

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Astrocytes are important cells within the medulloblastoma microenvironment. Therefore, we assessed how astrocyte secreted factors may alter Daoy (human MB cell line; ATCC HTB-186) cell gene expression.

overall_design: Astrocytes were isolated from the hippocampi of 1-2 day old Sprague Dawley rat pups and cultured in vitro. Supernatent, or astrocyte conditioned media (ACM) was collected from the astrocyte cultures every 2-3 days. This supernatent was used to culture Daoy (ATCC HTB-186) cells for 1 (P1) and 3 (P3)passages. Each passage was cultured for 48 h. For control samples, Daoy cells were cultured in the same manner but using full DMEM (DM) media. Three independant experiments were performed.

first: Emily

last: Gronseth


title: Role of BAP1 in pancreatic cancer (ChIP-seq Human)

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary: We found that BAP1 (BRCA1 Associated Protein-1) shows loss of heterozygosity in over 25% of pancreatic cancer patients and functions as tumor suppressor. Conditional deletion of Bap1 in murine pancreas led to genomic instability, accumulation of DNA damage, and an inflammatory response that evolved to pancreatitis with full penetrance. Concomitant expression of oncogenic KrasG12D led to malignant transformation and development of invasive and metastatic pancreatic cancer. At the molecular level, BAP1 maintains the integrity of the exocrine pancreas by regulating genomic stability and its loss confers sensitivity to radio- and platinum-based therapies.

overall_design: PANC1 and HPDE cells were treated with 10Gy of IR. One hour later cells were fixed and analyzed by ChIP-seq for BAP1 and H2AK119ub.

first: Yan

last: Kai


title: RNA sequencing results of cell migration and adhesion induced by modulated expression of paraspeckle protein PSPC1

city: Taipei, Taiwan

first: Tang

middle: K

last: Tang

state: Taiwan

address: 28 Sec. 2, Academia Rd. Nankang, Taipei 115

department: Institute of biomedical science

institute: Academia Sinica

summary: We found that PSPC1 potent facilitates HCC cells motility, adhesion, cytoskeleton assembling as well as cell spreading. To elucidate underlying mechanisms regulation by PSPC1, we performed the RNA-seq analysis of overexpression of PSPC1 in SK-Hep1 cell line and knockdown od PSPC1 in Hep3B cell line to evaluate its effects on gene expression.

overall_design: Gene expression profiles of PSPC1 with modulated knockdown in Hep3B cells were generated by Illumna RNA sequencing and compared to profiles derived from mock control cells.

first: Hsin-Wei

last: Jen

first: Yuh-shan

last: Jou


title: Role of BAP1 in pancreatic cancer (PrimeView)

summary:
Transcriptional profile of PANC1 cells with CRISPR/Cas9 mediated deletion of BAP1
We found that BAP1 (BRCA1 Associated Protein-1) shows loss of heterozygosity in over 25% of pancreatic cancer patients and functions as tumor suppressor. Conditional deletion of Bap1 in murine pancreas led to genomic instability, accumulation of DNA damage, and an inflammatory response that evolved to pancreatitis with full penetrance. Concomitant expression of oncogenic KrasG12D led to malignant transformation and development of invasive and metastatic pancreatic cancer. At the molecular level, BAP1 maintains the integrity of the exocrine pancreas by regulating genome stability and its loss confers sensitivity to radio- and platinum-based therapies.

overall_design: PANC1 cells with CRISPR/Cas9 mediated deletion of BAP1 were exposed to 10Gy of IR. RNA was collected 3 days later. Gene expression was analyzed with the Affymetrix platform to identify differentially regulated genes.


title: Peri-pancreatic LN cDC1 KPC

first: Jeffrey

last: Lin

summary: Bulk RNA sequencing of sorted peri-pancreatic LN cDC1s from different stages of neoplastic development in the KPC mouse model of pancreatic adenocarcinoma.

overall_design: n=3 per group. Groups: healthy, PanIN-draining, tumor-draining.

middle: H

first: Robert

last: Vonderheide


title: Role of BAP1 in pancreatic cancer

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


title: Role of BAP1 in pancreatic cancer (MoGene-2_0)

summary:
Transcriptional profile of murine Bap1 null pancreatic cancer cell lines
We found that BAP1 (BRCA1 Associated Protein-1) shows loss of heterozygosity in over 25% of pancreatic cancer patients and functions as tumor suppressor. Conditional deletion of Bap1 in murine pancreas led to genomic instability, accumulation of DNA damage, and an inflammatory response that evolved to pancreatitis with full penetrance. Concomitant expression of oncogenic KrasG12D led to malignant transformation and development of invasive and metastatic pancreatic cancer. At the molecular level, BAP1 maintains the integrity of the exocrine pancreas by regulating genome stability and its loss confers sensitivity to radio- and platinum-based therapies

overall_design: Wild type and Bap1 null cell lines were established from murine pancreata in the context of oncogenic Kras. Gene expression profile using the Affymetrix platform was performed to identify differentially expressed genes.


title: The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

status: Public on Apr 13 2020

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

summary: We conducted reduced representation bisulfite sequencing (RRBS) on myonuclei and interstitial nuclei and observed stark differences in methylation patterns during adaptation

overall_design: Examination of DNA methylation in myonuclei and interstitial cells of sham and 3-day overloaded mice

first: Ferdinand

last: von Walden


title: Dissection of the 4D chromatin structure of the alpha-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution [CITE-seq]

city: Oxford

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: Precise gene expression patterns during mammalian development are controlled by regulatory elements in the non-coding genome. Active enhancer elements interact with gene promoters within Topologically Associating Domains (TADs). However, the precise relationships between chromatin accessibility, nuclear architecture and gene activation are not completely understood. Here, we present Tiled-C, a new Chromosome Conformation Capture (3C) technology, which allows for the generation of high-resolution contact matrices of loci of interest at unprecedented depth, and which can be optimized for as few as 2,000 cells of input material. We have used this approach to study the chromatin architecture of the mouse alpha-globin locus through in vivo erythroid differentiation. Integrated analysis of matched chromatin accessibility and single-cell expression data shows that the alpha-globin locus lies within a pre-existing TAD, which is established prior to activation of the domain. During differentiation, this TAD undergoes further sub-compartmentalization as regulatory elements gradually become accessible and specific interactions between enhancers and promoters are formed. As these chromatin changes develop, gene expression is progressively upregulated. Our findings demonstrate that chromatin architecture and gene activation are tightly linked during development and provide insights into the distinct mechanisms contributing to the establishment of tissue-specific chromatin structures.

overall_design: single-cell RNA-seq was performed on fetal liver cells from e13.5 C57BL/6 mouse embryos. Barcoded antibodies were added to simultaneously determine cellular immunophenotype (CITE-seq).

first: Douglas

middle: R

last: Higgs


title: The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain

city: St. Louis

first: Jared

last: Goodman

state: MO

address: 4523 Clayton Ave

institute: Washington University in St. Louis School of Medicine

summary: The development and function of the brain require tight control of gene expression. Genome architecture is thought to play a critical regulatory role in gene expression, but the mechanisms governing genome architecture in the brain in vivo remain poorly understood. Here, we report that conditional knockout of the chromatin remodeling enzyme Chd4 in granule neurons of the mouse cerebellum increases accessibility of gene regulatory sites genome-wide in vivo. Conditional knockout of Chd4 promotes recruitment of the architectural protein complex cohesin preferentially to gene enhancers in granule neurons in vivo. Importantly, in vivo profiling of genome architecture reveals that conditional knockout of Chd4 strengthens interactions among developmentally repressed contact domains as well as genomic loops in a manner that tightly correlates with increased accessibility, enhancer activity, and cohesin occupancy at these sites. Collectively, our findings define a role for chromatin remodeling in the control of genome architecture organization in the mammalian brain.

overall_design: Cerebella were dissected from P22 mice. For ChIP-seq, protein-DNA complexes were isolated from sonicated lysates. For Hi-C, nuclei were digested and blunt-end ligated in the presence of a biotinylated nucleotide. Ligation complexes were then isolated from sonicated DNA by streptavidin pull-down. For DNaseI-seq, nuclei were digested with DNaseI, then DNA under 500bp were selected. For nuclear RNA-seq, total RNA was extracted from nuclei.

first: Tomoko

last: Yamada

first: Yue

last: Yang

first: Lingchun

last: Kong

first: Dennis

last: Wu

first: Guoyan

last: Zhao

first: Harrison

last: Gabel

first: Azad

last: Bonni


city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary: We used eXcision Repair-sequencing (XR-seq) to map UV induced damage in U2OS cells and in U2OS cells in which CSA or UVSSA genes were knocked out. Complementation of UVSSA knockout with WT or mutant proteins shows UVSSA is a core component of human transcription coupled repair.

overall_design: We performed CPD XR-seq in U2OS WT, UVSSA-KO and CSA-KO, UVSSA-KO+GFP-UVSSA WT, UVSSA-KO+GFP-UVVSA-CIR, UVSSA-KO+GFP-UVVSA-TIR cells treated with UV irradiation (20J/m2).

first: H

last: Golan Berman

first: E

last: Heilbrun

first: M

last: Luijsterburg

first: S


title: Dissection of the 4D chromatin structure of the alpha-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution [ATAC-seq]

first: Robert

middle: A

overall_design: ATAC-seq was performed on primary erythroid progenitor cells FACS sorted from e13.5 C57BL/6 mouse fetal livers and on primary haematopoietic stem and progenitor cells FACS sorted from adult C57BL/6 mouse bone marrow.

first: Jelena

last: Telenius

first: Jim

last: Hughes


title: Global gene expression profiling of K-RasLSL-G12D and K-RasLSL-G12D;Mll4fl/fl lung tumors using RNA sequencing

city: Waltham

first: Ming

last: Tang

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

institute: Immunitas Therapeutics

summary: Here, we show that the histone H3 lysine (H3K4) methyltransferase MLL4 (a COMPASS/SET1-like enzyme; also called KMT2D) is ranked the most highly inactivated epigenetic modifier in NSCLC tumors lung-specific loss of Mll4 accelerates K-RasG12D-induced lung tumorigenesis in mice while reducing their survival time. Mll4 loss upregulated tumor-promoting programs, such as glycolysis, which is also enriched in human lung tumors with low MLL4 levels or MLL4 inactivation. The inhibition of glycolysis selectively impeded the proliferation and tumorigenic growth of NSCLC cells bearing human MLL4-inactivating mutation. Mll4 loss caused widespread impairment of super-enhancer signals, including super-enhancer associated with the circadian transcriptional repressor gene Per2 which represses glycolysis genes in NSCLC cells.

last: Alam

last: Amin

first: K

last: Rai

middle: G

last: Lee


title: Transcriptomic study of NR8383 cells following exposure to zinc oxide nanoparticles NM110

status: Public on Apr 12 2020

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanoparticle exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 2 µg/mL of NP ZnO (20 % cell viability). This project (SmartNanoTox) has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 686098.

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (2 µg/mL) of NP ZnO for 4 h were measured. For each condition, three biological replicates, at less, were performed : C1; C2; C3; C4 as controls, Z1; Z2; Z3, as exposed cells to 2 µg/mL respectively.

first: Ramia

last: Safar

first: Zahra

last: Doumandji

first: Bertrand

last: Rihn


title: RNA editing profile in miRNA loci in human [breast]

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

summary: We utilized the targeted RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

overall_design: Targeted RNA-seq for 10 pairs of breast normal and turmor samples

first: Lishi

last: Li

first: Wanying

last: Chen

first: Yulong

last: Song


title: Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

institute: Korea National Institute of Health

summary:
Purpose : We investigated RNA-seq-based broad-range genetic quality tests on GMP-compliant human leucocyte antigen (HLA)-homozygous hiPSCs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control.
Methods : Transcriptome profiling of the differentiated cell lines in three lineages, including neuronal cells, cardiomyocytes and hepatocytes, at early and late passages, respectively, were carried out using RNA sequencing.
Results :  We performed SNV, indel, CNV, ekaryotyping, HLA genotyping and transcriptomic analyses in which differentiated cells were compared with hiPSCs using RNA-seq data from undifferentiated and differentiated cultures returned from multiple centres. In particular, we evaluated whether prolonged culture conditions have the potential to give rise to genomic and phenotypic changes in the CMC3 hiPSC line, a candidate line for manufacturing cell therapies.
Conclusion : RNA-seq analysis appears to offer an informative genetic quality testing approach for cell types and allows the early screening of candidate hiPSC seed stocks for clinical use by facilitating safety and potential risk evaluation

overall_design: The hiPSC lines were expanded and differentiated into neuronal cells, cardiomyocytes, and hepatocyte-like cells. Transcriptome profiling of the differentiated cells of three lineages and the original human induced pluripotent stem cells (hiPSCs) were performed at early and late passages.

first: Hye-Yeong

last: Jo

first: Jung-Hyun

last: Kim


title: Genome-wide maps of chromatin state in K-RasLSL-G12D and K-RasLSL-G12D;Mll4fl/fl  induced lung tumors  in mice

overall_design: Examination of 6 different histone modifications in 2 different tumor types with replicates.

first: H

first: M

last: Maitituoheti

first: S


title: RNA editing profile in miRNA loci in human [ADAR1 KO, Drosha KD]

summary: We utilized the stranded RNA-seq and small RNA-seq to identify and quantify RNA editing events located in miRNA and mRNA loci.

overall_design: Stranded RNA-seq for ADAR1 knockout and control HEK293 cells and Drosha knockdown and control HeLa cells; small RNA-seq for Drosha knockdown and control Hela cells.

first: Wenbing

last: Yang


title: Gene expression profile (GEP) of CALR-overexpressing CD34+ cells and CALR-silenced CD34+ cells

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

overall_design: Refer to individual Series


title: Dissection of the 4D chromatin structure of the alpha-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution [Tiled-C]

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

overall_design: Tiled-C is a new 3C-based approach which generates high-resolution contact matrices of selected regions of interest. Tiled-C uses a panel of capture oligonucleotides tiled across all restriction fragments of specified genomic regions, combined with an adapted Capture-C based protocol, to efficiently enrich for 3C contacts within this region. This allows for deep, targeted sequencing of chromatin interactions within regions of interest and thus for the generation of high-resolution, high-depth Hi-C-like data, across multiplexed samples and genomic regions. The combination of the efficient tiled enrichment strategy with previous Capture-C library preparation optimizations allows Tiled-C to generate high-resolution contact matrices from as few as 2,000 cells.

first: A

first: Robert

last: Beagrie

first: Jelena

last: Telenius

first: Douglas

last: Higgs

first: Jim

last: Hughes


title: Gene expression profile (GEP) of CALR-overexpressingCD34+ cells

summary:
In this work, we compared gene expression profile (GEP) of CD34+ cells transduced with the retroviral vector LCALRIDN with CD34+ cells transduced with the empty vector control LXIDN and of CD34+ cells treated with CALR siRNA with control cells transfected with a Non-Targeting siRNA
In order to explore the role of CALR in the proliferation and differentiation of hematopoietic stem/progenitor cells (HPSCs), we studied the effects of CALR overexpression in Cord Blood (CB) CD34+ cells. Assessment of cell differentiation unveiled that CALR enforced expression is able to skew the haematopoietic commitment towards the MK and erythroid cell lineages. Conversely, CALR silencing induced a marked repression of MK and erythroid differentiation. In order to characterize the effects of CALR mutations on human hematopoietic cells at the molecular level, we analyzed the coding RNA profiles of CB CD34+ overexpressing CALR. This analysis identified a list of differentially expressed genes. Among upregulated genes, we found genes involved in platelet aggregation, inflammation and erythroid differentiation, potentially related to the characteristics of the disease.

overall_design: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments on NGFR-posiitve cells isolated 36h after last retroviral transduction

first: Simona

last: Salati

first: Zelia

last: Prudente

first: Valentina

last: Pennucci

first: Sebastiano

last: Rontauroli

first: Samantha

last: Ruberti

first: Elena

last: Genovese

first: Chiara

last: Rossi

first: Roberta

last: Zini

first: Elisa

last: Bianchi

first: Greta

last: Barbieri


title: Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment

status: Public on Apr 11 2020

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary: Tumor cells interact with the microenvironment that specifically supports and promotes tumor development. Key components in the tumor environment have been linked to various aggressive cancer features and can further influence the presence of subpopulations of cancer cells with specific functions, including cancer stem cells and migratory cells. To model and further understand the influence of specific microenvironments we have developed an experimental platform using cell-free patient-derived scaffolds (PDSs) from primary breast cancers infiltrated with standardized breast cancer cell lines. This PDS culture system induced a series of orchestrated changes in differentiation, epithelial-mesenchymal transition, stemness and proliferation of the cancer cell population, where an increased cancer stem cell pool was confirmed using functional assays. Furthermore, global gene expression profiling showed that PDS cultures were similar to xenograft cultures. Mass spectrometry analyses of cell-free PDSs identified subgroups based on their protein composition that were linked to  clinical properties, including tumor grade. Finally, we observed that an induction of epithelial-mesenchymal transitionrelated genes in cancer cells growing on the PDSs were significantly associated with clinical disease recurrences in breast cancer patients. Patient-derived scaffolds thus mimics in vivo-like growth conditions and uncovers unique information about the malignancy-inducing properties of tumor microenvironment.

overall_design: RNA samples from two breast cancer cell lines, MCF7 and MDA-MB-231, extracted from three different culture conditions: adherent 2D culture (6 replicates for each cell line), patient-derived scaffolds (3 replicates for each cell line), mice xenografts (3 replicates for each cell line).

first: Anna

last: Gustafsson

first: Anders

last: Ståhlberg


title: Gene expression profile (GEP) of CALRsiRNA CD34+ cells

first: Rossella

last: Manfredini

overall_design: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments on CD34+ cells 24h after last nucleofection


title: Transcriptomic analysis of premature termination codon mutation in the zebrafish gene psen2

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

summary: PRESENILIN 2 (PSEN2) is one of the genes mutated in early onset familial Alzheimer’s disease (EOfAD). PSEN2 shares significant amino acid sequence identity with another EOfAD-related gene PRESENILIN 1 (PSEN1), and partial functional redundancy is seen between these two genes. However, the complete range of functions of PSEN1 and PSEN2 is not yet understood. In this study, we performed targeted mutagenesis of the zebrafish psen2 gene to generate a premature termination codon close downstream of the translation start with the intention of creating a null mutation. Homozygotes for this mutation, psen2S4Ter, are viable and fertile, and adults do not show any gross pigmentation defects, arguing against significant loss of γ-secretase activity. Transcripts containing the S4Ter mutation do not appear to be destabilized by nonsense-mediated decay. Forced expression in zebrafish embryos of fusions of psen2S4Ter 5’ mRNA sequences with sequence encoding green fluorescent protein (GFP) indicated that the psen2S4Ter mutation permits utilization of cryptic, novel downstream translation start codons. These likely initiate translation of N-terminally truncated Psen2 proteins that obey the “reading frame preservation rule” of PRESENILIN EOfAD mutations. Transcriptome analysis of entire brains from a 6-month-old family of wild type, heterozygous and homozygous psen2S4Ter female siblings revealed profoundly dominant effects on gene expression likely indicating changes in mitochondrial and (possibly) ribosomal function.

overall_design: 4 whole brain samples from each of 3 psen2S4Ter genotypes (WT, Heterozygous, Homozygous) were obtained from 6 month old zebrafish. All 12 zebrafish were the result of the same parental breeding event, minimising genetic heterogeneity, and were raised in the same tank as each other.

first: Haowei

last: Jiang

first: Morgan

last: Newman

first: Michael

middle: T

last: Lardelli


title: RNA editing profile in miRNA loci in human

first: Rui

last: Zhang


title: Effective FTO inhibitors with potent anti-tumor efficacy suppress cancer stem/initiating cell self-renewal and overcome immune evasion

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: We conducted RNA sequencing with poly A RNA isolated from NOMO-1 cells upon shRNA induced FTO knockdown and small molecules (CS1 and CS2) mediated FTO inhibition .

overall_design: The NOMO-1 cells were infected with lentivirus targeting FTO and the stable cells were selected with 1ug/ml puromycin for 1 week. As FTO inhibitors treatment, the NOMO-1 cells were treated with 100nM CS1 and 500nM CS2 for 72 hours. Then, the total RNAs were extrated from each samples and polyA RNAs were enriched for sequencing. Each group contains at least 3 biological replicates.

last: Su

first: Lei

last: Dong


title: Gene Expression of purified murine splenic CD205+CD8+ Dendritic Cells

city: Toronto

first: Dave

last: Prescott

state: ON

address: 1 King's College Circle, Room 7336

department: Immunology

institute: University of Toronto

summary:
We assessed the gene expression profile of purified CD205+CD8+ Dendritic Cells isolated from murine spleens.
Mice were injected 5 days previously with B16 melanoma cells expressing recombinant FLT3L in order to boost CD205 DC populations

overall_design:
DCs were FACS sorted based on the expression level of CD103 (High vs. Low) and were collected from mice with or without injection with muramyl dipeptide (MDP), a peptidoglycan-derived ligand of the innate immune receptor NOD2 (PBS vs. MDP).
Only samples with sufficient RNA quality as determined by 2100 Bioanalyzer were included in microarray analysis

first: Dana

middle: J

last: Philpott


title: Targeting FTO suppresses cancer stem cell maintance and immune evasion

summary: We conducted RNA sequencing with poly A RNA isolated from spleen mononuclear cells of MLL-AF9 (MA9) mouse models after treatment with PBS and FTO inhibitor CS1.

overall_design: MLL-AF9 (MA9) primary leukemic mouse bone marrow cells (CD45.2+) were collected and sorted by flow cytometry when the mice developed full-blown AML. The cells were injected into sub-lethally irradiated (320 rads) secondary recipient mice with 0.05x106 donor cells per mouse via tail vein injection. One week after BMT, the mice were randomly divided into CS1 and control groups. The recipient mice were injected with PBS control and 5mg/kg CS1 i.p. every other day for 20 days. Spleens were removed from mice at the end point, and homogenized into a single-cell suspension using RPMI 1640 supplemented with 2% FBS. Red blood cells were lysed using ammonium chloride (07850, STEMCELL Technologies), washed with cold PBS. Cell pellet were then resuspended in 45 μL pre-cold MACS buffer (0.5% BSA and 2mM EDTA in PBS) per 10⁷ total cells. Biotin-labeled CD45.2 (130-101-903, Miltenyi Biotec) were added to the cells and incubated for 10 minutes in the refrigerator (2−8 °C). Cells Cells were subsequently washed with MACS buffer and resuspended in MACS buffer (1 × 108 cells/mL). Streptavidin microbeads were added (MSPB-6003-74, Thermo Fisher Scientific) and the cell mixture was incubated at room temperature for 10 minutes. Cells were washed again and resuspended in 500 μL MACS buffer and then isolated with the MACS seperation Columns (130-042-201, Miltenyi Biotec). After collecting the CD45.2 positive cells, total RNA was extracted using miRNeasy Mini Kit (217004, Qiagen) and polyA RNA were enriched for RNA sequence.


title: High-throughput automated organoid culture via stem-cell aggregation in microcavity arrays

status: Public on Apr 10 2020

city: Lausane

first: Nathalie

last: Brandenberg

state: VD

address: AI 1116 (Bâtiment AI) Station 15

department: SV IBI-SV

country: Switzerland

institute: Ecole Polytechnique Federale de Lausane

summary: Stem-cell-derived epithelial organoids are routinely used for the biological and biomedical modelling of tissues. However, the complexity, lack of standardization and quality control of stem cell culture in solid extracellular matrices hampers the routine use of the organoids at industrial scale. Here, we report the fabrication of microengineered cell-culture devices and scalable and automated methods for the suspension culture and real-time analysis of thousands of individual gastrointestinal organoids trapped in microcavity arrays within a polymer-hydrogel substrate. The absence of a solid matrix significantly reduces organoid heterogeneity, as we show for mouse and human gastrointestinal organoids. We used the devices to screen for anticancer drug candidates with patient-derived colorectal cancer organoids, and high-content image-based phenotypic analyses to reveal insights into drug-action mechanisms. The scalable organoid-culture technology should facilitate the use of organoids in drug development and diagnostics.

overall_design: Examination of RNA expression profiles (bulk analysis) between human colorectal cancer (hCRC) organoids exposed to 1μΜ Afuresertib and DMSO (dilution 1:1000) in organoids arrays versus Matrigel domes.

first: Sylke

last: Hoehnel

first: Fabien

last: Kuttler

first: Matthias

middle: P

last: Lutolf


title: METTL3 and N6-methyladenosine Promotes Homologous Recombination Mediated Repair of DSBs by Facilitating R-loop Formation [RIP-Seq]

city: GuangZhou

first: Zhang

last: Feng

address: Graduate school, building 493, 135 xingang west road

institute: Sun Yat-sen University

summary: The goals of this study are to compare the level of YTHDC1 associated nascent RNA at chromatin between DMSO and zeocin treatment.

overall_design: YTHDC1 associated RNA were isolated form HEK293T with or without zeocin teatment using Flag beads for pair-end sequening on HiseqXten

first: Chen

last: Ping

first: Jiang

last: Ao

first: Peng

last: Di


title: Role of BAP1 in pancreatic cancer (ChIP-seq Mus musculus)

city: Washington

first: Alexandros

last: Tzatsos

address: 800 22nd St NW SEH 8850

institute: George Washington University

summary: We found that BAP1 (BRCA1 Associated Protein-1) shows loss of heterozygosity in over 25% of pancreatic cancer patients and functions as tumor suppressor. Conditional deletion of Bap1 in murine pancreas led to genomic instability, accumulation of DNA damage, and an inflammatory response that evolved to pancreatitis with full penetrance. Concomitant expression of oncogenic KrasG12D led to malignant transformation and development of invasive and metastatic pancreatic cancer. At the molecular level, BAP1 maintains the integrity of the exocrine pancreas by regulating genomic stability and its loss confers sensitivity to radio- and platinum-based therapies.

overall_design: Murine cell lines were estabished from Bap1 null pancreata expressing KrasG12D and analyzed by ChIP-seq for H3K4me1, H3K4me3, H3K27me3, H3K27ac, H2AK119ub, and H2BK120ub.

first: Yan

last: Kai


title: Analysis of FGF20-regulated genes in differentiating cochlear hair and supporting cell progenitors via ribosome affinity purification

first: Lu

last: Yang

state: Missouri

address: 660 S. Euclid Avenue Campus Box 8103

department: Developmental Biology

institute: Washington University School of Medicine

summary:
Background: Understanding the developmental mechanisms that regulate hair cell differentiation in the cochlea is essential to designing genetic therapies for acquired hearing loss due to hair cell loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in hair cell and supporting cell differentiation and patterning in the mouse cochlear sensory epithelium. To investigate the genetic landscape regulated by FGF20 signaling in hair cell and supporting cell progenitors, we employ Translating Ribosome Affinity Purification (TRAP) combined with Next Generation mRNA Sequencing (TRAPseq).
Methods: In mice, we used Fgf20-Cre to activate ROSA-fsTRAP in hair cell and supporting cell progenitors, and then collected translating mRNA using TRAP from Fgf20+/- (control) and Fgf20-/- cochleae. Library preparation and sequencing were done in two separate experiments, each with 12 samples that included 2 pre-TRAP (pre-immunoprecipitation) Fgf20+/- samples, 2 TRAP Fgf20+/- samples, 4 pre-TRAP Fgf20-/- samples, and 4 TRAP Fgf20-/- samples. Samples were sequenced via Illumina HiSeq 3000. We compared pre-TRAP (pre-immunoprecipitation) samples with TRAP mRNA samples to validate the TRAP technique as well as identify genes enriched in our target cell population. We also compared Fgf20+/- and Fgf20-/- TRAP mRNA samples to identify differentially expressed genes downstream of FGF20 during hair cell and supporting cell differentiation.
Results: TRAPseq targeting the prosensory cell population effectively enriches for translating mRNA within this rare cell population. TRAPseq comparing Fgf20+/- and Fgf20-/- samples identified differentially expressed genes downstream of FGF20. These included FGF-response genes Etv4, Etv5, Etv1, and Dusp6, as well as genes associated with cochlea development and hearing, such as Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, and cell cycle regulators such as Cdc20.

overall_design: E14.5 cochlear mRNA collected with translating ribosome affinity purification from Fgf20+/- and Fgf20-/- mouse cochleae. Expression of L10a-eGFP protein was targeted to the Fgf20-Cre lineage. Each sample is pooled from 3-7 embryos of the same genotype.

first: David

last: Ornitz


title: Genome-wide analysis reveals mucociliary remodeling of the airway epithelium induced by PM2.5

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

summary: Air pollution particulate matter <2.5 microns (PM2.5) is associated with poor respiratory outcomes. Mechanisms underlying PM2.5-induced lung pathobiology are poorly understood, but likely involve cellular and molecular changes to the airway epithelium. We extracted and chemically characterized the organic and water-soluble components of contemporary ambient air pollution PM2.5 samples. We then determined the whole transcriptome responses of human mucociliary airway epithelial cultures (n=12) to a dose series  of PM2.5 extracts. We found PM2.5 organic, but not water-soluble, constituents elicited a potent, dose-dependent transcriptomic response from the mucociliary epithelium. Epithelial exposure to a moderate organic extract (OE) dose modified the expression of 424 genes, which included activation of aryl-hydrocarbon receptor (AHR) signaling and an interleukin-1 inflammatory program. We generated an OE response network composed of 8 metagroups, which exhibited high connectivity through the CYP1A1, IL1A, and IL1B genes. This OE exposure also robustly activated a mucus secretory expression program (>100 genes), which included transcriptional drivers of mucus metaplasia (SPDEF, FOXA3). Exposure to a higher OE dose modified the expression of 1,240 genes and further exacerbated expression responses observed at the moderate dose, including the mucus secretory program. Moreover, the higher OE dose significantly increased the MUC5AC/MUC5B gel-forming mucin expression ratio and strongly downregulated ciliated cell expression programs, including key ciliating cell transcription factors (FOXJ1, MCIDAS). Our results suggest organic chemicals in PM2.5 likely drive cellular remodeling of the airway epithelium, punctuated by mucus metaplasia and loss of ciliated cells. This epithelial remodeling may underlie poor respiratory outcomes associated with high PM2.5 exposure.

overall_design: Three separates doses (Low, Moderate, High) of PM2.5 with their control. Additionally, there are 4 NIST samples and 4 water extract controls. In total, there are 42 samples

first: Michael

last: Montgomery

first: Seung-Hyun

last: Cho

first: Cydney

last: Rios

first: Jamie

last: Everman

first: Katherine

last: Goldfarbmuren

first: Nathan

middle: D

last: Jackson

first: Benjamin

last: Saef

first: Meghan

last: Cromie

first: Alicia

last: Adams

first: Celeste

last: Eng

first: Vivian

last: Medina

first: Jennifer

last: Elhawary

first: Sam

last: Oh

first: Jose

last: Rodriguez-Santana

first: Esteban

last: Burchard

first: Max

last: Seibold


title: Slug feeding triggers dynamicmetabolomic and transcriptomic responses leading to induced resistance in Solanum dulcamara

city: Nijmegen

first: Onno

middle: Wouter

last: Calf

address: Heyendaalseweg 135

department: Molecular Interaction Ecology

country: Netherlands

institute: Radboud University

summary: Induced plant responses to insect herbivores are well studied, but we know very little about responses to gastropod feeding. We aim to identify the temporal dynamics of signalling- and defence-related plant responses after slug feeding in relation to induced resistance. We exposed Solanum dulcamara plants to feeding by the grey field slug (GFS; Deroceras reticulatum) for different periods and tested discs of local and systemic leaves in preference assays. Induced responses were analysed using metabolomics and transcriptomics. GFS feeding induced local and systemic responses. Slug feeding for 72h more strongly affected the plant metabolome than 24h feeding. It increased the levels of a glycoalkaloid (solasonine), phenolamides, anthocyanins, and trypsin protease inhibitors as well as polyphenol oxidase activity. Phytohormone and transcriptome analyses revealed that jasmonic acid, abscisic acid and salicylic acid signalling were activated. GFS feeding upregulated more genes than that it downregulated. The response directly after feeding was more than five times higher than after an additional 24h without feeding. Our research showed that GFS, like most chewing insects, triggers anti-herbivore defences by activating defence signalling pathways, resulting in increased resistance to further slug feeding. Slug herbivory may therefore impact other herbivores in the community.

overall_design: Four seed batches were selected from S. dulcamara populations in the Netherlands (Goeree and Friesland) and Germany (Erkner and Siethen). Plants were randomly assigned to one of four treatments (n = 16 plants / population / treatment). Leaf number 10 from the apex was exposed to feeding by GFS for 24h or fitted with an empty clip cage for the same time period (undamaged control). Harvest took place directly (0h) after removing the slugs or after an additional 24h without exposure to GFS. RNA from four plants of a single plant population at each time point were pooled, resulting in four total RNA samples per treatment (control or induced) for both time points.

middle: W

first: Tobias

last: Lortzing

first: Alexander

last: Weinhold

first: Yvonne

last: Poeschl

first: Janny

last: Peters

first: Heidrun

last: Huber

first: Anke

last: Steppuhn

first: Nicole

last: van Dam


title: Molecular mechanisms for Krüppel-like factor 13 actions in hippocampal neurons

status: Public on Apr 09 2020

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

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


title: Molecular mechanisms for Krüppel-like factor 13 actions in hippocampal neurons [ChSP-seq]

summary: Krüppel-like factors (KLFs) play key roles in nervous system development and function. Several KLFs are known to promote, and then maintain neural cell differentiation. Our previous work focused on the actions of KLF9 in mouse hippocampal neurons. Here we investigated genomic targets and functions of KLF9’s paralog KLF13, with the goal of understanding how these two closely related transcription factors influence hippocampal cell function, proliferation, survival and regeneration. We engineered the adult mouse hippocampus-derived cell line HT22 to control Klf13 expression with doxycycline. We also generated HT22 Klf13 knock out cells, and we analyzed primary hippocampal cells from wild type and Klf13-/- mice. RNA sequencing showed that KLF13, like KLF9, acts predominantly as a transcriptional repressor in hippocampal neurons and can regulate other Klf genes. Pathway analysis revealed that genes regulated by KLF13 are involved in cell cycle, cell survival, cytoarchitecture regulation, among others. Chromatin-streptavidin sequencing conducted on chromatin isolated from HT22 cells expressing biotinylated KLF13 identified 9506 genomic targets; 79% were located 1 kilobase upstream of transcription start sites. Transfection-reporter assays confirmed that KLF13 can directly regulate transcriptional activity of its target genes. Comparison of the target genes of KLF9 and KLF13 found that they share some functions that were likely present in their common ancestor, but have also acquired distinct functions during evolution. Flow cytometry showed that KLF13 promotes cell cycle progression, and it protects cells from glutamate-induced excitotoxic damage. Taken together, our findings establish novel roles and molecular mechanisms for KLF13 actions in mammalian hippocampal neurons.

overall_design:
Identification of KLF13 association in chromatin across the genome of HT22 cells analyzed by chromatin streptavidin precipitation sequencing (ChSP).
The mouse hippocampus-derived neuronal cell line HT22 was engineered to stably express the biotin ligase BirA. Cells were then transfected with pTO-Klf13Bio plasmid to express a biotinylated form of KLF13. Chromatin streptavidin precipitation was applied to chromatin extracted from cells 24 hr after transfection and subjected to deep sequencing.

first: José

last: Ávila-Mendoza

first: Arasakumar

last: Subramani

first: Christopher

last: Sifuentes


title: Expression data from adult zebrafish

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

institute: National Health Research Institutes

summary:
Oligo-fucoidan (OF), a sulfated polysaccharide extracted from brown seaweed, exhibits anti-inflammation and antitumor effects, however, knowledge concerning the detailed mechanism of oligo-fucoidan on liver cells is obscure. In this study, we investigate the effect of oligo-fucoidan in normal hepatocytes using transcriptomic analysis.
Using an oligo-fucoidan oral gavage in adult wild-type zebrafish, we then used microarrays to detail the global programme of gene expression after fucoidan treatment and identified distinct classes of up- and down-regulated genes during this process.

overall_design: 5-month-old wild-type fish (N = 40) were divided into 2 groups, either no treatment (mock) or OF administrations via an oral gavage with OF (300 mg/kg) thrice a week for one month. The fish were sacrificed and the hepatic tissue was immediately frozen in liquid nitrogen and stored at −80 °C for later RNA extraction and hybridization on Affymetrix microarrays. Two batches of wild-type fish fed with OF were performed.

first: Chun-Chia

last: Cheng

first: Wan-Yu

last: Yang

first: Ming-Chen

last: Hsiao

first: Kuan-Hao

last: Lin

first: Hao-Wei

last: Lee


title: Defective SEC61α1 underlies a novel cause of autosomal dominant severe congenital neutropenia

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

institute: The Babraham Institute

summary: The molecular cause of severe congenital neutropenia (SCN) is unknown in 30-50% of patients. SEC61A1 encodes the α subunit of the heterotrimeric SEC61 complex, which governs endoplasmic reticulum (ER) signal peptide-dependent protein transport and passive calcium leakage. Recently, autosomal dominant mutations in SEC61A1 were reported to be pathogenic in common variable immunodeficiency (CVID) and glomerulocystic kidney disease. However the full spectrum of clinical manifestations in SEC61A1 mutations is yet to be explored. We investigated a SCN patient, the only child of healthy non-consanguineous Belgian parents. We identified a de novo private missense mutation in SEC61A1 (c.A275G;p.Q92R; CADD 24.5; msc 6.099) in the patient. The mutation results in diminished expression of the protein in PBMC and fibroblasts, and an increase in calcium leakage from the ER. In vitro differentiation of CD34+ cells recapitulated the patient’s clinical arrest in granulopoiesis. The impact of Q92R-SEC61α1 on neutrophil maturation was validated using HL-60 cells, where transduction reduced differentiation into CD11b+CD16+ cells. A potential mechanism for this defect is the uncontrolled initiation of the unfolded protein stress response (UPR), with single-cell analysis of primary bone-marrow revealing perturbed UPR in myeloid precursors, and in vitro differentiation of primary CD34+ cells into neutrophils revealing upregulation of the pro-apoptotic CHOP and BiP UPR-response genes. Together, these results support specific autosomal dominant mutations in SEC61A1 causing SCN through dysregulation of the UPR.

overall_design: Two RBC depleted whole bone marrow aspirates; one patient with severe congenital neutropenia with a de novo mutation in SEC61A1, one healthy gender-matched control


title: Expression data from mice bladder with MB49-induced cancer treated with alpha1-oleate.

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

summary: Potent chemotherapeutic agents are required to counteract the aggressive behavior of cancer cells and patients often experience severe side effects, due to tissue toxicity. This study addresses if a better balance between efficacy and toxicity can be attained using the tumoricidal complex alpha1-oleate, formed by a synthetic, alpha-helical peptide comprising the N-terminal 39 amino acids of alpha-lactalbumin and the fatty acid oleic acid. Bladder cancer was established, by intra-vesical instillation of MB49 cells on day 0 and the treatment group received five instillations of alpha1-oleate (1.7-17mM) on days 3-11. A dose-dependent reduction in tumor size, bladder size and bladder weight was recorded in the alpha1-oleate treated group, compared to sham-treated mice. Tumor markers Ki-67, Cyclin D1 and VEGF were inhibited in a dose-dependent manner, as was the expression of cancer-related genes. Remarkably, toxicity for healthy tissue was not detected in alpha1-oleate-treated, tumor bearing mice or in healthy mice or rabbits, challenged with increasing doses of the active complex. The results define a dose-dependent therapeutic effect of alpha1-oleate in a murine bladder cancer model.

overall_design: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. The treatment group received alpha1-oleate by intravesical instillation (1.7 mM, 8.5 mM or 17 mM) on days 3, 5, 7, 9 and 11. Sham treated mice received PBS and healthy mice bladders were used as control. Bladder samples were collected after 12 days. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis. For toxicity testing in healthy mice, alpha1-oleate was instilled intravesically in C57BL/6J female mice (17 mM) and bladders were collected for RNA isolation after 24 hours or 7 days. Controls received PBS.

first: Hien

last: Tran

first: Catharina

last: Svanborg


title: Subcellular RNA fractions of primary human fibroblasts infected with the HSV-1 delta-ICP27 mutant

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with the ICP27 null mutant of herpes simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RNA-seq

overall_design: HFF were infected with the ICP27-null mutant of HSV-1 strain 17 for 8h. Subcellular RNA fractions were prepared combining the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013) as described in Hennig et al., PLoS Pathogens 2018  (https://doi.org/10.1371/journal.ppat.1006954). Two independent biological replicates were analysed. Data for HFF infected with wild-type HSV-1 strain 17 for 8h (or mock) found under accession GSE100576 were re-analyzed for this study.

first: Adam

last: Whisnant

first: Thomas

last: Hennig

first: Marco

last: Michalski

first: Andrzej

last: Rutkowski

first: Lara

last: Djakovic

first: Marie-Sophie

last: Friedl

first: Bhaskar

last: Jha

first: Marisa

last: Baptista

first: Anne

last: L'Hernault

first: Florian

last: Erhard

first: Lars

last: Dölken


title: Microglia actively remodels adult hippocampal neurogenesis through the phagocytosis secretome

city: Leioa

first: Amanda

last: Sierra

address: Parque Científico (UPV/EHU) Barrio Sarriena s/n

country: Spain

institute: Achucarro Basque Center for Neuroscience

summary: During adult hippocampal neurogenesis, the majority of newborn cells undergo apoptosis and are rapidly phagocytosed by resident microglia in order to avoid disturbing the surrounding neurons. Here, we propose that phagocytosis is not merely a passive process of corpse removal but has an active role in maintaining adult hippocampal neurogenesis. First, we found that neurogenesis was disrupted in three defective microglial phagocytosis KO models in vivo (P2Y12, MerTK/Axl , GPR34). We then followed an in vitro approach to perform a transcriptomic analysis of microglial phagocytosis and identified genes involved in metabolism, chromatin remodeling, and neurogenesis-related functions. Finally, we determined that the phagocytic microglia secretome limits the production of new neurons both in vivo and in vitro. Our data suggest that reprogrammed phagocytic microglia acts as a sensor of local cell death, modulating the balance between cell proliferation and cell survival in the neurogenic niche, supporting the long-term maintenance of adult hippocampal neurogenesis.

overall_design: We performed a mouse-specific full genome-wide transcriptomic analysis using gene expression mouse-specific arrays comparing naïve vs. phagocytic microglia. We developed a xenogeneic in vitro model of phagocytosis of apoptotic cells (Beccari et al., 2018), in which mouse primary microglia were fed for two different time points (3 and 24h) with a human neuronal line (SH-SY5Y), previously labeled with CM-DiI and treated with staurosporine (STP; 4h, 3µM) for apoptosis induction. The experiment was performed in the presence of a control group of naïve microglia which were not exposed to any phagocytic stimuli. N=3 independent experiments were performed for this transcriptomic analysis.

first: Irune

last: Diaz-Aparicio

first: Iñaki

last: Paris

first: Victor

last: Sánchez-Zafra

first: Virginia

last: Sierra-Torre

first: Ainhoa

last: Plaza-Zabala

first: Noelia

last: Rodríguez-Iglesias

first: Mar

last: Márquez-Ropero

first: Sol

last: Beccari

first: Oihane

last: Abiega

first: Elena

last: Alberdi

first: Carlos

last: Matute

first: Irantzu

last: Bernales

first: Angela

last: Schulz

first: Lilla

last: Otrokocsi

first: Beata

last: Sperlagh

first: Kaisa

middle: E

last: Happonen

first: Greg

last: Lemke

first: Mirjana

last: Maletic-Savatic

first: Jorge

last: Valero


title: Investigation of different gene expression of putative tt mutants under AIC condition using RNA-seq

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

country: USA

institute: Michigan State University

summary: Characterization of transparent testa mutants from large T-DNA collections

overall_design: Total RNA of candidate tt mutant lines was extracted from seedlings,all under AIC conditions for four days.mRNA libraries were prepared using Illumina kit and sent for RNA-seq analysis by strand specific 50SE.TT samples have no replicates. Comparison for different gene expression between col-0 and candidate tt mutants

last: Jiang

first: Yun

middle: S

last: Lee

first: Eric

last: Maina


title: Effects of a quadruplex-binding compound on gemcitabine resistant pancreatic cancer cells

status: Public on Apr 07 2020

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

institute: UCL

summary: Changes in gene expression in a pancreatic cancer cell line and a chemoresistant line on treating with the drug CM03

overall_design: Changes at 6 h and 24 h were evaluated with RNA-seq with respect to controls

first: Ahmed

last: Ahmed


title: Tumor Necrosis Factor Alpha Regulates Skeletal Myogenesis by Inhibiting SP1 Interaction with cis-Acting Regulatory Elements within the Fbxl2 Gene Promoter

status: Public on Apr 08 2020

city: Pittsburgh

first: Michael

middle: Emmet

last: O'Brien

state: PA

address: 200 Lothrop Street

department: Pulmonary, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

summary: Using NGS technology we describe the transcriptomic effecs of TNFα stimulation on skeletal myogenesis and, through gene sliencing techniques, compare the effects of TNFα with the loss of a critical cell cycle regulator, Fbxl2, on the process of myogenic proliferation and differentiation.

overall_design: RNA sequencing was performed on C2C12 cells during the stage of myoblast proliferation (proliferation), at 48 h post induction of differentiation (control),  in the presence of 10 ng/ml TNFα stimulation (TNF) at 48 h, and after Fbxl2 gene silencing at 48 h post induction of differentiation.


title: Zonation of ribosomal DNA transcription defines a stem cell hierarchy in colorectal cancer

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

summary: Colorectal cancers (CRCs) are composed of an amalgam of cells with distinct genotypes and phenotypes. Here we reveal a previously unappreciated heterogeneity in the biosynthetic capacities of CRC cells. We discover that the majority of ribosomal DNA transcription and protein synthesis in CRCs occur in a limited subset of tumor cells that localize in defined niches. The rest of the tumor cells undergo an irreversible loss of their biosynthetic capacities as a consequence of differentiation. Cancer cells within the biosynthetic domains are characterized by elevated levels of the RNA Polymerase 1 subunit A - POLR1A. Genetic ablation of POLR1A-high cell population imposes an irreversible growth arrest to CRCs. We show that elevated biosynthesis defines stemness in both LGR5+ and LGR5- tumor cells. Therefore, a common architecture in CRC is a simple cell hierarchy based on the differential capacity to transcribe ribosomal DNA and synthesize proteins.

overall_design: Full-length single cell RNA sequencing libraries were prepared using the Smart-seq2 protocol with minor modifications.

first: Eduard

last: Batlle

first: Holger

last: Heyn


title: TLA: Targeted Locus Amplification interaction libraries from TLA viewpoints in the GFP construct from GFP(CAG) cells.

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: University of Lausanne

department: Center for Integrative Genomics

institute: University of Lausanne

summary: We performed Targeted Locus Amplification (TLA) to map the insertion site of a stably integrated, hemizygous ectopic locus that contains CAG repeats (15 or 270 repeats) in clonal populations of HEK293-derived cells (GFP(CAG)15 or GFP(CAG)270).

overall_design: TLA experiments with two TLA viewpoints located 3 kb downstream and 4 kb upstream of the ectopic CAG repeat locus in HEK293-derived cells.

first: Jennifer

middle: Y

last: Tan

first: Ana

last: Marques

first: Vincent

last: Dion


title: SNP confirmation: Sequencing of PCR amplicons that contained potential biallelic SNPs in HD-B and DM1-A patient cells.

summary: We performed DNA sequencing of potential biallelic SNPs in HD-B and DM1-A patient cell lines. These potential biallelic SNPs were identified in the 4C-seq interaction data. We selected a subset of these SNPs for confirmation by PCR, so we amplified the genomic regions that contained these potential SNPs and performed 2 x 150 bp paired-end sequencing on Illumina MiSeq nano.

overall_design: The HD family individuals used were: GM02180 (UN-C, unaffected mother), GM02164 (HD-A, HD father), and GM03620 (HD-B, HD daughter). For the HD family individuals' cell lines, we sequenced 16 genomic regions in a 1 Mb region around the HTT gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.The DM1 family individuals used were: GM04604 (UN-B, unaffected father) and GM06077 (DM1-A, DM1 daughter). For the DM1 family individuals, we sequenced 14 genomic regions in a 1 Mb region around the DMPK gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.

first: Flavia

last: Marzetta


title: Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

summary:
Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders.

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