title: Transcriptome analysis of SATB1- and SATB1+ Hematopoietic stem cells.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Hematopoietic stem cells (HSCs) are now recognized as a heterogeneous population in self-renewing and differentiation capabilities. However, fundamental mechanisms governing the heterogeneity remain uncertain. We here show that special AT-rich sequence-binding protein 1 (SATB1), a global chromatin organizer, is involved in the mechanisms. Analyzing hematological lineage-restricted SATB1 knock out mice proved that SATB1 is indispensable for both self-renewal and normal differentiation of adult HSCs. Using SATB1/Tomato knock-in mice, we subdivided HSCs according to SATB1 intensity. Culture experiments and RNA-sequencing revealed essential differences between SATB1- and SATB1+ HSCs regarding lineage potential.

overall_design: Total RNAs isolated from SATB1- and SATB1+ CD150+ Flt3- LSK cells were applied for RNA-sequencing, and then amount of change of each genetic expression in SATB1+ HSCs compared with SATB1- HSCs were calculated.

first: Yukiko

last: Doi

first: Takafumi

last: Yokota


title: The kinase/ATPase Rio1 coordinates yeast metabolism, physiology, growth and cell division at multiple levels

status: Public on Jun 14 2018

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq of ten guinea pig tissues from breeders and non-breeders

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: Comparison of gene expression level by Illumina sequencing of ten different guinea pig tissue from breeders and non-breeders.

overall_design: 238 samples: 10 tissues (heart, skin, liver, kidney, cerebellum, hypothalamus, pituitary, thyroid, adrenal, gonad),  5-6 animals per group, 4 groups: 1) female non-breeder, 2) female breeder, 3) male non-breeder, 4) male breeder

first: Martin

last: Bens

first: Karol

last: Szafranski

first: Susanne

last: Holtze

first: Arne

last: Sahm

first: Thomas

middle: B

last: Hildebrandt

first: Matthias

last: Platzer


title: Genome-wide mapping of Cnp1 of wild-type and various deletion strains in fission yeast.

status: Public on Jun 13 2018

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

country: China

institute: Zhejiang University, Life Sciences Institute

summary: ccp1Δ, gar2Δ showed wild-type level of genome-wide Cnp1 distribution.

overall_design: ChIP-seq (anti-Cnp1) were performed to specific deletion strains and wild type strain.

first: Xiangwei

last: He


title: IL-22 impedes the proliferation of Schwann cells and influence nerve regeneration

status: Public on Jun 15 2018

city: Shanghai

first: Shengming

last: Xu

address: No.415, Fengyang Road, Huangpu District

department: Department of Orthopaedics

institute: Changzheng Hospital, Second Military Medical University

summary: Schwann cells (SCs) proliferation is crucial for axonal guidance and nerve regeneration following nerve injury. This study aims to investigate the in vitro effects of interleukin-22 (IL-22) on SCs and the corresponding mechanism.

overall_design: Rat SCs were treated with 100 ng/ml rat IL-22.

first: Junping

last: Ao


title: mRNA profiles of JMJD3 overexpression- and JMJD3 knockout- HL-60 cells

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

summary: Next Generation Sequencing Facilitates Quantitative Analysis of HL-60 cells transduced with control or JMJD3-expression vector, and HL-60 parental and JMJD3 knockout cells

overall_design: mRNA profiles of HL-60 cells were generated by deep sequencing, in triplicate, using  Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Shan-he

last: Yu

first: Jiang

last: Zhu


title: Whole blood RNA-seq of pediatric cases of natural Chikungunya infection

city: New York

first: Andrew

last: Kasarskis

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: The primary aim of this study was to characterize the transcriptomic changes between the acute and convalescent phase of natural Chikungunya infections in pediatric patients as observed in peripheral blood samples.

overall_design: 43 pediatric cases of natural Chikungunya infection were sampled for whole blood at two timepoints (1-2 and 15-17d post symptom onset). Two technical replicates were sequenced per blood sample.

first: Theodore

middle: R

last: Pak

first: Daniela

middle: H

last: Michlmayr

first: Adeeb

last: Rahman

first: El-Ad

middle: D

last: Amir

first: Eun-Young

last: Kim

first: Seunghee

last: Kim-Schulze

first: Maria

last: Suprun

first: Mayte

last: Suarez-Fariñas

first: Steven

last: Wolinsky

first: Eva

last: Harris


title: mRNA expression profiling of siDBP-mesangial cells

city: Beijing

first: Yang

last: Lu

address: 8th fuxing road

institute: PLA general hospital

summary: The goals of this study are to compare the difference between DBP knock-down group and control group in mesangial cells

overall_design: DBP was knock-down by siRNA and NC siRNA was set as control.


title: Genome-wide mapping of fission yeast

first: Min


title: Murine Norovirus Infection Initiates Interferon and TNF Signaling with Significant Alteration of Lipid and Cell Cycle Homeostasis

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Murine norovirus (MNV) is genetically similar to human norovirus (HuNoV), and offers both an efficient in vitro cell culture system and animal model by which to investigate the molecular basis of replication.  Here, we present a detailed global view of the cellular alterations that occur during the progression of a norovirus infection. The transcriptome of a synchronously infected population of MNV-infected murine macrophage-like cell line (RAW264.7) was determined at 8, 14, and 20 hours post infection. The cellular genetic response was analyzed both globally and by specific pathways. Viral replication was monitored by RNA-seq and quantitative real-time PCR in context of the cellular phenotypic response.  The majority of transcriptionally up regulated genes were related to the IFN response. Additionally, there was a global increase in gene transcripts associated with immune response and inflammation. A transcriptional decrease was observed across many cellular processes, but particularly for genes involved in lipid homeostasis and cell cycle. The peak of the transcriptional immune response correlated with detected viral genome copies and changes in cellular phenotype including nuclear condensation. A more complete understanding of host response to norovirus infection will help to highlight the cellular pathways critical for a more effective immune response as well as those that may be exploited by the virus for therapeutic development.

overall_design: Time course study of murine macrophage-like cell line gene expression infected with Murine nororvirus.

first: Eric

middle: A

last: Levenson

first: Kishore

last: Kanakabandi

first: Charles

last: Turner

first: Stanislav

middle: V

last: Sosnovtsev

first: Stacy

last: Ricklefs

first: Jordan

last: Johnson

first: Stephan

middle: F

last: Porcella

first: Kim

middle: Y

last: Green


title: RNA-seq of nine naked mole-rat tissues from breeders and non-breeders

first: Marco

last: Groth

summary: Comparison of gene expression level by Illumina sequencing of nine different naked mole-rat tissue from breeders and non-breeders.

overall_design: 215 samples: 9 tissues (heart, skin, kidney, cerebellum, hypothalamus, pituitary, thyroid, adrenal, gonad),  5-6 animals per group, 4 groups: 1) female non-breeder, 2) female breeder, 3) male non-breeder, 4) male breeder

first: Martin

last: Bens

first: Karol

last: Szafranski

first: Susanne

last: Holtze

first: Arne

last: Sahm

first: Thomas

last: Hildebrandt

first: Matthias

last: Platzer


title: The fate of CD8+ T cells during infection is linked to their developmental origin [Naïve_Timestamp]

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: During immune ontogeny the thymus is colonized by distinct waves of hematopoietic stem cells that give rise to unique lineages of immune cells.  In this report, we asked whether the developmental origin of CD8+ T cells influences their response to infection later in adulthood.  To answer this question, we developed a system to ‘timestamp’ CD8+ T cells in situ at various stages of development (1d and 28d) and examined their behavior at 8 weeks of age.  We found that neonatal-derived CD8+ T cells have an intrinsic propensity to become memory phenotype cells prior to infection and are the first cells to proliferate and become effectors after microbial challenge. These data indicate that there are developmental layers in the adult CD8+ T cell response to infection and that the heterogeneity in the effector pool is linked to the variation in the developmental origins of the responding cells. This dataset profiles gene expression in 1day- and 28day-timestamped naïve CD8+ T cells in 8 week old mice.

overall_design: gene expression profiling of naïve CD8+ T cells in 8 week old mice, looking at two samples: cells made at 1 day or 28 days of life, in duplicate.

first: Norah

last: Smith

first: Brian

last: Rudd


title: Genome-wide mapping of Ccp1 association sites in fission yeast

first: Min

last: Lu

summary: In our genetic screen, we found that Ccp1 is an epigenetic stability modulator in centromeres and heterochromatin in S. pombe. In interphase cells,Ccp1-GFP enriched at centromeres. To determine the association sites of Ccp1 with the centromeres and to characterize the global distribution pattern of Ccp1 throughout the genome, ChIP-seq were performed for Myc-tagged Ccp1 (C-terminal fusion protein). The result revealed that Ccp1 associates with the central core regions (cnt and imr) within every single centromere.

overall_design: ChIP-seq (anti-Myc) were performed to wild-type (no tag) and ccp1-myc (C-terminal fusion) starins simultaneously.

first: Xiangwei

last: He


title: Comparative transcriptomic response of primary and immortalized macrophage to murine norovirus infection

first: Craig

last: Martens


title: Stromal PTEN determines mammary epithelial response to radio-therapy

city: Columbus

first: Gina

last: Sizemore

state: OH

address: 460 W. 12th Avenue

institute: Ohio State University

summary: It is well-described that the tumor stroma participates in cancer progression, but whether stromal factors can initiate breast tumorigenesis remains unclear. Using our previously described stromal-specific phosphatase and tensin homolog (PTEN) deletion mouse model, we investigated transformative events in young, non-tumor bearing animals. Here, we show stromal PTEN deletion initiates radiation-induced genomic instability on neighboring mammary epithelium through paracrine epidermal growth factor receptor (EGFR) activation. In these mice, a single low dose of whole-body radiation induces mammary hyperplasia, a result that is prevented by pre-treatment with an EGFR inhibitor. We reveal that stromal PTEN is lost in a subset of normal breast samples and is predictive of recurrence in breast cancer patients. Combined, these data suggest both diagnostic and therapeutic chest wall radiotherapy may inadvertently predispose patients with focal stromal PTEN loss to secondary breast cancer, and that this predisposition may be treated prophylactically through EGFR inhibition.

overall_design: Each biological replicate of FACS sorted Lin-CD24+CD29loCD61- mature luminal epithelial subpopulations was collected by pooling pre-neoplastic mammary tissue from 6-8 virgin ErbB2;Ptenfl/fl or ErbB2;Fsp-cre;Ptenfl/fl (8-9 weeks of age) mice. Microarray on three mature luminal samples from both genetic groups was performed with GeneChip® Mouse Transcriptome Assay 1.0 (Affymetrix, Santa Clara, California, USA) at the OSUCCC Genomics Facility.

middle: M

first: Subhasree

last: Balakrishnan

first: Michael

middle: C

last: Ostrowski


title: Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for resistance and virulence

status: Public on Jun 10 2018

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: With the global increase in the use of carbapenems, several gram-negative bacteria have acquired carbapenem resistance, thereby limiting treatment options. Klebsiella pneumoniae is one of such notorious pathogen that is being widely studied to find novel resistance mechanisms and drug targets. These antibiotic-resistant clinical isolates generally harbor many genetic alterations, and identification of causal mutations will provide insights into the molecular mechanisms of antibiotic resistance. We propose a method to prioritize mutated genes responsible for antibiotic resistance, in which mutated genes that also show significant expression changes among their functionally coupled genes become more likely candidates. For network-based analyses, we developed a genome-scale co-functional network of K. pneumoniae genes, KlebNet (www.inetbio.org/klebnet). Using KlebNet, we could reconstruct functional modules for antibiotic-resistance, and virulence, and retrieved functional association between them. With complementation assays with top candidate genes, we could validate a gene for negative regulation of meropenem resistance and four genes for positive regulation of virulence in Galleria mellonella larvae. Therefore, our study demonstrated the feasibility of network-based identification of genes required for antimicrobial resistance and virulence of human pathogenic bacteria with genomic and transcriptomic profiles from antibiotic-resistant clinical isolates.

overall_design: We used two strains of K. pneumoniae clinical isolates from a single patient who had undergone meropenem treatment: YMC2014/2/R777 (K26) and YMC2014/3/P345 (K56) that were isolated before and after the meropenem administration, respectively. A significant increase in meropenem minimum inhibitory concentration (MIC) was observed in K56 compared with K26 from 0.5 µg/ml to ≥16 µg/ml.

first: Naina

last: Pinto

first: Chan Yeong

last: Kim

first: Roshan

last: D’Souza

first: Dongeun

last: Yong

first: Insuk


title: Targeting CREBBP/EP300 in cancer

status: Public on Jun 12 2018

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

country: Spain

institute: ISCIII

summary: Antiprolifereative effects of CREBBP/EP300 inhibitors were tested in human leukemia and lymphoma cell lines and the molecular mechanisms responsible for such effects were explored.

overall_design: K562 cells were treated with CBP-30 (CREBBP/EP300 bromodomain inhibitor), C646 (CREBBP/EP300 HAT activity inhibitor) and JQ1 (BRD4 inhibitor) and changes in gene expression were evaluated by RNA-seq.

first: Veronica

last: Garcia-Carpizo

first: Osvaldo

last: Graña

middle: J


title: RNA-sequencing of human mammary epithelial cells (HMLEs) transduced in vitro with a shRNA against SOX4 or a scrambled shRNA in untreated and TGF-β-treated (16 hours) conditions

status: Public on Jun 11 2018

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

summary: In order to identify SOX4- and TGF-beta dependent genes, human mammary epithelial cells (HMLEs) were transduced with shRNA scrambled (control) or shRNA targeting SOX4 (TRCN0000018213, Sigma Aldrich, St. Louis, MS) and selected with puromycin for at least 2 weeks. SOX4 knockdown was confirmed by qRTPCR and western blotting. Cells were plated in 6 well plates and either left untreated or treated with TGF-beta (2.5ng/ml) for 16 hours in biological duplicate (different passages). Samples were harvested and total RNA was isolated using RNAeasy kit (Qiagen). Samples were sequenced on the NextSeq 500 (Illumina), SE75.

overall_design: Through RNA-sequencing we analysed the differentially expressed genes upon in vitro knockdown of SOX4 and TGF-β pathway activation in human mammary epithelial cells using one shRNA against SOX4

first: S

last: Vervoort

first: A

first: P

last: Coffer


title: Platelet Transcriptome Profiling in HIV and ABCC4 as a Biomarker of Platelet Activity

first: Jeffrey

middle: Stuart

last: Berger

address: 522 First Avenue

department: Cardiology

institute: NYU Langone Medical Center

summary:
The purpose of this study was to perform an unbiased RNA expression profile in platelets from HIV subjects under ART and healthy controls to identify a gene signature for the HIV hyperactive phenotype.
Methods: Rna-Sequencing was performed in leukocyte-depleted platelet RNA from 6 HIV subjects and 3 healthy controls.  qRT–PCR validation was performed to validate our candidate transcripts.
Results: Across the 9 platelet samples, there was an average of 28.3 million mapped reads per sample with an average unique mapping rate of 91.6 %. Using a cut-off of normalized counts ≥1 across the 9 samples, we found 11988 expressed transcripts.
Conclusions: Our study represents a detailed analysis of platelet transcriptome generated by RNA-seq technology in HIV patients under ART. Further experiments identified the mechanism of our transcript target in mediating platelet activity and platelet cell effector function.

overall_design: Platelet mRNA profiling in HIV subjects under ART vs helthy controls to identify candidate transcripts with differential expression.

first: Emanuela

last: Marcantoni

first: Nicole

last: Allen

first: Matthew

last: Cambria

first: Rebecca

last: Dann

last: Cammer

first: Tenzin

last: Lhakhang

first: Meagan

last: O’Brien

first: Benjamin

first: Tilla

last: Worgall

first: Adriana

last: Heguy

first: Aristotelis

last: Tsirigos

middle: S


title: Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [Chromium 10X]

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity.

overall_design:
Single-cell transcriptome analyses of two HCC cell lines (HuH-1 and HuH-7) and one patient-derived circulating tumor cells by using Chromium 10X protocol.

***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***

middle: W


title: Single cell analysis reveals cancer cell heterogeneities in hepatcellular carcinoma

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

overall_design: Refer to individual Series


title: Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [SMART-seq]

overall_design:
Single-cell transcriptome analyses of two HCC cell lines (HuH-1 and HuH-7) and one patient-derived circulating tumor cells by using SMART-Seq protocol

***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***


title: KhpA and KhpB Regulate Peptidoglycan Synthesis and Cell Division in the “Superbug” Streptococcus pneumoniae

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

summary: Streptococcus pneumoniae is a human commensal bacterium that causes serious diseases. Peptidoglycan (PG) is the critical component of bacteria that maintains cell shape, size, chaining, and turgor resistance. Because of its surface exposure and eubacterial-specific mechanism of biosynthesis, PG biosynthesis remains an outstanding target for discovery of new antibiotics to resistant “superbugs,” like S. pneumoniae. Pneumococcal PG biosynthesis is carried out by a balance of septal and peripheral (side-wall-like) PG synthesis mediated by bPBP2x and bPBP2b, respectively, that emanates from midcell regions. We selected for additional suppressor mutations, besides mltG, that eliminate the requirement for essential bPBP2b in peripheral PG synthesis. We found that mutations that inactivate a putative RNA binding protein, designated KhpA, suppressed the requirement for some, but not all of the essential proteins required for peripheral PG synthesis. KhpA was used as bait in co-IP experiments to demonstrate interactions with a second RNA binding protein, designated KhpB, in cells. Mutations in khpA or khpB phenocopy each other and result in slower growth rates, smaller cell size with normal aspect ratios, and induction of cell wall stress responses. RIP-Seq analyses confirmed KhpAB as RNA binding protein in cells. Another suppressor of Δpbp2b implicated induction of a cell division operon as a way to bypass the requirement for bPBP2b. We show that increased expression of this cell division operon occurs in ΔkhpAB mutants and that this induction is necessary and sufficient to account for suppression of Δpbp2b. Comparisons of relative transcript amounts and protein levels indicate that induction of this cell division operon in ΔkhpAB mutants occurs primarily at the post-transcriptional level. Together, our results show that KhpAB, which are virulence factors in S. pneumoniae and are conserved in other Gram-positive pathogens, acts as a new class of RNA binding protein, with properties analogous to Hfq in Gram-negative bacteria.

overall_design: RNA was prepared from cultures of IU1824 (parent) and IU9036 (∆khpA) strains grown exponentially in BHI media at 37ºC to OD620 ≈0.15 to 0.2. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Jiaqi

last: Zheng

first: Ho-Ching

middle: T

last: Tsui

middle: E


title: Lkb1 interacts with a ciliopathy complex to regulate inflammation (RNA-Seq)

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Ciliopathies comprise a spectrum of inherited disorders involving different organ systems such as the central nervous system, the skeleton, and the kidney1. The cilium is a hair-like organelle at the cell surface that acts as a sensor and signal transducer2. Many ciliopathy manifestations can be linked to deficient cilia function, yet it is unclear how a cilium defect results in nephronophthisis (NPHP), the most prevalent renal manifestation in children, characterized by inflammation, interstitial fibrosis, and renal cysts3. Here, we report that deletion of the serine threonine kinase Lkb1 in the mouse kidney results in cardinal features of nephronophthisis. An in-vivo proteomic interaction screen revealed ANKS3, a known interaction partner of the nephronophthisis protein NPHP1, and its interactor NEK7 as novel binding partners of LKB1. Lkb1 genetically interacts with Nphp1 in zebrafish. Unbiased transcriptional analysis in-vitro and in-vivo revealed that the chemokine CCL2 is upregulated in Lkb1 deficiency and is accompanied by recruitment of CCR2 expressing mononuclear cells in the kidney. CCL2 regulation requires NPHP1, ANKS3 and NEK7. These findings link LKB1 and ciliopathy proteins to immune regulation and explain how mutations in NPHP proteins result in fibrosis of the kidney.

overall_design: The transcriptomes of WT MDCK cells was compared Stk11 (Lkb1) KD MDCK cells by RNAseq.

first: Melanie

last: Boerries

first: Amandine

last: Viau

first: Wolfgang

last: Kuehn

first: Frank

last: Bienaimé


title: SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis

status: Public on Jun 09 2018

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEAD-box pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences pri-miRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also enhances the abundance of the DCL1 protein levels through promoting the splicing of the DCL1 pre-mRNAs. Collectively, our data provide new insights into the function of SMA1/Prp28 in regulating miRNA abundance in plants.

overall_design: Non-coding RNA deep sequencing

first: Shengjun

last: Li

first: Ran

last: Xu

first: Aixia

first: Yunhai

first: Bin

last: Yu


title: Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation

city: Jerusalem

first: Eran

last: Rosenthal

address: Givat Ram

department: Computer Science

country: Israel

institute: Hebrew University

summary:
Histone H2B monoubiquitylation (H2Bub1) is localized to transcribed regions of genes and spread in parallel with the progress of RNA polymerase II (Pol II). H2Bub1 levels are highly correlated both with transcription and elongation rates of mammalian genes. Although H2Bub1 correlate with elongation rates, it is not clear whether the correlation is due to causative role of H2Bub1 in regulating elongation rate or the vice versa.
By utilizing our recently developed method to measure genomewide elongation rate – 4sUDRB-seq, we tested genomewide elongation rates in H2Bub1 depleted cells. Our results show that H2Bub1, although widely appreciate as an elongation factor, is not needed for proper transcription elongation. Although H2Bub1 depletion does not affect transcription elongation, its depletion results in the upregulation of more than 1000 genes. Our findings show that H2Bub1 regulates the pause release of Pol II at these genes. This specificity might be mediated through the relatively high proximity of H2Bub1 to paused Pol II at these genes. Overall, our data shed light on the regulation of transcription by H2Bub1 and suggest that the role of H2Bub1 in transcription elongation should be reconsidered.
-------------------------------------------
see also: Fuchs G, Voichek Y, Benjamin S, Gilad S et al. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol 2014 May 9;15(5):R69. PMID: 24887486
see also Dataset GSE57116, Samples GSM1375518 – GSM1375525

overall_design: Pol II ChIP-seq, mRNA and 4sUDRB-seq were derived for different replicates of RNF20 siRNA and control siLacZ

first: Gilad

last: Fuchs


title: Enteric bacteria increase the defenses against oxidative stress in Entamoeba histolytica

status: Public on Jun 08 2018

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Characterization of the human microbiota is providing new insightsinto the complexity of host–parasite–bacterium relationships. Amoebiasis (an intestinal infection affecting a large proportion of the population in many countries worldwide) is caused by the amoebic parasite Entamoeba histolytica. During amoebiasis, the parasite encounters several types of stress as a result of the host’s response to infection. Given that E. histolytica phagocytises bacteria in the intestinal lumen, we hypothesized that enteric bacteria can influence the course of an amoebic infection. Hence, we used live Escherichia coli O55 as a pertinent model of the bacterial community’s contribution to amoebic responses during host- induced stress. By measuring amoebic survival, we found that live E. coli protected E. histolytica against oxidative stress (OS) but not against nitrosative stress. E. coli– associated protection is correlated with massive transcriptionalchanges in amoebic genes acquired through lateral transfer from the bacterial kingdom, including genes coding for proteinscontaining leucine-rich repeat (LRR) motifs. The transcriptome profile triggered by OS and E. coli was also observed with other enteric bacteria, including pathogens and non-pathogens. In contrast, exposure to a probiotic resulted in a different transcriptome profile. The present study shows that OS and live bacteria together modulate 84 of E. histolytica’s 137 LRR protein genes. The LRR proteins are involvedin protein-ligand and protein-protein interactions – especially in proteins that interact with bacteria as part of the innate immune response in mammals and plants, such as Toll-like receptors. The structural and functional homology of LRRs and TLRs identified here suggest that despite its old age in evolutionary terms, the protozoan E. histolytica displays key characteristics of higher eukaryotes’ innate immune systems. We conclude that components of innate immunity existed in the common ancestor of plants and animals

overall_design: RNA-seq analysis of Entamoeba histolytica parasites in different states: live, killed, non-infected or infected by some bacteria (E.coli, E.faecalis, L.acidophilus, S.enterica), in presence or absence of oxydative stress.

first: Hugo

last: Varet

first: Yana

last: Shaulov

first: Odile

last: Sismeiro

first: Meirav

last: Geffen

first: Jean-Yves

last: Coppée

first: Serge

last: Ankri

first: Nancy

last: Guillen


title: Aberrant expression of histone homocysteinylation: Implications for neural tube defects (RNA-seq)

first: Qin

address: 2 YaBao Road，Chao Yang Distinct

institute: Capital Institute of Pediatrics

summary: Neural tube defects (NTDs) are serious congenital malformations. Excessive maternal homocysteine (Hcy) increases the risk of NTDs, while its mechanism remains elusive. In this study, we evaluated the role of histone homocysteinylation in neural tube closure (NTC). A total of 39 histone homocysteinylation sites were identified in samples from human embryonic brain tissue using mass spectrometry. Elevated levels of histone KHcy and H3K79Hcy were detected at increased cellular Hcy levels in human fetal brains. Using ChIP-seq and RNA-seq assays, we demonstrated that increase in H3K79Hcy level downregulated the expression of selected NTC-related genes including Cecr2, Smarca4, and Dnmt3b. In human NTD brain tissues, decrease in expression of Cecr2, Smarca4, and Dnmt3b was also detected along with high levels of Hcy and H3K79Hcy. Our results suggest that higher levels of Hcy contribute to the onset of NTDs through upregulation of histone H3K79Hcy, leading to abnormal expression of selected NTC-related genes.

overall_design: NE4C cells mRNA profiles of HTL treatment and normal control were generated by deep sequencing,using BGISEQ-500 .


title: Characterize novel lncRNAs responding to stresses in Oryza sativa at transcriptional and post-transcriptional levels

first: Jiapei

last: Yuan

state: Beijing

address: Tsinghua Yuan

institute: Tsinghua University

summary: We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

overall_design: We treated the seedlings under the stress conditions, including cold, drought, heat, high-salt, and high-light. Also, we choose two tissues, roots and panicles for RNA sequencing.

first: Jia

middle: P

first: Zhi

last: Lu


title: Genome-wide mapping of H3K9me2 of wild-type and various deletion strains in fission yeast.

city: Hangzhou

first: Min

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

summary: ccp1Δ affects the genome-wide distribution of H3K9me2.

overall_design: ChIP-seq (anti-H3K9me2) were performed to specific deletion strains and wild type strain.

first: Xiangwei

last: He


title: Aged Hematopoietic Stem Cells Drive Aging-Associated  Immune Remodeling

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: Phenotypic and functional changes seen in the aged adaptive immune system are primarily driven by aging of hematopoietic stem cells (HSCs), pharmacological rejuvenated aged HSCs were able to reconstituted a youthful immune system

overall_design: We employed RNA-seq to assess similarities/differences between naive CD4+ T cells and CD19+ B cells isolated from RAG1-/- recipients transplanted with either young, old or old rejuvenated (CASIN treated) HSCs


title: Murine mammary epithelial cell methylome and ATAC-seq analyses

city: Toronto

first: Rama

last: Khokha

state: ON

address: Princess Margaret Research Tower, 101 College Street

department: Medical Biophysics

country: Canada

institute: Princess Margaret Cancer Centre

type: Methylation profiling by high throughput sequencing

summary: The following data comes from two separate experiments. In the initial experiment, luminal and basal murine mammary epithelial cells were analyzed by reduced representation bisulfite sequencing (RRBS) to generate methylome profiles. In the second experiment, luminal and basal murine mammary epithelial cells were analyzed by ATAC-seq.

overall_design: Luminal and basal primary mammary epithelial cells were FACS-purified from WT FVB mice and subjected to methylome (via RRBS) or ATAC-seq analyses (n=2; prior to cell extraction mice were ovariectomized and treated with 17β-oestradiol + progesterone [EP] for 2 weeks).

first: Alison

last: Casey

first: Daniel

last: De Carvalho

first: Rajat

last: Singhania

first: Mathieu

last: Lupien

first: Swneke

last: Bailey

first: Genevieve

last: Deblois


title: Enhancer profiling in metastatic cancer [RNA-Seq]

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: Metastases cause the majority of cancer-related deaths. Yet, the origins of metastatic cancer phenotypes remain poorly understood. Few metastasis-specific driver mutations have been identified [1-3], raising the possibility that metastatic transcriptional programmes may emerge from perturbations in the oncogenic signalling cascades that support the development of primary tumours. Here, using genome-wide histone modification profiling, high-throughput chromatin conformation capture by Hi-C and functional analysis in human-derived metastasis models of renal and breast cancers, we identify transcriptional enhancers that drive metastatic cancer progression. We demonstrate that specific enhancers and enhancer clusters are activated in metastatic cancer cell populations. The activation status of these enhancers is associated with gene expression patterns predictive of poor patient outcome in clinical samples. CRISPRi-mediated inhibition of enhancer activity and genetic ablation of enhancer sequences demonstrated the requirement of metastasis-associated regulatory elements for metastatic colonization in vivo. We further show that metastatic cancer clones co-opt evolutionarily conserved enhancers that converge on shared metastasis driver genes, such as CXCR4. Thus, we provide functional evidence for the requirement of specific enhancers for metastatic colonization and show that metastatic traits can arise through tissue-specific commissioning of distal gene regulatory elements.

overall_design: mRNA profiling in experimental models of metastasis.

first: Paulo

last: Rodrigues


title: FBXL19 recruits CDK8-Mediator to CpG islands and primes developmental genes for activation during lineage commitment

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford


title: FBXL19 transcriptionally primes promoters of developmental genes via CDK8-Mediator recruitment [ChIP-seq 1]

summary: Regulatory elements called CpG islands (CGIs) are associated with the majority of mammalian gene promoters and have been proposed to play an important role in gene expression. The regulatory capacity of CGIs is thought to rely upon a family of proteins that recognise CGIs through their ZF-CxxC DNA binding domains to recruit chromatin-modifying activities to gene promoters. Through studying FBXL19, a poorly characterized ZF-CxxC domain-containing protein, we have discovered that it specifically interacts with the CDK8-Mediator complex in mouse embryonic stem cells (ESCs). Intriguingly, FBXl19 recruits CDK8-Mediator to a subset of CGI-associated promoters of repressed developmental genes in ESCs. We show that FBXL19-dependent recruitment of CDK8 in ESCs is required for the proper induction of the associated genes during ESC differentiation. This is consistent with early embryonic lethality of in FBXl19 deficient mice. Together, our observations highlight a novel role for FBXL19 in priming developmental gene expression, via recruitment of CDK8 to their CGI promoters, in order to support normal gene induction during differentiation and development.

overall_design: Binding profile of FBXl19 and its dependency of a functional CxxC domain was determined via performing ChIPseq for epitope-tagged wild type, CxxC point mutant FBXL19 and ΔCxxC FBXL19 in ES cells.

first: Robert

last: Klose


title: Decoupling the influence of growth and defense in the yeast stress response

city: madison

first: Audrey

last: Gasch

state: wi

address: 425G Henry mall

department: genetics

institute: university of wisconsin, madison

summary: We demonstrate that ESR activation upon stress cannot be simply explained by cell cycle distribution or growth arrest. We further study translation regulations under cel cycle arrested condition and  upon stress via polysome-seq.

overall_design: RNA-seq, polysome-seq and transcriptome analysis of yeasts. Biological replicates were perfomed.

first: Yi-Hsuan

last: Ho


title: FBXL19 transcriptionally primes promoters of developmental genes via CDK8-Mediator recruitment [RNA-seq]

overall_design: Gene expression analysis of wild type (Fbxl19fl/fl) and mutant (ΔCxxC Fbxl19) cells in pluripotent state and and during retinoic acid differentiaion performed by 4sU-RNA sequencing.


title: FBXL19 transcriptionally primes promoters of developmental genes via CDK8-Mediator recruitment [ChIP-seq 2]

overall_design: Fbxl19fl/fl embryonic stem cells were used to delete the CXXC domain of FBXL19. CDK8 occupancy was then profiled by ChIP-seq in biological duplicates to assess the contribution of FBXL19 to CDK8 binding to chromatin.


title: The thyroid hormone receptors regulate the expression of microRNAs with key roles in skin homeostasis

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

institute: CIEMAT

summary: The role of the nuclear receptors (TRs) of thyroid hormones in cutaneous miRNA has been studied using RNAseq in a mice model

overall_design: We have used RNAseq to compare the skin miRnome of wild-type mice and genetically modified mice lacking both TRα1 and TRβ the main thyroid hormone binding isoforms

first: Lidia

last: Ruiz-Llorente

first: Constanza

last: Contreras-Jurado

first: Mónica

last: Martínez-Fernández

first: Jesús

last: Paramio

first: Ana

last: Aranda


title: Lkb1 interacts with a ciliopathy complex to regulate inflammation

first: Hauke

last: Busch

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus

overall_design: Refer to individual Series


title: Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

summary: Lineage segregation in the mouse embryo is a finely controlled process dependent upon coordination of signalling pathways and transcriptional responses. We employed conditional deletion of Oct4 to investigate consequences of interference with embryonic patterning and lineage specification. Nanog becomes upregulated in the first epiblast cells to lose Oct4, leading to an expanded Nanog-positive domain. The primitive streak forms in the presumptive proximal posterior region, but epithelial to mesenchymal transition is impeded by dramatic increase of E-cadherin, leading to complete disorganisation and failure to generate germ layers. Formerly, expression domains of lineage markers were disrupted. Specifically, definitive endoderm expanded, the boundaries between presumptive anterior and posterior domains blurred and an ectopic posterior-like region appeared anteriorly, suggesting a role for Oct4 in maintaining the embryonic axis. Despite intermixing of lineage marker domains in mutants, cells co-expressing distinct lineage genes were not observed, suggesting that Oct4 deletion does not alter the connectivity of the transcription networks which underlie cell fate decisions in vivo. Molecular profiling corroborated genome-wide posteriorisation of mutants and disrupted expression of genes involved in gastrulation. Lastly, we confirmed a requirement for Oct4 in self-renewal of post-implantation epiblast ex vivo

overall_design: mRNA profiling of OCT4- and OCT4+ mouse in post implantation stage

first: Gloryn

last: Chia le Bin

first: Carla

last: Mulas

first: Kenneth

last: Jones

middle: G

first: Jennifer

last: Nichols


title: Major Facilitator Superfamily Domain Containing 7C (Mfsd7c) Mediates the Effects of Heme on Cell Metabolism, Motility and Transcription

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Dysfunctional mutations of major facilitator superfamily domain containing 7C (Mfsd7c) are associated with Fowler's Syndrome. However, beyond its reported activity in heme importation, the function of Mfsd7c is unknown. Herein, we show that Mfsd7c forms complexes with proteins in both mitochondrial and cytoplasmic membranes including components of the electron transport chain (ETC), Fc receptors, and integrin. Cells deficient in Mfsd7c exhibit altered ETC activities with an elevated oxygen consumption rate and heat generation, decreased ATP synthesis and production of reactive oxygen species, and attenuated responses to heme stimulation. Mfsd7c-deficient cells are more motile with increased antibody-dependent cellular phagocytosis (ADCP) activity and exhibit an altered transcriptional response to heme stimulation through transcriptional factors CREB and NF-kB. These results show that Mfsd7c mediates the effects of heme in cell metabolism, motility and transcription, and shed light on how dysfunctional Mfsd7c mutations may contribute to Fowler’s syndrome.

overall_design: Assay the transcriptional impact of Heme treatment by comparing gene 3 sets of CD11c+ Siglec-F+ alveolar macrophages treated with 40 μM heme in for 2 hours with 3 sets of similar but untreated cells.

first: Yingzhong

last: Li

first: Marianna

last: Kleyman

first: Guangan

last: Hu

first: Walter

last: Chen

first: Dimitrios

last: Papageorgiou

first: Lucas

middle: B

last: Sullivan

first: Mandeep

last: Kaur

first: Nikola

last: Ivica

first: Amanda

last: del Rosario

middle: A

first: Jianzhu


title: Low Cell-Matrix Adhesion Reveals Two Subtypes of Human Pluripotent Stem Cells

city: Kyoto

first: Leqian

last: Yu

address: 205 Room, International Science Innovation Building

country: Japan

institute: Kyoto university

summary: The human pluripotent stem cells cultured on Low-adhesion substrates formed two morphologically different subtypes (Monolayer and Domed).  The dome-like cells showed higher proliferation capacity and KLF4/5 expression than the monolayer cells. A serum response factor based regulatory double loop was proposed to explain how cell-matrix adhesion mediates the interaction between cell morphology and pluripotency genes

overall_design: Compare the two type cells with RNA-seq to investigate the different expression

first: Yujiao

last: Dang

first: Yu

last: Hou

first: Li

last: Liu


title: Differentially transcribed miRNAs in stress-induced premature senecence (SIPS)

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: Detection of senescence-associated miRNAs differentially transcribed during early (D7) and late stages (D21) of human dermal fibroblast (HDF) senescence

overall_design: 12 samples in total. Three different HDF strains from different donors, each quiescent control (Q) and SIPS,  two different timepoints (day 7 and day 21)

first: Lucia

last: Terlecki-Zaniewicz

first: Johannes

last: Grillari

first: Julie

last: Latreille


title: RNA-seq: weight cycling time series (eWAT)

status: Public on Jun 07 2018

city: Seoul

first: Je Kyung

last: Seong

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

summary: Gene expression change on weight cycling mice eWAT

overall_design: transcriptome profiling from diet-induced weight gain, loss and re-gain (weight cycling time series) mice eWAT

first: Je

middle: K

first: Dong

last: Kyeong


title: Dissection of influenza infection in vivo by single-cell RNA-sequencing

status: Public on Jun 06 2018

city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

institute: Tel-Aviv University

summary: The influenza virus is a major cause of morbidity and mortality worldwide, yet, the impact of intracellular viral invasion and the cellular response diversity remain uncharacterized. By massively parallel single-cell RNA-seq we comprehensively mapped the host lung response to in-vivo influenza infection in wild-type and Irf7-knockout mice across nine immune and non-immune cell types. We found an unexpected high prevalence of infected cells in all cell types, showed that infection is a characteristic property of cell types that is independent of type-I interferon activity, and demonstrated that all cell types responded primarily with a robust generic transcriptional response. Analysis of the viral and host transcriptomes in the same single cell enabled us to resolve the heterogeneity of bystander (exposed but uninfected) as compared to viral-infected cells. Our results highlight novel markers specific for influenza-infected as opposed to bystander cells, opening new avenues for targeted therapy aimed exclusively at infected cells.

overall_design: We used Massively parallel single-cell RNA-seq (MARS-seq) to characterize single cell RNA-seq of immune (CD45+) and non-immune (CD45-) cells derived from the lungs of influenza-treated and PBS-treated mice.

first: Ido

last: Amit

first: Yael

last: Steuerman

first: Merav

last: Cohen

first: Liran

last: Valadarsky

first: Eyal

last: David

first: Amit

last: Frishberg


title: Transcriptomic insight into molecular processes of light-induced rapid darkening of non-obligative cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura) and their genetic basis of pigmentation strategy

city: Chengdu

first: xungang

last: wang

address: No.9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

summary: O. rhodostigmatus are non-obligative cave dwellers, whose tadpoles keep albinistic phenotype in caves but rapidly darken in light within 24 hours. Their coloration system is an excellent model for exploring the processes and mechanisms of light-induced pigmentation and revealing the genetic adaptation for non-obligative cave dwelling due to complicated life history. Using comparative transcriptomics, we found that melanocyte MCC (including melanogenesis and melanocytes proliferation) was responsible for the rapid skin darkening in was activated in O. rhodostigmatus. Light exposure induced robust activation of growth signals (including growth factor signals, MAPK signal pathways and PIK3-Akt signal pathways) at transcriptional levels, which were likely the upstream activation signals of melanocyte MCC in O. rhodostigmatus tadpoles. These results evidenced that amphibians and mammals likely share similar regulatory signals for light-induced melanocyte MCC. The conservation of pigmentation mechanisms across lower vertebrates and mammals imply that knowledge based on simpler models could also provide implications for causations and therapies of human pigmentation disorders and pigmented tumors. In aspect of genetic adaptation, an in-frame deletion of four amino acids in the membrane/extracellular junctions of the second and third transmembrane domains of O. rhodostigmatus MC1R, the receptor for melanogenesis signal, was identified. This mutation increases the negative charge of the ligand pocket of MC1R and results stereo-tandem of three aspartate residues aligning towards its ligand pocket. The ligand pocket of O. rhodostigmatus MC1R resembles a trap for positively charged ligands (α-MSH and ACTH) and likely increases the ligands-dependent activity of MC1R, providing an explanation for the rapid MCC of O. rhodostigmatus in light. Meanwhile, increased negative charge of ligand pocket likely decreased the constitutive activity of MC1R, in in supporting the albinistic phenotype of cave dwelling tadpoles. Therefore, genetic change of MC1R explains, at least to some extent, how the pigmentation system of O. rhodostigmatus coordinates the capacity of rapid melanogenesis (or other types of pigment production) and pigment regression, a couple of seemingly contradictory coloration requirements. To our knowledge, this is the first study reporting the association between pigmentation phenotype adaptation and MC1R mutations in amphibians or in non-obligative cave dwellers.

overall_design: The light-induced skin darkening in the cave-adapted tadpoles of O. rhodostigmatus was investigated based on comparative transcriptomics. Firstly, genes showed a light-depended expression pattern were screened, and functional enrichment analyses were conducted to present the primary cellular processes in response to light exposure; Secondly, the expression pattern of genes involved in pigmentation were analyzed exclusively to determine the coloration types in O. rhodostigmatus tadpoles; Thirdly, genes showed close correlation with critical effector genes responsible for skin darkening in O. rhodostigmatus tadpoles were screened and a functional enrichment analysis were underwent to highlight the potential upstream regulation pathways; Finally, genes potentially contributing to genetic adaptation of coloration were analyzed by sequence aligning and protein homologous modeling to screen functional evolution responsible for the life history of O. rhodostigmatus. Based on the results, we mainly attempt to answer three questions:

first: Wei

last: Zhu

first: Lusha

first: Xungang

last: Wang

first: Xinyu

last: Gao

first: Jianping

last: Jiang

first: Bin


title: Role of Hmgb1 in hepatocarcinogenesis

city: New York

first: Robert

middle: F

last: Schwabe

address: 1150 st Nicholas Av

department: Medicine

institute: Columbia University

summary: The gene expression of normal and tumor tissues isolated from WT mice were compared with tumor tissues isolated from mice harboring liver specific deletion of HMGB1

overall_design:
a. Hepatocellular carcinoma from HMGB1 floxed control mice, treated with the combination of DEN (25 mg/kg i.p. given a day 15 postpartum) and CCl4 (0.5 ul/g, dissolved in corn oil, given weekly starting at week 8 postpartum for 15 weeks) (Hgmb1fl/fl , n=6)
b. Hepatocellular carcinoma from mice with liver-specific HMGB1 deletion (HMGB1fl/fl mice expressing Albumin-Cre), treated with the combination of DEN (25 mg/kg i.p. given a day 15 postpartum) and CCl4 (0.5 ul/g, dissolved in corn oil, given weekly starting at week 8 postpartum for 15 weeks) (Hgmb1Dhep , n=6)
c. Normal liver from C57Bl/6 control mice (n=3)

first: Celine

last: Hernandez

first: Peter

last: Huebener

first: Daniel

last: Antoine

first: Richard

last: Friedman


title: Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: MYC genes are frequently amplified and correlate with poor prognosis in MB. BET bromodomains recognize acetylated lysine residues and often promote and maintain MYC transcription. Certain cyclin-dependent kinases (CDKs) are further known to support MYC stabilization in tumor cells. In this report, MB cells were suppressed by combined targeting of MYC expression and MYC stabilization using BET bromodomain inhibition and CDK2 inhibition, respectively. Such combination treatment worked synergistically and caused cell cycle arrest as well as massive apoptosis. Immediate transcriptional changes from this combined MYC blockade were found using RNA-Seq profiling and showed remarkable similarities to changes in MYC target gene expression when MYCN was turned off with doxycycline in our MYCN-inducible animal model for Group 3 MB. In addition, the combination treatment significantly prolonged survival as compared to single agent therapy in orthotopically transplanted human Group 3 MB with MYC amplifications. Our data suggests that dual inhibition of CDK2 and BET bromodomains can be a novel treatment approach for suppressing MYC-driven cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 50 samples in total were analyzed. Four MB002 stimulated for 6h with DMSO, JQ1, Milciclib, and JQ1 and Milciclib. Five GTML2 stimulated for 6h with DMSO, JQ1, Milciclib, JQ1 and Milciclib, and doxycycline. Seven cell lines stimulated for 2h with DMSO. Two samples with human astrocytes from cerebellum and from spine. AF22 cell line. All samples in biological triplicates except doxycycline (duplicate), astrocytes and AF22 (single).

first: Sara

last: Bolin

first: Anna

last: Borgenvik

first: Camilla

middle: U

last: Persson

first: Anders

last: Sundström

first: Jun

last: Qi

first: James

last: Bradner

first: William

last: Weiss

first: Yoon-Jae

last: Cho

first: Holger

last: Weishaupt


title: Cerebellar gene expression from Mecp2-null and WT mice

status: Public on Jun 05 2018

first: Ayush

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

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


title: Biochemical and structural insights into the function of small RNA methyltransferase Hen1 in animals

city: Shanghai

first: Fengjuan

last: Zhang

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: HUA ENHANCER 1 (Hen1) is a RNA 2'-O-methyltransferase that modifies small non-coding RNAs (sncRNAs) by adding a methyl group to the 2'-OH of 3'-terminal nucleotides, thereby protecting them from other modifications and degradation. The molecular mechanism underlying the methylation of small RNA duplexes has been revealed by the crystal structure of Hen1 in Arabidopsis (AtHen1). However, the molecular basis of single-stranded RNA methylation by mammalian Hen1 homologues, especially p-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs), remains elusive. Here we show that mouse Hen1 (mHen1) is responsive for the 3’ end methylation of classical piRNAs, as well as for the non-canonical piRNAs derived from ribosomal RNA (rRNAs), small nuclear RNAs (snRNAs) and transfer RNAs (tRNAs) in mouse spermatogonial stem cells (SSCs). Moreover, we identified a class of transfer RNA (tRNA)-derived sncRNAs as novel substrates of mHen1, which we refer to as Hen1-methylated tRNA-derived small RNAs. We determined the crystal structure of the catalytic domain of human Hen1 (HsHen1) in complex with its cofactor AdoMet at 1.8 Å resolution. Comparisons of the structures of HsHen1 and AtHen1 reveal a similar active site for binding a divalent cation and AdoMet. An in vitro methyltransferase assay indicated that the complete catalytic domain of HsHen1 is sufficient to methylate a specific length of single-stranded RNAs in a manganese-dependent manner. In conclusion, our functional and structural findings provide important insights into the methylation details of sncRNAs in mouse SSCs, and the catalytic mechanism of mammalian Hen1

overall_design: Small RNA profiling of wild-type, mhen1-/- and mili-/- SSC, and which small RNAs have 3' modification by treatment with NaIO4.

first: Renfu

last: Shang

first: Hongdao

first: Ligang

last: Wu


title: Cerebellar gene expression from Mecp2-null and WT mice [RNA-Seq data set]

summary: Several recent studies have suggested that genes that are longer than 100 kb are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in Mecp2 mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, the statistical significance of these results needs to be re-evaluated. Here, we show that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-Sequencing datasets, particularly in genes with low-fold changes, disappeared when compared to randomized control samples. As we found no similar bias with Nanostring technology, this bias seems to be particular to PCR amplification-based platforms. Transcriptional alterations with large fold-change values, however, can reveal an authentic long gene bias. Discriminating authentic from artefactual length-dependent trends requires establishing a baseline from randomized control samples.

overall_design: RNA-seq cerebellum dataset

first: Huda

middle: Y

last: Zoghbi

first: Amy

last: Pohodich

first: Laura

last: Lavery

first: Ying-Wooi

last: Wang

first: Zhandong

last: Liu


title: MACROD2 haploinsufficiency promotes chromosome instability and growth of intestinal tumors

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

summary: RNA-Seq data from intestinal tumors of ApcMin/+/Macrod2-/-,ApcMin/+/Macrod2-/+ and ApcMin/+/Macrod2+/+ mice (6 tumors per group)

overall_design: Examine mRNA expression level changes between tumors by Macrod2 genotype

middle: M


title: Bases of antisense lncRNA-associated regulation of gene expression in fission yeast

status: Public on Jun 04 2018

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: Antisense (as)lncRNAs can regulate gene expression but the underlying mechanisms and the different cofactors involved remain unclear. Using Native Elongating Transcript sequencing, here we show that stabilization of antisense Exo2-sensitivite lncRNAs (XUTs) results in the attenuation, at the nascent transcription level, of a subset of highly expressed genes displaying prominent promoter-proximal nucleosome depletion and histone acetylation. Mechanistic investigations on the catalase-coding gene ctt1 revealed that its induction following oxidative stress is impaired in Exo2-deficient cells, correlating with the accumulation an asXUT. Interestingly, expression of this asXUT was also activated in wild-type cells upon oxidative stress, concomitant to ctt1 induction, indicating a potential attenuation feedback. This attenuation correlates with asXUT abundance, it is transcriptional, characterized by low RNAPII-ser5 phosphorylation, and it requires an histone deacetylase activity and the conserved Set2 histone methyltransferase. Finally, we identified Dicer as another RNA processing factor acting on ctt1 induction, but independently of Exo2. We propose that asXUTs could modulate the expression of their paired-sense genes when it exceeds a critical threshold, using a conserved mechanism independent of RNAi.

overall_design: NET-Seq analysis in exo2-delta cells of S. pombe

first: Camille

last: Gautier

first: Marc

last: Descrimes

first: Mayuko

last: Yoda

first: Valérie

last: Migeot

first: Damien

last: Hermand

first: Antonin

last: Morillon


title: DNA methylation regulates the neonatal CD4+ T-cell response to pneumonia in mice

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

summary: Lung CD4+ T cell responses may determine outcomes in pediatric pnuemonia. We therefore sought to define the transcriptional response and underlying DNA methyaltion landscape of lung CD4+ T cells by treating neonatal (~5 days of age) and juvenile (~15 days of age) mice with 2.8 million CFUs of E. coli or PBS (control) by aspiration. 48 hours later, lung CD4+ T cells were isolated by magnetic bead pre-enrichment and fluorescence-activated cell sorting for RNA-sequencing (RNA-seq) and modified reduced representation bisulfite sequencing (mRRBS).

overall_design: 3 replicates per group, each representing pooled cells from 3 neonatal and 2 juvenile mice/replicate.

middle: D

first: Sharon

last: McGrath-Marrow


first: McGrath-Marrow

last: Sharon A.


title: Human-specific features of special gene expression and regulation in eight brain regions

city: Okazaki

first: Yasuhiro

last: Go

address: 38 Nishigonaka Myodaiji

department: Department of Brain Sciences, Center for Novel Science Initiatives

institute: National Institutes of Natural Sciences

summary: Despite the substantial efforts made to compile the molecular maps of the human brain, they do not fully inform us of the features unique to humans. Yet, identification of these features might help us to understand both the evolution and nature of the human cognitive traits. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, gibbon and macaques. Integrated analysis of these data revealed existence of 1,851  human-specific transcriptome differences affecting one or multiple brain regions, in contrast to 240 chimpanzee-specific ones. More than a half of these differences represented elevated expression in human hippocampus, while the rest affected microglial functions in neocortex. Analysis of predicted regulatory interactions driving these differences revealed role of transcription factors in species-specific transcriptome changes, while epigenetic modifications were linked to spatial expression differences conserved across species.

sample_organism:
Hylobates lar
Gorilla gorilla
Pan troglodytes
Homo sapiens

overall_design: Transcriptome across eight brain regions (dorsolateral prefrontal cortex, ventrolateral prefrontal cortex, anterior cingulate cortex, premotor cortex, primary visual cortex, striatum, hippocampus, cerebellum) of humans, chimpanzees, gorillas and gibbon were measured using RNA-seq.

first: Chuan

last: Xu

first: Qian

last: Li

first: Olga

last: Efimova

first: Liu

last: He

first: Shoji

last: Tatsumoto

first: Takao

last: Oishi

first: Toshifumi

last: Udono

first: Katsushi

last: Yamaguchi

first: Shuji

last: Shigenobu

first: Akiyoshi

last: Kakita

first: Hiroyuki

last: Nawa

first: Philipp

last: Khaitovich


title: The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [ATAC-seq Grh mutants and Human GRHL]

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

institute: Institute of molecular Pathology

summary: Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. We show that deletion or ectopic expression of Grh causes loss or gain of DNA accessibility, respectively. However, while Grh binding is necessary for enhancer accessibility, it is insufficient to activate enhancers. Finally, we show that human Grh homologs, GRHL1/2/3, function similarly. We conclude that Grh binding is necessary and sufficient for the opening of epithelial enhancers, but not for their activation. Our data support the model that complex spatiotemporal expression patterns are controlled by regulatory hierarchies in which pioneer factors, such as Grh, establish tissue-specific accessible chromatin landscapes upon which other factors can act.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
ATAC-seq on control and Grh mutant eye-antennal discs.
ATAC-seq on control larval brains and larval brains that ectopically express  the epithelial isoform of Grh.
Omni-ATAC-seq on control MCF7 cells and on MCF7 cells with GRHL1,2,3 knockdown.
Experiments to establish the pioneering role of Grainyhead.

first: J

first: S

last: Aerts


title: The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [scATAC-seq]

overall_design: Single-Cell-ATAC-seq on eye progenitor cells (Optix-GFP positive) from the drosophila 3rd instar wandering larvae eye-antennal disc

first: K

last: Davie


title: Heterogeneity in early lymphoid compartments [CLP]

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

summary: In order to understand the developmental trajectories of early lymphocyte differentiation it is crucial to identify linage-restricted progenitors. It has become clear that the classical early lymphoid progenitor compartments in the bone marrow are molecularly and functionally heterogeneous which warrants further investigation to refine the marker combinations used to isolate these progenitors. Herein, an initial antibody screen revealed extensive surface marker heterogeneity amongst early lymphoid progenitors. This heterogeneity was resolved using single cell gene expression assays and single cell in vitro differentiation assays, identifying marker combinations that isolate functionally distinct populations. In addition, surface markers that could be used alone or in combination with classical targets to capture specific stages of B-cell development were identified in the screen. The data provides a greater resolution of the complexity of the lymphoid progenitor compartment within the bone marrow than has been understood to date and provides novel tools for the further identification of cell populations in B-lineage development.

overall_design: Investigation of the transcriptome in 3 different bone marrow CLP compartments by RNASeq (3-6 replicates/cell type)

first: Christina

middle: T

last: Jensen

first: Tobias

last: Strid

first: Mikael

last: Sigvardsson


title: QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

institute: Technion

summary: The finding that small non-coding RNAs (sRNAs) can affect cellular processes by regulating gene expression had a significant impact on biology research and clinical diagnosis. Yet, the ability to quantify and profile sRNAs, especially miRNAs, using high-throughput sequencing is especially challenging because of their repetitive nature. We have developed QsRNA-seq a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling separation of fragments differing only by 20nt in length and implementing barcode and unique molecular identifiers for multiplexing and accurate quantification. We show that this method gives very accurate, comprehensive and reproducible results. Using QsRNA-seq to study the miRNA repertoire in C. elegans embryo and L4 larval developmental stages, we found many miRNAs that are expressed in a developmental-specific manner. Interestingly, when profiling miRNA length, we found that miRNAs 23-nt long are predominantly expressed in L4 developmental stage and not embryo.

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: RNA was extracted from wildtype C. elegans synchronized to embryo or L4 larval stage. For each stage, 3 independent biological replica RNA samples were used for construction of small RNA libraries. One of the 3 samples was also used for preparation of three technical replica libraries and, in addition, for preparation of 3 technical replicas of libraries without UMI (0N) at 5-adaptor. One library was prepared from human brain total RNA (Life technologies).

first: AyeletT

first: Alla

last: Fishman

first: Dean

last: Light


title: Glucose competition between immune cells and microbial pathogens controls infections

status: Public on Jun 03 2018

city: Clayton

first: Traude

last: Beilharz

address: Wellington Rd

department: Biomedicine Discovery Institute

institute: Monash University

summary: To understand the dynamic physiological changes in host and pathogen that occur during infection, some of which might be driving the ability of C. albicans to trigger macrophage cell death, we performed dual RNA-seq of C. albicans-infected bone marrow-derived mouse macrophages over a time course. We chose three time points corresponding to: (i) early events post-phagocytosis of C. albicans (approximately 1 h post infection), (ii) fungal escape following caspase 1-dependent pyroptosis (approximately 6 h post infection), and (iii) the transition to the rapid Phase II death (approximately 9 h post-infection).

sample_organism:
Candida albicans
Mus musculus

platform_organism:
Candida albicans
Mus musculus

overall_design: Analysis of dual RNA-seq  in C. albicans

first: Ana

last: Traven

first: Paul

last: Harrrison

middle: H


title: RNA-sequencing of shSRC-1 and shNT tamoxifen treated LY2 cells

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

summary: The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. SRC-1's role in affecting the transcriptome of the breast cancer endocrine resistant setting is uncovered through this RNA-seq analysis of LY2 cells grown with or without the presence of SRC-1

overall_design: We report the RNA-sequencing of tamoxifen treated LY2 breast cancer cells treated with non-targeting shRNA or SRC-1 (NCOA1) targeting shRNA and examine the gene expression differences.

middle: S

first: Ailis

last: Fagan

first: Elspeth

last: Ward


title: Neuronal integrity, not activity, drives synaptic material clearance by microglia after CNS injury

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Phagocytosis of synaptic debris by microglia is critical for CNS development and homeostasis. Less well understood are microglial functions in injured adult brain, where their presumed role is clearance of neuronal debris. Assay of this process is challenging, because the resulting peripheral myeloid-cell engraftment is difficult to dissociate from microglial clearance. The model used here, optic nerve crush injury in adult mouse, stimulates rapid engulfment of synaptic material by microglia residing in the lateral geniculate nucleus (LGN), sufficiently distant from the injury to preclude peripheral-cell engraftment. Pre-injury pharmacological depletion of microglia causes post-injury accumulation of synaptic debris, suggesting that these, not astrocytes, are the dominant post-injury phagocytes. Genetic and pharmacological manipulations revealed that neuronal activity, which regulates microglial engulfment of synaptic debris in development, does not do so in post-injury synaptic material clearance in adulthood, where such clearance depends instead on axonal integrity. RNAseq reveals C1q involvement in clearance of debris by LGN-resident microglia, supporting our finding of its impaired clearance in C1qa-/- and Itgam-/- mice. Our results demonstrate how neurodegenerative debris is cleared by microglial phagocytosis, and offer a model for assaying microglial phagocytic activity and studying its mechanisms and physiological roles.

overall_design: Microglia were isolated from the LGN of adult (2-3 months old) male c57BL/6 mice in either uninjured, one, or three days post bilateral optic nerve crush injury. Cells were isolated by MACS using CD11b magnetic beads.

first: Geoffrey

last: Norris

first: Igor

last: Smirnov

first: Anthony

last: Filiano

first: Hannah

last: Shadowen

first: Kris

last: Cody

first: Kodi

last: Ravichandran

middle: C

first: Jonathan

last: Kipnis


title: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

city: Nedlands

first: Christian

last: Pflueger

state: Western Australia

address: 6 Verdun Street

department: Harry Perkins Institute of Medical Research

institute: University of Western Australia

summary: DNA methylation is a covalent modification of the genome that plays important roles in genome regulation and vertebrate development. Although detection of this modification in the genome has been possible for several decades, the ability to deliberately and specifically manipulate local DNA methylation states  in the genome has been extremely limited. Consequently, this has impeded the direct determination of the consequence of DNA methylation on transcriptional regulation and transcription factor binding in the native chromatin context. Thus, highly specific targeted epigenome editing tools are needed to address this outstanding question. Recent adaptations of genome editing technologies, such as the fusion of the DNMT3A methyltransferase catalytic domain to catalytically inactive Cas9 (dC9-D3A), have aimed to provide new tools for altering DNA methylation at desired loci. Here, we performed a deeper analysis of the performance of the tools at a genome wide level which revealed consistent off-target binding events and DNA methylation deposition throughout the genome, limiting the capacity of these tools to generate unambiguous determination of the functional consequences of DNA methylation. To address this issue, we developed a modular dCas9-SunTag (dC9Sun-D3A) system that can recruit multiple DNMT3A catalytic domains to a target site for editing DNA-methylation. dC9Sun-D3A is tunable, specific and exhibits much higher induction of DNA methylation at target sites than the dC9-D3A direct fusion protein. Importantly, genome-wide characterization of dC9Sun-D3A binding sites and DNA methylation revealed minimal off-target protein binding and induction of DNA methylation with dC9Sun-D3A, compared to pervasive off-target binding and methylation by the dC9-D3A direct fusion construct. Furthermore, we used dC9Sun-D3A to test the impact of DNA methylation upon the DNA binding of CTCF and NRF1 upon targeted methylation of their core binding sites, demonstrating the binding sensitivity of these proteins to DNA methylation in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the least amount of off-target DNA methylation reported to date, allowing accurate functional determination of the role of DNA methylation at single loci.

overall_design: A direct fusion dCas9-DNMT3A construct was compared to a modular, highly specific dCas9-SunTag + aGCN4-DNMT3A catalytic domain (dC9Sun-D3A) system, where on- and off-target DNA methylation deposition was measured by bsPCR-seq at select loci. dC9Sun-D3A was found to have less off-target effects compared to direct fusion dCas9-DNMT3A while not compromising its high on-target performance. Consequently, the response of targeted DNA methylation at CTCF and NRF1 core binding sites in HeLa cells by dC9Sun-D3A was measured by bsPCR-seq, ChIP-seq and ChIP-BS-seq to assess CTCF and NRF1 DNA methylation tolerance. dC9Sun-D3A was introduced by “hit-and-run epigenetic editing”, using transient transfection, and expression was selected for by either 48h puromycin treatment or cell sorting. DNA or chromatin was extracted from the cells after treatment and selection with controls (DNMT3AMut or mCherry aGCN4 coupled effectors) or dC9Sun-D3A for on-target DNA methylation deposition. WGBS, targeted solution capture bisulfite sequencing (TSC-bs-seq), ChIP-seq and ChIP-BS-seq libraries were prepared for sequencing on the Illumina HiSeq1500. bsPCR-seq libraries were sequenced on Illumina MiSeq.

first: Dennis

last: Tan

first: Tessa

last: Swaine

first: Trung

last: Nguyen

first: Jahnvi

last: Nefzger

first: Jose

last: Polo

first: Ryan

last: Lister


title: High-throughput transcriptome sequencing analysis provides insights into preliminary biotransformation mechanism of Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnose

city: Taiyuan

first: lei

last: Bi

address: xinjian south road

institute: Shanxi medical university

summary: In this paper, we present the first comparative transcriptome profiles with ARR treated and control of R. palustris. Moreover, putative two ARR biotransformation mechanisms in R. palustris were first given. All of these provided a valuable genomic resource for further studying molecular mechanism of biotransformation and genetic modification of R. palustris.

overall_design: mRNA profiles of the control of R. palustris (RPS) and alpha-rhamnetin-3-rhamnose (ARR) treated of R. palustris (RPB)  were generated by deep sequencing using Illumina Hiseq2000.

first: Lei

first: Guane

last: Yang


title: Heterogeneity in early lymphoid compartments [LP]

first: Shamit

last: Soneji

overall_design: Investigation of the transcriptome in 3 different bone marrow LP compartments by RNASeq (2-5 replicates/cell type)

first: Christina

last: Jensen

first: Tobias

last: Strid

first: Mikael

last: Sigvardsson


title: Epigenetic Drift of H3K27me3 in Aging Links Glycolysis to Healthy Longevity

first: Hui

last: Wang

email: wanghuisimm@sioc.ac.cn, mazj@sioc.ac.cn

address: Qiuyue Road 26

institute: Chinese Academy of Science

summary: We adapted ChIP-Rx method established in cells to fly tissues for quantitative ChIP-seq. We found the deposition of H3K27me3 during aging loses fidelity, resulting its propagation across the epigenome; lowering H3K27me3 by PRCs-deficiency promotes healthy lifespan by mitigating this trend.  Quantitative multi-omic analysis converges on a central role of glycolysis, linking H3K27me3 dynamics to the regulation of glycolytic genes, which correspondingly rewire cellular metabolic homeostasis including energy and redox potential that impact lifespan and adult fitness.

overall_design: Compare H3K27me3 distribution with age and in two PRC2 trans-heterozygous double mutants. Compare transcriptome changes in normal aging and PRC2 mutants, 3 replicates for each genotype at given age.

last: Liu

first: Zaijun

last: Ma


title: RNA-Seq profiling in PBMCs and spinal cord from ALS patients and healthy controls

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

overall_design: Refer to individual Series


title: Rett Syndrome in a dish model

city: Cambridge

first: Ayush

last: Raman

overall_design: RNA-Seq iPSC, NPC and Neuron dataset of Rett Syndrome

first: Bill

last: Lowry

first: Zhandong


title: PRMT5-regulates developmental myelination

status: Public on Jun 02 2018

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

institute: ASRC-CUNY

summary: PRMT5 is important for gliomas, however its physiological function in oligodendrocyte progenitors (OPCs), remains poorly understood. Here we report PRMT5 to be responsible for symmetric di-methylation of histone H4R3 (H4R3me2s) in OPC. PRMT5 depletion via CRISPR/Cas9 decreased H4R3me2s, altered the OPC transcriptome, and decreased OPC survival. Strikingly, these changes were associated with a marked increase of H4K5ac in OPC, but not in gliomas. Consistently, ChIP-sequencing analysis revealed increased genome-wide distribution of H4K5ac in PRMT5 knockout cells. In vitro acetylation assays demonstrated reciprocal inhibition between symmetric arginine methylation and lysine acetylation. Low H4R3me2s and high H4K5ac levels were also detected in OPC in mice with lineage-specific ablation of Prmt5 (Olig1-Cre;Prmt5fl/fl), resulting in severely impaired developmental myelination. Importantly, pharmacological inhibition of acetyltransferase activity partially rescued the effect of Prmt5 deletion on oligodendrocyte-specific gene transcripts. Collectively, we identify PRMT5 as a critical modulator of histone acetylation and OPC differentiation in early developmental myelination.

overall_design: (1) mRNA profiles of OPCs with or without PRMT5 expression were generated by deep sequencing, in tetraplicates, using Illumina HiSeq 2500.

first: Jialiang

last: Liang


title: Whole transcriptome profiling by RNA-sequencing of RNA from N2 and F01D4.5(baf20) C. elegans

status: Public on Jun 01 2018

city: San Antonio

first: Alfred

middle: L

last: Fisher

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center

summary: A forward genetic screen identified a mutation in the previously uncharacterized gene F01D4.5--homologous with human TCF20 and RAI1--that suppresses the adverse phenotypes observed in m-tyrosine-treated tyrosine aminotransferase mutant C. elegans. To gain insights into the function of F01D4.5. RNA was isolated from N2 and F01D4.5(baf20)  mutants and used for whole transcriptome profiling by RNA sequencing. Analysis of the data reveals a signficant reduction in the expression of ribosome protein encoding genes suggesting a diminution in protein synthesis as a compensatory mechansims to abate the adverse effects of m-tyrosine

overall_design: mRNA profiles of N2 and F01D4.5(baf20) C. elegans 48 hours post-L1 arrest generated by deep sequencing, five biological replicates per strain, using the Illumina HiSeq 3000 platform

first: Brett

middle: R

last: Ipson


title: The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and aploplastic immunity

city: Thuwal

first: Naganand

last: Rayapuram

address: KAUST

country: Saudi Arabia

institute: KAUST

summary: Arabidopsis G3BP1 mutants showed enhanced resistance to the virulent bacterial pathogen Pseudomonas syringae Pv. tomato. Pathogen resistance was mediated in Atg3bp1 mutants by altered stomatal and apoplastic immunity.

overall_design: Transcriptome profiling of PstDC3000 hrcC- treated and untreated WT and Atg3bp1 mutants

first: Aala

last: Abulfaraj

first: Kiruthiga

last: Mariappan

first: Jean

last: Bigeard

first: Prabhu

last: Manickam

first: Ikram

last: Blilou

first: Xuijie

last: Guo

first: Salim

last: Albabili

first: Delphine

last: Pflieger

first: Heribert

last: Hirt


title: Acid suspends the circadian clock in hypoxia through inhibition of mTOR

city: Philadelphia

first: Chi

middle: Van

last: Dang

state: PA

address: 3601 Spruce St

institute: Wistar Institute

summary: Recent reports indicate hypoxia influences the clock through the transcriptional activities of hypoxia inducible factors (HIFs) at clock genes. Unexpectedly, we uncover a profound disruption of the circadian clock and diurnal transcriptome when hypoxic cells are permitted to acidify, recapitulating the tumor microenvironment. Buffering against acidification or inhibiting lactic acid production fully rescues circadian oscillation. Acidification of several human and murine cell lines, as well as primary murine T cells, suppresses mechanistic target of rapamycin complex 1 (mTORc1) signaling, a key regulator of translation in response to metabolic status. We find acid drives peripheral redistribution of normally perinuclear lysosomes, inhibiting lysosome-bound mTOR. Restoring mTORc1 signaling and the translation it governs rescues clock oscillation, revealing a model in which lactic acid produced during the cellular metabolic response to hypoxia suppresses the circadian clock through diminished translation of clock constituents.

overall_design: RNA-sequencing was performed over a 52-hour timecourse using total RNA collected every 4 hours from U2OS human osteosarcoma cells in media of pH 7.4 or pH 6.3

first: Zandra

middle: E

last: Walton

first: Rebekah

last: Brooks

first: Lin

last: Zhang

middle: V


title: Expression of mRNA from MCF10A and UFH-001 human cell lines

city: Gainesville

first: Susan

middle: Cooke

last: Frost

state: Florida

address: 1200 Newell Drive

department: Biochemistry and Molecular Biology

institute: University of Florida

summary:
UFH-001 cells, a newly isolated breast cancer line, have an STR profile that is most similar to that of the control MCF10A cells.  Yet, the UFH-001 line is tumor forming with a triple negative phenotype. These cells have a unique transcriptome profile associated numerous breast cancer marker genes.
We used microarrays to detail the global programme of gene expression underlying the metastatic behavior of the UFH-001 cells compared to the MCF10A cells.

overall_design: UFH-001 cells were isolated using carbonic anhydrase IX expression as a tag in FACS analysis.  RNA was isolated from the sorted cells and authenticated MCF10A cells for microarray analysis using the Affymetrix platform to identify genes underlying the aggressive behavior of the UFH-001 cells.

first: Zhijuan

last: Chen

first: Mam

last: Mboge

first: Lingbao

last: Ai

first: Coy

last: Heldermon

first: Christopher

middle: J


title: mRNA sequencing of msh1 memory line in arbidopsis

city: State College

first: Sally

middle: A

last: Mackenzie

address: 362 North Frear

institute: Penn State University

summary: MSH1 depletion caused whole genome wide gene expression changes in Arabidopsis, to conduct comparative genomic analysis, here we generate gene expression profile for wild type and  msh1 memory line

overall_design: 3 wildtype plants ,and 3 msh1 memory plants been sequenced

first: Hardik

last: Kundariya


title: Bisulfite methylome sequencing of msh1 memory line in arbidopsis [Bisulfite-seq]

summary: MSH1 depletion caused whole genome wide Methylome changes in Arabidopsis, to conduct comparative genomic analysis, here we generate methylome for  MSH1-RNAi line and transgene segregated out msh1 memory line

overall_design: 3 wildtype plants,and 3 msh1 memory plants been sequenced


title: Effect of larval nutrition on maternal mRNA contribution to the Drosophila egg

city: Davis

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

summary: Transcriptomes of stage 2 Drosophila embryos, from mothers with different food conditions during the larval stage

overall_design: RNA-Seq data from eggs from mothers with 100%, 25% or 5% of standard diet (standard cornmeal food recipe diluted with agar/water)

first: Amanda

last: Crofton


title: Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [bulk]

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Gastruloids are small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017).  We analyzed the transcriptomic profiles of gastruloids at different time-points after aggregation (AA), showing that they are capable of organizing a post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression.

overall_design: RNA-seq analysis of bulk gastruloids collected at different time-points after aggregation

first: L

first: N

last: Boris

first: M

last: Girgin


title: RNAseq of FACS-sorted C.elegans neurons from wildtype and thoc-5(wy822) mutant animals.

city: STANFORD

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr.

department: Genetics

country: USA

institute: Stanford University

summary: We sorted approx. 10000 neurons per sample from day one adult worms. We collected two wildtype samples and three thoc-5(wy822) mutant samples.

first: Celine

middle: I

last: Maeder

first: Qin


title: Next Generation Sequencing  Quantitative Analysis of altered expression of genes in lncRNA LNMAT1 knockdown bladder cancer cells

city: Guang zhou

first: Changhao

state: Guangdong

address: yanjiang road

department: Department of Urology

country: China

institute: Sun Yat-Sen Memorial Hospital

summary: Bladder cancer is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. LNMAT1 is reported to play diverse roles in the development and progression of human cancer. However, its function and underlying mechanism in bladder cancer remains unclear. The goal of this study is to identify the target genes of LNMAT1 in bladder cancer. Our results indicate that the genes regulated by LNMAT1 associated in a variety of biological functions, such as proliferation and metastasis.

overall_design: To investigate the functional roles of LNMAT1 in bladder cancer, the UM-UC-3 and 5637 bladder cancer cell lines were established to stably downregulate LNMAT1 expression. The RNA of the transfected cells was extracted and hybridized on illumina Hiseq 2000. We indentified the putative target genes of LNMAT1 in both LNMAT1 shRNAs by comparing the different expressed genes among NC, sh-LNMAT1-1 and sh-LNMAT1-2. We further validated the data of next generation sequencing in UM-UC-3 and 5637 bladder cancer cells by qRT-PCR and western bloting.

first: Tianxin

last: Lin


title: De novo transcriptome of the mayfly Cloeon viridulum and transcriptional signatures of Prometabola

city: Nanjing

first: Changfa

last: Zhou

state: Jiangsu

address: Wenyuan Road 1st

institute: Nanjing Normal University

summary: we used next-generation sequencing technology to characterize mRNA-seq of Cloeon viridulum (Ephemeroptera: Baetidae) among the young larva (YL), mature larva (ML), subimago (SI), imago (IM) stages, and mixture sampling (composite group, CG).

overall_design: Examination of 4 different stages during prometabola.

last: Si


title: Comparing the Transcriptomes of Wild Type and Mtor-Gdf9-Cre mediated Oocyte-Conditional Knockout Mouse ovaries by RNA-Seq Analysis

first: You-Qiang

last: Su

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: The goal of this study is to identify the differentially expressed genes in Gdf9-Cre mediated Mtor oocyte-specific knockout (CKO) ovaries by comparing the transcriptomes of  Mtor Wild-Type (WT) and CKO Mouse ovaries via RNA-Seq Analysis.

overall_design: Seven WT- and 5 Mtor-CKO ovarian samples were collected from 6-month old mice that were initially primed with eCG (5 IU/mouse) for 46 h. Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and 500 ng was then taken out from each of them and subjected to mRNA isolation using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment. The  ovarian mRNA libraries were sequenced on an Illumina HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).


title: Transcriptomic analysis by Next Generation Sequencing of mouse bone marrow derived macrophages (BMDMs) infected by Wild-Type and gra18 mutant strains of T. gondii.

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

summary:
Purpose: T. gondii is an obligate intracellular parasite that remodels host transcriptome during infection. How T. gondii provokes these changes is not fully understood. In the present study we found that GRA18 is secreted in the infected host cell and associates with the β-catenin destruction complex to induce β-catenin levels, notably in the host nuclei. Therefore, we  hypothesized that GRA18 could modulate the expression of β-catenin-dependent genes. To determine whether GRA18 induces changes in the host cell gene expression, we performed a transcriptomic analysis of BMDMs infected by Wild-Type and gra18 mutant strains of T. gondii.
Methods: RNA profiles were generated from BMDMs (BALB/c mice) that were left uninfected or infected with the Pru ku80, Pru ku80 Δgra18, and Pru ku80 Δgra18, GRA18+++ strains (MOI = 6) for 18 hours and subsequently subjected or not to LPS stimulation for 4 hours.Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). The RNA quality was checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California, USA) and Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer's recommendations (Illumina, San Diego, CA, USA). The samples were paired-end multiplex sequenced (2 × 125 bp) on the Illumina Hiseq 2500 platform and generated at least 70 million reads for each sample. The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 14 (DNASTAR, Madison, WI, USA) using default parameters. The paired-end reads were uploaded onto the SeqMan NGen (version 14, DNASTAR. Madison, WI, USA) platform for reference-based assembly using either the Mus musculus genome package (GRCm38.p3) or the Toxoplasma Type II ME49 strain (ToxoDB-24, ME49 genome) as reference template. The ArrayStar module (version 14, DNASTAR. Madison, WI, USA) was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters. The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Conclusion: This approach identifies a specific set of genes that are regulated in a GRA18-dependent fashion in BMDM upon T. gondii infection. Particularly, GRA18 promotes the expression of chemokines Ccl17, Ccl22, and Ccl24.

sample_organism:
Toxoplasma gondii
Mus musculus

platform_organism:
Toxoplasma gondii
Mus musculus

overall_design: A total of 8 samples were analyzed. The experiment contains two sets of data: in the absence of LPS stimulation and after LPS stimulation. Cells that were left uninfected (ui) and without LPS stimulation were used as controls.

first: Huan

last: He

first: Marie-Pierre

last: Brenier-Pinchart

first: Laurence

last: Braun

first: Alexandra

last: Kraut

first: Bastien

last: Touquet

first: Yohann

last: Couté

first: Isabelle

last: Tardieux

first: Mohamed-Ali

last: Hakimi


title: Light and G Protein Coordinate Regulation of Arabidopsis Photomorphogensis

status: Public on May 31 2018

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: Seeds were germinated on 1/2 MS plates plus 1% sucrose and placed at 4°C for 3 days and then transferred to white light for 12 h before placed in blue light for another 4 days. Total RNA was extracted from samples including WT, agb1, cry1 cry2 and hy5 with RNAprep plant kit (TIANGEN), and followed by DNase I (Takara) treatment. This study reveals the molecular basis for light and G-protein crosstalk by analyzing gene expression profile under control of both signals.

overall_design: mRNA from wild type, agb1, hy5 and cry1 cry2 mutants, which were grown in blue light, was sequenced to analyze the genes regulated by CRY- and HY5-mediated blue signaling and AGB1-mediated G protein signaling.

first: Hong-Li

last: Lian

first: Hong-Quan

last: Yang