title: Effects of Hif1a mutation and maternal diabetes on the offspring heart

city: Vestec by Prague

first: Gabriela

last: Pavlínková

address: Průmyslová 595

department: Laboratory of Molecular Pathogenetics

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i

summary: We analysed the combined effects of  exposure to maternal diabetes and disrupted HIF-1 signaling on the transcriptom in cardiac left ventricles of 12 weeks old male mice. This approach provides the information about the long term changes originating in utero due to maternal diabetes and inefficient response to hypoxia which develops as a result of hyperglycemia. The majority of changes were detected in Hif1a insufficient mice exposed to maternal diabetes.

overall_design: Streptozotocin induced diabetic FVB females were mated with non-diabetic males with global heterozygous deletion of Hif1a (Hif1a+/-). Total RNA was extracted from the LV of the hearts of 12-week-old male offspring in biological triplicates per each group (wt, non-diabetic pregnancy; wt, diabetic pregnancy; Hif1a+/-, non-diabetic pregnancy; Hif1a+/-, diabetic pregnancy). RNA profiles were generated by deep sequencing using Illumina NextSeq.

first: Romana

last: Bohuslavová

first: Pavel

last: Abaffy

first: Radka

last: Čerychová


title: The RNA exosome adaptor protein ZFC3H1 functionally competes with nuclear export activity to retain target transcripts

status: Public on May 14 2018

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

type: Expression profiling by high throughput sequencing

summary: Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short-lived due to their nuclear degradation by the ribonucleolytic RNA exosome.  Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA+) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA+ RNA foci with ‘pA-tail exosome targeting (PAXT) connection’ components MTR4, ZFC3H1 and PABPN1, but no overlap with known nuclear structures, such as Cajal bodies, speckles, paraspeckles or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence selected pA+ RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear RNA retention factor, counteracting nuclear export activity.

overall_design: Nuclear poly(A) selected RNA from HeLa cells was analysed by next generation sequencing upon depletion of EGFP(control) and RNA exosome core factor RRP40

first: Toomas

last: Silla

first: Dawid

last: Mąkosa

first: Michal

last: Lubas

first: Albin

last: Sandelin

first: Torben

middle: H

last: Jensen


title: A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila [GRO-seq]

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

country: USA

institute: Medical University of South Carolina

summary: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of anti-sense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway. Here, we show that nucleoporin 358 (Nup358) and Piwi interact with each other and that a germline knockdown (GLKD) of Nup358 with short hairpin RNA prevents Piwi entry into the nucleus. The Nup358 GLKD also activated transposons, increased genomic instability, and derailed piRNA biogenesis because of a combination of decreased piRNA precursor transcription and a collapse of the ping-pong cycle. Our results point to a critical role for Nup358 in the piRNA pathway, laying the foundation for future studies to fully elucidate the mechanisms by which Nup358 contributes to piRNA biogenesis and transposon silencing.

overall_design: Global Run-On RNA profiles from mat>Luc (Control) and Nup358 germline knockdown ovaries.


title: RNA-seq analysis of visceral fat Treg signature genes in aged WT and PPARg-2KR mice.

city: New York

first: Li

last: Qiang

state: NY

address: 1150 St. Nicholas Ave. Room 607A

department: Pathology and Cell Biology

institute: Columbia University

summary: We investigated PPARgamma deacetylation in regulating visceral fat Treg cell transcriptomes

overall_design: Epididymal fat Treg cells isolated from aged WT and PPARg-2KR mice, using spleen Treg cells as controls


title: Genome-wide analysis of cell cycle-specific SF3B1-chromatin interactions and its effect on RNA splicing

status: Public on May 15 2018

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report genome-wide analysis of SF3B1-chromatin interactions in cell cycle synchronized HeLa cells.  ChIP-Seq was performed on cell-cycle synchronized HeLa Cell for SF3B1 (G1S and G2M) in duplicates. RNA-Seq was performed on same cells, also in duplicates to determine changes in gene expression and RNA splicing. ChIP-Seq files were aligned to hg19 and peaks calls and comparisons performed by HOMER. RNA-Seq datasets were aligned using STAR aligner and differential expression determined by Cufflinks package. Alternative splicing was determined by rMATS algorithm

overall_design: Determination of cell cycle specific changes in chromatin interaction  of SF3B1 through SF3B1 ChIP-Seq and correlate results with changes in RNA expression and splicing with RNA-Seq from same samples

first: Tushar

last: Murthy

first: Alex

middle: C

last: Minella

first: Manoj

middle: M

last: Pillai


title: Transcriptome analysis of IFNγ producing and non-producing CD4 T cells during chronic intestinal inflammation.

status: Public on May 12 2018

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

summary:
Purpose: The goal of this study is to compare transcriptome profiles of IFNγ producing (Thy1.1+) and IFNγ non-producing (Thy1.1-) CD4 T cells during chronic intestinal inflammation using RNA sequencing.
Methods: Total mRNA was isolated from FACS sorted CD44+Thy1.1+ and CD44+Thy1.1-CD4 T cells and sequenced in duplicate using Illumina HiSeq 2500 (2x100 base pair, paired-end reads).  The sequence reads were aligned using mouse GRCm38.75 reference genome. DESeq2 software was used for differential expression analysis.
Results: Differential expression analysis with DESeq2 algorithm revealed that a total of 942 and 1091 genes were significantly increased in the IFNγ+ and IFNγ- effector CD4 T cells, respectively (adjusted p value <0.05).  We also performed gene set enrichment analysis (GSEA) by pre-ranking RNA sequencing data according to an adjusted p-value and the sign of differential expression.  GSEA regults suggested that IFNγ+ CD4 T cells had terminally differentiated phenotype, while IFNγ- CD4 T cells had transcriptional profile associated with self-renewal and stemness.
Conclusions: Our study suggests that effector CD4 T cells exist in a spectrum of differentiation status during chronic intestinal inflammation, which impacts pathogenicity of CD4 T cells.

overall_design: mRNA profiles of IFNγ producing and non-producing CD4 T cells during chronic intestinal inflammation.

first: Laurie

middle: E

last: Harrington

first: Robert

middle: L

last: Kress

first: Philip

middle: A

last: Kramer

first: Victor

last: Darley-Usmar

first: Susan

last: Bellis


title: Chromatin remodeling BAF155 subunit regulates the genesis of basal progenitors in developing cortex

status: Public on May 11 2018

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We have analyzed gene expression differences between control, BAF155 conditional knockout (cKO) and Pax6 cKO embryonic cortices at E15.5.

overall_design: The following comparisons were made: "Control vs BAF155 cKO", "Control vs Pax6 cKO".

first: Cemil

last: Kerimoglu

first: Andre

last: Fischer


title: Reprogramming of chromatin accessibility in somatic cell nuclear transfer is DNA replication independent

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Mammalian oocytes have the ability to reset the transcriptional program of differentiated somatic cells into that of totipotent embryos through somatic cell nuclear transfer (SCNT). However, the mechanisms underlying SCNT-mediated reprogramming are largely unknown. To understand the mechanisms governing chromatin reprogramming during SCNT, we profiled DNaseI hypersensitive sites (DHSs) in donor cumulus cells and 1-cell stage SCNT embryos. To our surprise, the chromatin accessibility landscape of the donor cells is drastically changed to recapitulate that of the in vitro fertilization (IVF)-derived zygotes within 12 hours. Interestingly, this DHS reprogramming takes place even in the presence of a DNA replication inhibitor, suggesting that SCNT-mediated DHS reprogramming is independent of DNA replication. Thus, the study not only reveals the rapid and drastic nature of the changes in chromatin accessibility through SCNT, but also provides a DNA replication-independent model for studying cellular reprogramming.

overall_design: Here we performed low-input DNase-Seq (liDNase-Seq) profilling of Donor cumulus cells, 1-Cell stage somantic nuclear Transfer (SCNT) embryos and in 1-Cell Aphidicolin treated SCNT embryos

first: Azusa

last: Inoue

first: Shogo

last: Matoba

first: Tsukasa

last: Suzuki

first: Chunxia

last: Zhang

first: Falong

last: Lu

first: Lan

last: Jiang

first: Yi


title: CHD4 and the NuRD complex directly control cardiac sarcomere formation

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Cardiac development relies on proper cardiomyocyte differentiation including expression and assembly of cell-type specific actomyosin subunits into a functional cardiac sarcomere. Control of this process involves not only promoting expression of cardiac sarcomere subunits but also repressing expression of non-cardiac myofibril paralogs. This level of transcriptional control requires broadly expressed multiprotein machines that modify and remodel the chromatin landscape to restrict transcription machinery access. Prominent among these is the Nucleosome Remodeling and Deacetylase (NuRD) complex, which includes the catalytic core subunit CHD4. Here, we demonstrate that direct CHD4-mediated repression of skeletal and smooth muscle myofibril isoforms is required for normal cardiac sarcomere formation, function, and embryonic survival early in gestation. Through transcriptomic and system genome-wide analyses of CHD4 localization, we identified novel CHD4 binding sites in smooth muscle myosin heavy chain, fast skeletal α-actin, and the fast skeletal troponin complex genes. We further demonstrate that in the absence of CHD4, cardiomyocytes in the developing heart form a hybrid muscle cell that contains cardiac, skeletal and smooth muscle myofibril components. These misexpressed paralogs intercalate into the nascent cardiac sarcomere to disrupt sarcomere formation and cause impaired cardiac function in utero. These results demonstrate the genomic and physiological requirements for CHD4 in mammalian cardiac development.

overall_design: mRNA profiles from cardiac tissue of 3 biological replicates of control Chd4flox/flox or CHD4-depleted Chd4Δflox/Δflox at E10.5 and 5 biological replicates of control Chd4flox/flox  or CHD4-depleted Chd4Δflox/Δflox at E9.5 were generated by high-throughput sequencing for transcriptome analysis. CHD4-bound genomic DNA from E10.0 cardiac tissue (2 biological replicates, 3 technical replicates from wild-type embryos) was isolated and sequenced for genomic localization analysis.

first: Caralynn

last: Wilczewski

first: Takashi

last: Shimbo

first: Lauren

last: Wasson

first: Zachary

last: Robbe

first: Ian

last: Davis

first: Paul

last: Wade

first: Frank

last: Conlon


title: Comparison of Ildr2 knockdown by (Adv-shRNA) and Ildr2 knockout (Adv-Cre) in mouse liver

city: Atlanta

first: Elizabeth

last: Millings

state: GA Georgia

address: 1510 Clifton Rd, Rm. G235

department: Biochemistry

institute: Emory University

summary: We observed that Ildr2 knockdown via adenovirally-delivered shRNA (Adv-Ildr2 shRNA) causes hepatic steatosis in mice. Acute, liver-specific Ildr2 knockout mice generated by infecting C57BL/6J mice segregating for a floxed allele of Ildr2 with adenoviral Cre recombinase (Adv-Cre) do not develop hepatic steatosis. However, administration of Adv-Ildr2 shRNA to Ildr2 knockout mice (Ildr2floxed; albumin-cre) did cause hepatic steatosis, indicating that the Adv-Ildr2 shRNA had apparent “off-target” effects on gene(s) other than Ildr2. To determine additional targets of Ildr2 shRNA that may regulate hepatic lipid metabolism, we performed RNA sequencing on liver samples from (1) Adv-Ildr2 shRNA knockdown mice, (2) Adv-lacZ shRNA control mice, and (3) Adv-Cre Ildr2 knockout mice. For the purposes of our study, we sought to identify genes downregulated by Adv-Ildr2 shRNA, but unchanged in Adv-lacZ shRNA control or Adv-Cre Ildr2 knockout mice. The hepatic steatosis observed in Adv-Ildr2 shRNA knockdown mice was likely due to shRNA targeting of other “off-target” genes. We propose that the genes candidates identified in this sequencing experiment may lead to identification of novel regulators of hepatic lipid metabolism.

overall_design:
Liver tissue from male, BL6 mice, 10 wks old. Adv-lacZ shRNA (n=4), Adv-Ildr2 shRNA (n=4), Adv-cre (n=4)

Submitter indicates the raw data files are no longer available.

first: Rudolph

last: Leibel


title: Sp8 and Sp9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression [ChIP-Seq]

city: Shanghai

first: Qifei

last: Liang

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

summary: D1- and D2-type medium spiny neurons (MSNs) are the principal projection neurons in the striatum, including in the dorsal striatum (caudate nucleus and putamen) and ventral striatum (nucleus accumbens and olfactory tubercle) that are generated by the lateral ganglionic eminence (LGE). Using conditional deletion, we show that mice lacking the Sp8 and Sp9 transcription factors (TFs) selectively have a severe reduction in D2 MSNs  due to reduced neurogenesis in the LGE. Sp8/9 together drive expression of the Six3 TF in a spatial restricted domain of the LGE subventricular zone. Conditional deletion of Six3 also prevents the formation of most D2 MSNs, phenocopying the Sp8/9 loss of function. Finally, ChIP-Seq reveals that SP9 directly binds to the promoter and a putative enhancer of Six3. This study provides evidence for components of a transcription pathway, in a regionally restricted LGE domain, that selectively drives the generation of D2 MSNs.

overall_design: We examined Sp9 binding (TF ChIP-seq) from basal ganglionic eminence in E13.5 and E16.5 wild type mice.

first: Z

last: Xu

first: Q

first: X

last: Song

first: S

last: Lindtner

last: Li

first: Y

last: Wen

first: G

last: Liu

first: T

last: Guo

first: D

last: Qi

first: M

last: Wang

first: C

first: H

last: You

last: Chen

last: Feng

first: J

last: Rubenstein

last: Yang


title: Expression data for High and Low permeable brain metastases in 231-BR mouse model

city: Bethesda

first: Patricia

middle: S

last: Steeg

state: MD

address: 37 Convent Dr

department: Women's Malignancies Branch

institute: National Cancer Institute

summary:
All highly and poorly permeable metastases from the same mouse brain were collected by laser capture microdissection. Total RNA from both metastatic lesions and immediate microenvironment was isolated from 5 mice bearing 231-BR metastases. As control 4 healthy mouse brains were included.
We used the microarray to compare the genes differentially expressed between highly vs poorly permeable metastases. This mouse microarray gives the changes in the microenvironment. The human microarray gives the profile of tumor cells in the metastases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Female athymic NIH nu/nu mice were injected intracardiacally with the brain-tropic MDA-MB-231-BR cells. Brain metastases were established after 4 weeks. Diffusion of 3 kDa Texas red dextran was used to determine highly and poorly permeable metastases.

first: Brunilde

last: Gril

first: Anurag

middle: N

last: Paranjape

first: Stephan

last: Woditschka

first: Xiaolin

last: Wu


title: Hemeatopoietic stem cells but not multipotent progenitors drive erythropoiesis during chronic erythroid stress in EPO transgenic mice

city: Toronto

first: Rashim Pal

last: Singh

address: 101, College Street

country: Canada

institute: Princess Margaret Cancer Centre, UHN

summary: The hematopoietic stem cell (HSC) compartment consists of a small pool of cells capable of replenishing all blood cells. Although it is established that the hematopoietic system is assembled as a hierarchical organization under steady-state conditions, emerging evidence suggests that distinct differentiation pathways may exist in response to acute stress. However, it remains unclear how different hematopoietic stem and progenitor cell subpopulations behave under sustained chronic stress. Here, by using adult transgenic mice over-expressing erythropoietin (EPO; Tg6) and a combination of in vivo, in vitro, and deep sequencing approaches, we found that HSCs respond differentially to chronic erythroid stress than their closely related multipotent progenitors (MPPs). Specifically, HSCs exhibit a vastly committed erythroid progenitor profile with enhanced cell division, while MPPs display erythroid and myeloid cell signatures and an accumulation of uncommitted cells. Thus, our results identify HSCs as master regulators of chronic stress erythropoiesis, potentially circumventing the hierarchical differentiation-detour.

overall_design: HSC and MPP from WT or Tg mice were analyzed in triplicates.

first: Rashim

middle: P

first: Mathias

last: Lesche

first: Ian

last: Henry

first: Ben

last: Wielockx


title: ChIRP-seq of lincDUSP in colon cancer cells

status: Public on May 17 2018

city: Cleveland

first: Ahmad

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The genome-wide occupancy of lincDUSP was determined by using chromatin isolation after RNA purification to detemine the genomic sites where lincDUSP directly interacts with chromatin.

overall_design: Colon cancer cells were grown to obtain over 500 million cells. After crosslinking with formaldehyde and sonication, half of the lysates were incubated with probes that bind to lincDUSP, and the second lysate was incubated with control non-specific probes over night. Purification of lincDUSP, DNA isolation and sequencing enabeled us to identify the genome-wide occupancy sites of lincDUSP.

first: Megan

last: Forrest


title: A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer

city: Boston

first: Matthew

last: Freedman

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

summary: Increased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of this locus presumably targeting the AR gene. Here, we identify and characterize a somatically acquired AR enhancer located 650 kilobases centromeric to the AR. Systematic perturbation of this enhancer using genome editing decreased proliferation by suppressing AR levels. Insertion of an additional copy of this region sufficed to increase proliferation under low androgen conditions and to decrease sensitivity to enzalutamide. Epigenetic data generated in localized prostate tumors and benign specimens support the notion that this region is a developmental enhancer. Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.

overall_design: Examination of H3K4me2 in 4 patient tumors, H3K27me3 in 4 patient tumors, H3K27Ac in 11 patient tumors, HOXB13 in 4 patient tumors, FOXA1 in 4 patient tumors

first: Xintao

last: Qiu

first: David

middle: Y

last: Takeda

first: Sandor

last: Spisak

first: Matt


title: Candidate Gene Identification Through RNA-Seq Analysis of (TRAMP x WSB/EiJ) F2 Primary Tumors

first: Derek

last: Gildea

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

summary: RNA-seq analysis of 115 randomly selected (TRAMP x WSB/EiJ) F2 prostates that had been harvested at experimental termination was performed to identify metastasis associated transcriptomic changes

overall_design: Total RNA expression profile of (TRAMP x WSB/EiJ) F2 prostate tumors

first: Jean

last: Winter

first: Nigel

last: Crawford


title: RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients

status: Public on May 10 2018

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

summary: We compared the transcriptome of keratoconus and control epithelium using RNA-Seq. Epithelial tissues were obtained prior to surgery from keratoconus and myopia control patients, undergoing collagen cross-linking and photorefractive keratectomy, respectively. We identified major differences in keratoconus linked to cell-cell communication, cell signalling and cellular metabolism. The genes associated with the Hedgehog, Wnt and Notch1 signaling pathways were down-regulated in keratoconus.

overall_design: Twenty samples were used for RNA-Seq including 10 KC and 10 controls. All 10 KC samples were from males, and there were 4 samples from females in the control group.  Samples were prepared and processed in 2 batches each with 5 control samples and 5 KC samples. The RNA samples were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA) according to the manufacturer’s instructions.  The libraries were sequenced on a NextSeq500 (Illumina) using a 75bp paired end read high output v2 run at the Ramaciotti Centre for Genomics UNSW.

first: Jingjing

last: You

first: Chris

last: Hodge

first: Marc

middle: R

last: Wilkins

first: Gerard

last: Sutton


title: Genome-wide occupancy of FLAG-ERG and FLAG-EHF in RWPE1 cells

city: Salt Lake City

first: Kathleen

last: Clark

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: We compared the genome occupancy for FLAG-tagged versions of the ETS factors ERG and EHF in the normal prostate epithelial cell line RWPE1. Our in vitro binding studies support a model whereby oncogenic ETS factors like ERG bind cooperativly with AP1 factors at closly spaced ETS-AP1 sites, while certain non-oncogenic factors like EHF bind anti-cooperatively with AP1 at the same sites. ETS and AP1 binding motifs were enriched in both ChIP datasets, but the ERG-FLAG bound reginos contained a much higher percentage of ETS-AP1 sites spaced in close proximity, consistent with our in vitro binding data.

overall_design: ChIP-seq with anti-FLAG antibody in RWPE1 cells expressing either FLAG-ERG or FLAG-EHF

first: Barbara

last: Graves


title: Inhibition of 2-AG hydrolysis differentially regulates blood brain barrier permeability after injury

city: Cambridge MA

first: Jie

last: Quan

address: 1 Portland St

institute: Pfizer

summary: Here we demonstrate that the neurovasculature exhibits a unique transcriptional signature following inflammatory insults, and pharmacological inhibition of monoacylglycerol lipase using a newly characterized inhibitor, rescues the transcriptional profile of brain vasculature, and restores its functional homeostasis.

overall_design: RNAseq of neurovasculature isolated from mice treated with lipopolysaccharides or PBS in the presence and absence of an inhibitor of monoacylglycerol lipase

first: Justin

last: Piro


title: ATAC-seq from A549 (ENCSR265ZXX)

status: Public on May 09 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Gld2-catalyzed 3' monoadenylation of miRNAs in the hippocampus has no detectable effect on their stability or on animal behavior.

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: Gld2, a noncanonical cytoplasmic poly(A) polymerase, interacts with the RNA binding protein CPEB1 to mediate polyadenylation-induced translation in dendrites of cultured hippocampal neurons. Depletion of Gld2 from the hippocampus leads to a deficit in long-term potentiation evoked by theta burst stimulation. At least in mouse liver and human primary fibroblasts, Gld2 also 3' monoadenylates and thereby stabilizes specific miRNAs, which enhance mRNA translational silencing and eventual destruction. These results suggest that Gld2 would be likely to monoadenylate and stabilize miRNAs in the hippocampus, which would produce measurable changes in animal behavior. We now report that using Gld2 knockout mice, there are detectable alterations in specific miRNA monoadenylation in the hippocampus when compared to wild type, but that these modifications produce no detectable effect on miRNA stability. Moreover, we surprisingly find no overt change in animal behavior when comparing Gld2 knockout to wild-type mice. These data indicate that miRNA monoadenylation-mediated stability is cell type-specific and that monoadenylation has no measurable effect on higher cognitive function.

overall_design: To assess the involvement of Gld2 in nontemplated nucleotide addition to miRNAs, hippocampi from six WT and six Gld2 KO male mice were isolated and cDNA libraries were constructed from gel-isolated RNAs between 18 and 32 bases in length, which primarily include miRNAs.

first: Maria

last: Ivshina

first: Yvonne

first: Joel

middle: D

last: Richter


title: Effects of FGFRL1 knockdown on gene expression in ovarian cancer cell lines

first: Haiyan

last: Tai

address: Fangxie Road, Huangpu district,

institute: Obstetrics and Gynecology hospital of Fudan University

summary:
Analysis of ovarian cancer cell lines after knockdown of FGFRL1 using SiRNA.
To elucidate the signaling pathways that were significantly altered following the silencing of FGFRL1 expression, we performed global gene profiling experiments of the OVCAR8 and ES2 cells after knockdown of FGFRL1 using siRNA. We conducted pathway analysis with the differentially expressed genes using R in two OC cells.

overall_design: Ovarian cancer cell line OVCAR8 and ES2 were transiently transfected with control or FGFRL1 siRNA, followed by RNA extraction by RNA extraction and analyses wth the Affymetric Human U133 Plus 2.0.

first: Zhiyong

last: Wu


title: Diverse reprogramming codes for neuronal identity

city: La Jolla

first: Kristin

last: Baldwin

address: 10550 North Torrey Pines Road

department: Department of Neuroscience

institute: The Scripps Research Institute

summary: The transcriptional programs that establish neuronal identity evolved to produce a rich diversity of neuronal cell types that arise sequentially during development. Remarkably, transient expression of certain transcription factors (TFs) can also endow non-neural cells with neuronal properties. To decipher the relationship between reprogramming factors and transcriptional networks that produce neuronal identity and diversity, we screened ~600 TF pairs and identified 76 that produce induced neurons (iNs) from fibroblasts. By intersecting the transcriptomes of iNs with those of endogenous neurons, we define a “core” cell-autonomous neuronal signature. The iNs also exhibit diversity; each TF pair produces iNs with unique transcriptional patterns that can predict their pharmacological responses. By linking distinct TF input “codes” to defined transcriptional outputs, this study uncovers cell autonomous features of neuronal identity and expands the reprogramming toolbox to enable more facile engineering of induced neurons with desired patterns of gene expression and related functional properties.

overall_design: RNA-Seq profiles for 35 TauEGFP-positive induced neuron populations, 1 embryonic fibroblast population, and 7 endogenous neural populations in biological duplicates. 2 endogenous neural populations were sequenced in biological triplicates. Single-cell RNA-Seq profiles for 4 TauEGFP-positive induced neuron populations and 1 Tau-EGFP-negative/positive mixed population.

first: Rachel

last: Tsunemoto

first: Sohyon

last: Lee

first: Pavel

last: Chubukov


title: Antileukemic Efficacy of BET Inhibitor in a Preclinical Mouse Model of MLL-AF4+ Infant ALL

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

summary: We investigated the anti-leukemic effects of the Bromodomain and Extra Terminal inhibitor I-BET151 on primary MLL-AF4 patient samples, using a xenotransplantation mouse model of MLL+ infant ALL in vivo. We reported that I-BET151 treatment impairs the engraftment and the disease burden of primary MLL+ infant ALL samples transplanted into immunedeficient mice. I-BET151 is able to arrest the growth of leukemic cells by blocking cell division and rapidly inducing apoptosis, through the deregulation of crucial target genes of the BRD4 and HOXA9/HOXA7 network. Moreover I-BET151 sensitizes glucocorticoid-resistant MLL+ cells to Prednisolone. Finally we observed that I-BET151 treatment is even more efficient when used in combination with HDAC inhibitor.

overall_design: Gene expression was measured using  Affymetrix platform in 28 samples treated with I-BET151 10uM or DMSO ex vivo for  6h

first: Michela

last: Bardini


title: Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity

city: San Francisco

first: Jason

last: Cyster

address: HSE 1001/Cyster Lab/Box 0414, 513 Parnassus Ave.

department: Microbiology and Immunology

institute: University of California, San Francisco

summary: Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing we identified 9 peripheral LNs non-endothelial SC subsets. Included are the established subsets Ccl19hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs) and perivascular cells. We also identified Ccl19lo TRCs, likely including cholesterol-25-hydroxylase+ cells located at the T-zone perimeter, Cxcl9+ TRCs in the T-zone and interfollicular region, CD34+ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase+ SCs in the medullary cords and Nr4a1+ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and they provide evidence that many SCs are in an activated state.

overall_design: Droplet-based scRNAseq on sorted mouse pLN CD45- CD31- cells from uninfected mice and mice at day 15 post-infection with LCMV-Armstrong.

first: Lauren

middle: B

last: Rodda

middle: G


title: A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila [ncRNA-seq]

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of anti-sense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway. Here, we show that nucleoporin 358 (Nup358) and Piwi interact with each other and that a germline knockdown (GLKD) of Nup358 with short hairpin RNA prevents Piwi entry into the nucleus. The Nup358 GLKD also activated transposons, increased genomic instability, and derailed piRNA biogenesis because of a combination of decreased piRNA precursor transcription and a collapse of the ping-pong cycle. Our results point to a critical role for Nup358 in the piRNA pathway, laying the foundation for future studies to fully elucidate the mechanisms by which Nup358 contributes to piRNA biogenesis and transposon silencing.

overall_design: Total small RNA profiles from mat>Luc (Control) and Nup358 germline knockdown ovaries.


title: Transcription Factor SOX30 Is a Key Regulator of Mouse Spermiogenesis

status: Public on May 13 2018

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: As Sox30 knockout arrests spermatogenesis at the step 3 round spermatid (rST) stage, we performed RNA sequencing to identify genes regulated by Sox30.

overall_design: We conducted RNA-sequencing (RNA-seq) analysis to identify SOX30-regulated genes that were differentially expressed in rST of Sox30 KO and WT mice. rST were isolated by FACS from 23 dpp (days postpartum) WT and KO mice, a stage where spermatogenesis progress to step 3 rST with no extra haploid cell types present.

first: Daoqin

last: Zhang

first: Xiwen

last: Lin


title: ATAC-seq from A549 (ENCSR220ASC)

first: ENCODE

last: DCC

summary:
ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from A549 (ENCSR139OYS)

summary:
ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from A549 (ENCSR074AHH)

summary:
ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Changes in mRMA/protein expression and signaling pathways in in vivo passaged mouse ovarian cancer cells

city: Indianapolis

first: Yan

last: Xu

state: Indiana

address: 1044 W. Walnut St

institute: Indiana University School of Medicine

summary: The cure rate for late stage epithelial ovarian cancer (EOC) has not significantly improved over several decades. New and more effective targets and treatment modalities are urgently needed. RNA-seq analyses of a syngeneic EOC cell pair, representing more and less aggressive tumor cells in vivo were conducted. Bioinformatics analyses of the RNA-seq data and biological signaling and function studies have identified new targets, such as ZIP4 in EOC. Many up-regulated tumor promoting signaling pathways have been identified which are mainly grouped into three cellular activities: 1) cell proliferation and apoptosis resistance; 2) cell skeleton and adhesion changes; and 3) carbohydrate metabolic reprogramming. Unexpectedly, lipid metabolism has been the major down-regulated signaling pathway in the more aggressive EOC cells. In addition, we found that hypoxic responsive genes were at the center stage of regulation and detected functional changes were related to cancer stem cell-like activities. Moreover, our genetic, cellular, biochemical, and lipidomic analyses indicated that cells grown in 2D vs. 3D, or attached vs. suspended had dramatic changes. The important clinical implications of peritoneal cavity floating tumor cells are supported by the data proved in this work. Overall, the RNA-seq data provide a landscape of genetic alterations during tumor progression.

overall_design: RNA-seq analyses of a syngeneic epithellial ovarian cancer cell pair, representing more and less aggressive tumor cells in vivo were conducted

first: Qingchun

last: Cai

first: Qipeng

last: Fan

first: Aaron

last: Buechlein

first: David

last: Miller

first: Kenneth

last: Nephew

first: Sheng

last: Liu

first: Jun

last: Wan


title: Transcriptome of CD8 T cells before and after PD-1 ICI therapy

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: We compared the transcriptom between respondrs and non-responders before and after PD-1 blockade therapy in melanoma patients, and defined their difference in context of T cell function.

overall_design: We had 4 sapmles from 2 cohorts of patients collected before and after PD-1 ICI therapy according to their responses to PD-1 ICI therapy.

first: Haidong

last: Dong


title: RNA-sequencing (RNA-seq) of non-manipulated ventricular tissue only of 1- (P1) and 2-day (P2) old neonatal mice

city: Barcelona

first: Mario

last: Notari

address: Hospital Duran i Reynals Gran Via de l'Hospitalet, 199-203

country: Spain

institute: Center of Regenerative Medicine in Barcelona (CMRB)

summary:
Purpose: The goal of this study is to compare the NGS-derived from ventricular trascriptome profiling (RNA-seq) of 1- and 2-day old mouse hearts to gain insight into the molecular bases responsible for the decline in the heart regeneration competence between P1 and P2 mice

Methods: Ventricular cardiac trascriptome profiling were generated by total RNA was extracted from only the ventricles of P1 (n=3) or P2 (n=3) hearts using Quiazol lysis reagent (Quiagen) and RNAeasy extraction kit (Qiagen) according to manufacturer’s instructions. Polyadenylated RNA was isolated from 1-5 μg of total RNA using Dynabeads mRNA purification kit (Invitrogen). Polyadenylated RNA was then fragmented, retro transcribed and finally re-synthetized to double strand DNA molecules using DNA polymerase I (Invitrogen). End-pair, A-tailing, adapter ligation and size selection were then performed. RNA-seq analysis was performed using the 50 nt long paired-end reads obtained from sequencing 6 samples of mice heart tissue at two different time points and using three biological replicates for each time point. Firstly, the quality of the reads was verified using FastQC v0.11.21. Then, the reads were mapped to Mus musculus reference genome vGRCm38 2, using tophat v2.0.143. Following mapping, the transcript and normalization counts were performed using cuffdiff v2.2.1 4. The differential expression analysis of normalized counts was performed using cummeRbund v2.12 5, a widely used R v3.2 package which works together with the cuffdiff software; the applied threshold on the parameter alpha in the function getSig of the package was <= 0.05.

Results: We found that most differentially-expressed transcripts encode extracellular matrix components and structural constituents of the cytoskeleton.

Conclusion: These results suggest that the stiffness of the local microenvironment, rather than cardiac cell-autonomous mechanisms, crucially determines the ability or inability of the heart to regenerate.

overall_design: Ventricular mRNA profiles of  (WT) of 1- and 2-day old neonatal mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.


title: A Retinoic Acid-dependent Stroma-Leukemia Crosstalk Promotes Chronic Lymphocytic Leukemia Progression [RNA-seq]

city: Milan

first: Linda

last: Pattini

address: piazza Leonardo da Vinci, 32

department: Department of Electronics, Information and Bioengineering

institute: Politecnico di Milano

summary: In B-cell chronic lymphocytic leukemia (CLL), the non-hematopoietic stromal microenvironment plays a critical role in promoting tumor cell recruitment, activation, survival and expansion. Using the Eμ-TCL1 mouse model, we demonstrate that leukemic cells induce the activation of retinoid acid synthesis and signaling in stromal cells of the lymphoid microenvironment.

overall_design: Four stromal samples treated with vehicle (DMSO) and four stromal samples treated with BMS493

first: Diego

last: Farinello

first: Andrea

last: Brendolan


title: Expression data from human hair follicles (ex vivo) incubated with cyclosporine A and vehicle control

city: Manchester

first: Nathan

middle: John

last: Hawkshaw

address: Oxford Road

department: Dermatology

country: United Kingdom

institute: University of Manchester

summary:
Since hair growth disorders can carry a major psychological burden, more effective human hair growth-modulatory agents need to be urgently developed.  Here, we used the hypertrichosis-inducing immunosuppressant, cyclosporine A (CsA), as a lead compound to identify new hair growth-promoting targets. Through microarray analysis we identified the Wnt inhibitor, SFRP1, as being downregulated in the dermal papilla (DP) of CsA-treated human scalp hair follicles (HFs) ex vivo. Therefore, we further investigated the function of SFRP1 using a pharmacological approach and found that SFRP1 regulates intrafollicular canonical Wnt/β-catenin activity through inhibition of Wnt ligands in the human hair bulb. Conversely, inhibiting SFRP1 activity through the SFRP1 antagonist, WAY-316606, enhanced hair shaft production, hair shaft keratin expression and inhibited spontaneous HF regression (catagen) ex vivo. Collectively, these data (a) identify Wnt signaling as a novel, non-immune-inhibitory CsA target; (b) introduce SFRP1 as a physiologically important regulator of canonical β-catenin activity in a human (mini-)organ; and (c) demonstrate WAY-316606 to be a promising new promoter of human hair growth. Since inhibiting SFRP1 only facilitates Wnt signaling through ligands that are already present, this “ligand-limited” therapeutic strategy for promoting human hair growth may circumvent potential oncological risks associated with chronic Wnt over-activation.
We used microarrays to identify novel hair growth promoting targets in human hair follicles through the use of cyclosporine A.

overall_design: Human hair follicles were treated for 6 hours with cyclosporine A (10-7M) to identify primary changes in gene transcription and total RNA was extracted using RNAeasy mini kit. Subsequently RNA was prepared for the Affymetrix U133 plus 2.0 genechip. Matched patient samples were treated with either vehicle control or cyclosporine A (from three independent male samples).


title: A Retinoic Acid-dependent Stroma-Leukemia Crosstalk Promotes Chronic Lymphocytic Leukemia Progression

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

overall_design: Refer to individual Series


title: Low density granulocytes and their gene signature associate with vascular inflammation and coronary atheroclerosis in systemic lupus erythematosus patients

city: Bethesda

first: Hong-wei

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Patients with systemic lupus erythematosus (SLE) display an increased risk of cardiovascular disease that is not fully explained by traditional risk factors. This study correlated RNA sequencing data from whole blood of patients with SLE and healthy controls with markers of cardiovascular risk including coronary plaque measured by CT angiogram and vascular inflammation by FDG-PET CT.

overall_design: This dataset includes a total of 53 individual samples from two independent RNAseq runs. This study sought to compare healthy controls to SLE patients and to determine transcriptomic differences in patients that developed vascular damage to those without vascular impairments. The first run compared SLE patients with high noncalcified plaque burdens (NCB) (>1.5 standard deviations of healthy control mean), measured by coronary CT angiography, and patients that had NCB comparable to healthy controls (within 1.5 standard deviations of healthy control mean). The second run validated these findings and compared patients with high vascular inflammation (>1.5 standard deviations of healthy control mean), as measured by target:background ratio (TBR) on FDG-PET/CT scans, to patients with vascular inflammation comparable to healthy controls (within 1.5 standard deviations of healthy control mean).

first: P

last: Carlucci

first: M

last: Purmalek

first: H

middle: W

first: G

last: Gutierrez-Cruz

first: N

last: Mehta

last: Kaplan


title: ATAC-seq from A549 (ENCSR288YMH)

first: ENCODE

last: DCC

summary:
ATAC-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Interferon-γ Converts Human Microvascular Pericytes into Negative Regulators of Alloimmunity through Induction of Indoleamine 2,3-Dioxygenase 1

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

summary: Early acute rejection of human allografts is mediated by circulating alloreactive host effector memory T cells (TEM). TEM infiltration typically occurs across graft post-capillary venules and involves sequential interactions with graft-derived endothelial cells (ECs) and pericytes (PCs). While the role of ECs in allograft rejection has been extensively studied, contributions of PCs to this process are largely unknown. This study aimed to characterize the effects and mechanisms of interactions between human PCs and allogeneic TEM. We report that unstimulated PCs, like ECs, can directly present alloantigen to TEM but while IFN-γ-activated ECs (γ-ECs) show increased ability to stimulate alloreactive T cells, IFN-γ-activated PCs (γ-PCs) instead suppress TEM proliferation but not cytokine production or signaling. RNA sequencing analysis of PCs, γ-PCs, ECs, and γ-ECs reveal induction of indoleamine 2,3-dioxygenase 1 (IDO1) in γ-PCs to significantly higher levels than in γ-ECs that correlates with tryptophan depletion in vitro. Consistently, shRNA knockdown of IDO1 markedly reduces -PC-mediated immunoregulatory effects. Adoptively transferred T cells induced PC expression of IDO1 in allogeneic human skin grafts on immunodeficient mice. We conclude that immunosuppressive properties of human PCs are not intrinsic but instead result from IFN-γ-induced IDO1-mediated tryptophan depletion.

overall_design: Examination of gene expression by unstimluated versus IFN-γ-stimulated endothelial cells or pericytes

first: Rebecca

first: Thomas

last: Manes

first: Jonathan

last: Merola

first: Lingfeng

last: Qin

last: Lopez-Giraldez

first: Caodi

last: Fang

first: Catherine

last: Xie

first: Ping-Min

last: Chen

first: Nancy

last: Kirkiles-Smith

first: Dan

last: Jane-wit

first: Jordan

last: Pober


title: Transcriptome analysis of developing mammalian postnatal intestinal crypts and villi

city: Durham

first: Terry

last: Lechler

institute: Duke University

summary: Villar and intervillar epithelial cells were FACs isolated from P0, P3, P6, or P10 CD1 mouse medial small intestine. Three biological replicates were used for e ach population, and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of compartment-specific and stage-specific genes.

overall_design: 8 distinct samples, with three replicates each. Crypt (Epcam+/CD44+) and Villar (Epcam+/CD44-) populations for CD1 mice at P0, P3, P6, P10.

first: Kaelyn

last: Sumigray


title: Genomewide mapping of Trim33 binding in Th17 cells

status: Public on May 08 2018

city: Fukuoka

first: SHINYA

last: TANAKA

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

country: Japan

institute: Kyushu University

summary: We report the genome-wide binding of Trim33  in Th17 cells. We found that more than 90% of Trim33 binding regions was located in non-conding sequence, and therefore reflect the role of Trim33 as a trancriptional co-factor. Trim33 was found to accumulate on cis-regulatory regions of genes that regulate the function of Th17 cells such as Il17a, Ccr6 and Il10. This study provides a basis for the comprehensive understanding of Trim33-mediated regulation of Th17 cells.

overall_design: Examination of Trim33 binding  in Th17 cells.

first: Shinya

last: Tanaka

first: Yu

last: Jiang


title: Protective role of oleic acid in angiotensin II-induced cardiac remodeling

city: beijing

first: li

last: Michael

address: beiqing road

institute: Basepedia

summary: To gain mechanistic insights into the protective effects of oleic acid (OA) on  angiotensin II(AngII)-induced cardiac remodeling, a whole transcriptomic analysis of heart were performed using RNA-seq.Comparing with heart of normal mice, a total of 1468 genes (987 upregulated and 481 down regulated) were differentially expressed (FDR<0.05) in heart of AngII-induced mice. Comparing with heart of AngII-induced mice,  a total of 785 genes (162 upregulated and 623 down regulated) were differentially expressed (FDR<0.05) in heart of OA treated mice. Importantly, among the 987 upregulated genes in heart of AngII-induced mice,388 genes  were significantly reversed in heart of OA treated mice.

overall_design: 15 samples. There are 3 groups: Veh_H group, mice were treated with saline. A_H group, mice were subcutaneously implanted  AngII pump (1000ng/kg/min). A_OA group, mice were ere subcutaneously implantated  AngII pump (1000ng/kg/min) and treated with OA (160mg/kg,0.3mL/mice per day). Heart were isolated and RNA sequencing.

first: Tian-long

last: Liu

first: Hao

last: Li

first: Hao-chen

last: Xu


title: Identifying the role of Acox1 in metabolism and inflammation in non-alcoholic fatty liver disease through mRNA-sequencing.

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: To identify the impact of Acox1 on cellular metabolism and inflammation related to non-alcoholic fatty liver disease, within the context of obesogenic dietary stress.
Methods: Hepatic mRNA profiles were obtained in triplicate for control and Acox1Lampe1  mice on chow diet or obesogenic diet. Profiles were generated using the Illumina HiSeq2000, reads that passed quality inspection were processed through the TopHap/Cufflinks pipeline.
Results: Approximately 20million reads per sample were aligned to the mm8 mouse genome, using annotations provided by Ensembl.  Testing between control and Acox1Lampe1 mice on control and obesogenic diets was performed using a 2-way ANOVA, with a p-value cutoff of 0.05 and FC of 1.5.  We observed a significant alteration of hepatic gene expression in Acox1Lampe1 mutant mice, a pattern that was exacerbated by the obesogenic diet.  Among significant genes, we observed an enrichment of those known to teb associated with inflammatory responses, leukocyte activation and adhesion, and abnormal liver physiology, regeneration, and development.
Conclusion: Through next generation sequencing of hepatic tissues from control and Acox1Lampe1 mutant mice on control and obesogenic diets, we demonstrate that Acox1 regulates both metabolism and inflammation, the interplay of which correlates with increased hepatocellular damage and impared hepatic mitochondrial function.

overall_design:
Hepatic mRNA profiles of control and Acox1Lampe1 mutant mice on control or obesogenic diets were obtained in triplicate.
--------------------------------------------------
Submitter states "There was an apparent breakdown in the long-term storage protocols, and the raw samples are no longer available."

first: Senad

last: Divanovic

first: Maria

last: Moreno-Fernandez


title: Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia

city: Stockholm

first: Erik

last: Fasterius

address: AlbaNova University Center

department: Proteomics and nanotechnology

country: Sweden

institute: KTH Royal Institute of Technology

summary: In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing the surrounding vasculature network. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O2) conditions, we observed that despite being highly similar, the four cell lines responded strikingly different to hypoxia. We demonstrate that the transcriptome adaptation to moderate hypoxia resembles the process of malignant transformation. The transformed cells displayed a distinct capability of metabolic switching, reflected in reversed gene expression patterns for several genes involved in oxidative phosphorylation and glycolytic pathways. By profiling the stage-specific responses to hypoxia, we identified ASS1 as a potential prognostic marker in hypoxic tumors. This study demonstrates the usefulness of the BJ cell model for highlighting the interconnection of pathways involved in malignant transformation and hypoxic response.

overall_design: 16 paired-end samples in total: 4 different cell lines sequenced in duplicate across 2 conditions each.

first: Frida

last: Danielsson

first: Devin

last: Sullivan

first: Kemal

last: Sanli

first: Cheng

last: Zhang

first: Adil

last: Mardinoglu

first: Cristina

last: Al-Khalili

first: Mikael

last: Huss

first: Mathias

last: Uhlén

first: Cecilia

last: Williams

first: Emma

last: Lundberg


title: Expression data from mouse monocyte- and common- dendritic progenitors (MDP and CDP) from Ikaros mutant in response to gamma-secretase inhibitor (GSI)

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

summary:
Ikaros hypomorphic mice (IkL/L) show plasmacytoid dendritic cell (pDC) defects with an absence of pDCs in the peripheral organs and a reduction of pDCs in the bone marrow (BM). Moreover in vitro differentiation of pDC from IkL/L total BM cells is also defective.
We found that GSI treatment of BM rescue IkL/L pDC differentiation in vitro and identified MDP and CDP as GSI sensitive cells in IkL/L BM cells.

overall_design: Purified dendritic progenitor MDP and CDP from IKL/L and WT BM (CD45.2+) were co-cultured with total BM cells (CD45.1+) in presence of GSI or vehicule DMSO. Expression data were obtained from purified CD45.2+ MDP and CDP 24h after GSI treatment.

first: P

first: J

last: Mastio

last: Kastner

first: S

last: Chan


title: Differential responses by human respiratory epithelial cell lines to respiratory syncytial virus reflect distinct patterns of infection control

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary: We compared constitutive gene expression between two respiratory epithelial cell lines

overall_design: Examination of mRNA transcriptome by Illumina NGS

first: Ronald

last: Rabin


title: Setd2 deficiency impairs hematopoietic stem cell self-renewal and causes malignant transformation

city: Shanghai

first: Qiuhua

last: Huang

address: 197 ruijin road II

institute: Shanghai Institute of Hematology

type: Methylation profiling by high throughput sequencing

summary:
Purpose: The histone H3 lysine 36 methyltransferase SETD2 is frequently mutated in various cancers, including leukemia. However, there has not been any functional model to show the contribution of SETD2 in hematopoiesis or the causal role of SETD2 mutation in tumorigenesis. In this study, using a conditional Setd2 knock-out (KO) mouse model, we show that Setd2 deficiency skews hematopoietic differentiation and impaired HSC (hematopoietic stem cell) self-renewal. Intriguingly, Setd2-deleted HSCs, through a latency period, can acquire abilities to overcome the growth disadvantage and eventually develop into hematopoietic malignancy characteristic of myelodysplastic syndrome (MDS). This study aimed at finding the mechanism controlled by Setd2, which was required for MDS formation.
Methods: Young and old Setd2 WT and KO LSKs (Lin-c-Kit+Sca1+) were generated by deep RNA-seq, using Illumina Hiseq2500. Using Stringtie (version:1.3.0) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed using SYBR Green assays. Young Setd2 WT and KO LSKs were also generated by whole genome bisulfite sequencing (WGBS), using Illumina Hiseq2500.
Results: Using an optimized data analysis workflow, 246 genes down-regulated and 226 up-regulated, showed significant differential expression (fold change, FC ≤ 0.5 or FC ≥ 2; p < 0.05) between young WT and KO LSKs. Old LSKs displayed about 1112 down-regulated and 777 up-regulated genes between WT and KO. The results of WGBS showed that the Setd2 KO genome carries a much larger number of hypomethylated DMRs (different methylation regions) relative to hypermethylated ones (5,839 versus 1,294).
Conclusions: Through RNA-seq, gene expression profile of young Setd2-deleted LSKs partially resembles the Dnmt3a/Tet2 double knock-out. WGBS also indicated that Setd2 deficiency can regulate the distribution of whole genome DNA methylation. Furthermore, young Setd2 deficiency also induces DNA replication stress in HSCs, as reflected by activated E2F gene regulatory network and repressed ribonucleotide reductase subunit Rrm2b. Old Setd2-deleted LSKs displayed a MDS related transcriptional signature.

overall_design: I) Total RNA seq of young Setd2 WT and KO conditional knockout LSKs using Illumina HiSeq 2500. II) Total RNA seq of old Setd2 WT and KO LSKs using Illumina HiSeq 2500. III) Whole genome bisulfite sequencing of young Setd2 WT and KO LSKs using Illumina HiSeq 2500.

first: Yuanliang

first: Jiewen

last: Sun

first: Xiaojian


title: Characterization of tissue-specific BMAL1 cistromes reveals new roles for enhancer-enhancer interactions in regulating rhythmic transcription [ChIA-PET]

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

summary: The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes and enable biological functions to anticipate the daily environmental variations. Consistent with the wide range of biological functions under clock control, rhythmic gene expression is tissue-specific, and this even if the clockwork mechanism is identical in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, through mechanisms involving differences in chromatin accessibility between tissues as well as co-binding of tissue-specific transcription factors. Our results also indicate that the ability of BMAL1 to drive tissue-specific rhythmic transcription not only relies on the activity of BMAL1 cis-regulatory elements (CREs), but also on the activity of neighboring CREs. Characterization of the physical interactions between BMAL1 CREs and other CREs by RNA Polymerase II ChIA-PET in the mouse liver reveals that most interactions are stable over the course of the day, and suggests that BMAL1-mediated rhythmic transcription relies on its ability to regulate the transcriptional activity of other CREs. Our data therefore suggest that much of BMAL1 target gene transcription depends on BMAL1 capacity at rhythmically regulating a network of enhancers.

overall_design: Detection of mouse liver chromatin interactions mediated by RNA Polymerase II

first: Joshua

last: Beytebiere


title: Generation of tissue-specific circadian transcriptional programs by BMAL1 [ChIP-seq]

overall_design:
Examination of BMAL1 DNA binding in the mouse liver, kidney, and heart by Chromatin Immunoprecipitation with sequencing.
Please note that each processed bed, bw file was generated from all ChIP and input replicates together and is linked to the corresponding 'ChIP replicate 1' sample records.


title: Characterization of tissue-specific BMAL1 cistromes reveals new roles for enhancer-enhancer interactions in regulating rhythmic transcription


title: Different Chromatin and DNA Sequence Characteristics Define Glucocorticoid Receptor Binding Sites that are Blocked or Not Blocked by Coregulator Hic-5

city: Los Angeles

first: Brian

middle: Hae Kang

last: Lee

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

institute: University of Southern California


title: Smad4 deficiency impairs chondrocyte hypertrophy via the Runx2 transcription factor in mouse skeletal development [ChIP-seq]

status: Public on May 07 2018

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Smad4 is a central mediator of canonical TGF/BMP signaling and plays important roles in mesenchymal cell aggregation, chondrocyte differentiation, osteoblast differentiation and maturation. However, the regulatory mechanism of Smad4 underlying chondrocyte hypertrophy during skeletal development is unknown. To elucidate the molecular mechanism by which Smad4 deficiency impairs chondrocyte hypertrophy, we performed high-throughput Chip-seq to identify target genes involved in Smad4-regulated chondrocyte hypertrophy. Our results suggest that Smad4 controls chondrocyte hypertrophy through regulating Runx2 expression during skeletal development.

overall_design: We performed ChIP-seq with E12.5 and E13.5 forelimbs to determine Smad4 direct downstream targets in chondrocyte hypertrophy development.

first: Chen-Leng

last: Cai


title: Activation of the p53-MDM4 regulatory axis defines the anti-tumour response to PRMT5 inhibition through its role in regulating cellular splicing.

city: Collegeville

first: Shawn

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

summary:
Here we describe broad anti-proliferative activity of potent, selective, reversible inhibitors of protein arginine methyltransferase5 (PRMT5) including GSK3326595 in human cancer cell lines representing both hematologic and solid malignancies.
Interestingly, PRMT5 inhibition activated the p53 pathway via the induction of alternative splicing of MDM4. The MDM4 isoforms witch and subsequent p53 activation are critical determinants of the response to PRMT5 inhibition suggesting that the integrity of the p53-MDM4 regulatory axis defines a subset of patients that could benefit from treatment with GSK3326595.

overall_design:
RNA-seq from PRMT5 inhibitor treated or control (DMSO) treated lymphoma cell lines performed in duplicate post 3 and 6 days.

** Please note that processed data was generated from control and GSK595 sample pairs and linked to the corresponding GSK595 sample records.

first: Wendy

last: Kellner

first: Sarah

last: Gerhart

first: Christine

last: Thompson

first: Melissa

last: Pappalardi

first: Ping

last: Zhang

first: Rocio

last: MontesdeOca

first: David

last: Soong

first: BaoChau

last: Le

first: Chris

last: Carpenter

first: Neil

last: Johnson

first: Ryan

last: Kruger

first: Olena

last: Barbash


title: Different Chromatin and DNA Sequence Characteristics Define Glucocorticoid Receptor Binding Sites that are Blocked or Not Blocked by Coregulator Hic-5 [ChIP-seq]

summary: The glucocorticoid-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid regulation of some genes, but not others, and blocks regulation of a third gene set. Hic-5 inhibits GR binding to blocked genes but not other glucocorticoid-regulated genes. Site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. We investigate whether ATPases CHD9 and BRM were required for GR occupancy at GR binding sites near Hic-5 blocked genes.

overall_design: Since Hic-5 inhibits the actions of CHD9 and BRM, we performed double depletion of Hic-5 and CHD9 or Hic-5 and BRM in U2OS-GR⍺ cell using siRNA and examined GR occupancy at 1 hour dexamethasone treatment. Single depletion of CHD9, BRM, Hic-5 and control siRNA (siNS) followed by hormone treatment were performed as contrast and control.

middle: H

first: Michael

last: Stallcup


title: Different Chromatin and DNA Sequence Characteristics Define Glucocorticoid Receptor Binding Sites that are Blocked or Not Blocked by Coregulator Hic-5 [ATAC-seq]

first: Brian

last: Lee

summary: The glucocorticoid-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid regulation of some genes, but not others, and blocks regulation of a third gene set. Hic-5 inhibits GR binding to blocked genes but not other glucocorticoid-regulated genes. Site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. We investigate the effects of Hic-5 and dexamethasone on chromatin accessibility at GR binding sites near Hic-5 blocked genes and non-blocked genes.

overall_design: U2OS-GR⍺ cells were transfected with either siRNA for Hic-5 (siHic5) or control siRNA (siNS) and then treated with 1 hour of dexamethasone or ethanol as control.


title: Smad4 deficiency impairs chondrocyte hypertrophy via the Runx2 transcription factor in mouse skeletal development [RNA-seq]

first: Chengguo

last: Wei

summary: Smad4 is a central mediator of canonical TGF/BMP signaling and plays important roles in mesenchymal cell aggregation, chondrocyte differentiation, osteoblast differentiation and maturation. However, the regulatory mechanism of Smad4 underlying chondrocyte hypertrophy during skeletal development is unknown. To elucidate the molecular mechanism by which Smad4 deficiency impairs chondrocyte hypertrophy, we performed high-throughput RNA-seq to identify target genes involved in Smad4-regulated chondrocyte hypertrophy. Our results suggest that Smad4 controls chondrocyte hypertrophy through regulating Runx2 expression during skeletal development.

overall_design: We performed high-throughput RNA-seq to examine genes with altered expression in Smad4-/- forelimbs at E11.5-E14.5.

first: Chen-leng


title: Smad4 deficiency impairs chondrocyte hypertrophy via the Runx2 transcription factor in mouse skeletal development

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

overall_design: Refer to individual Series


title: Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity and specificity, in part due to the use of reverse transcription stops. We sought to use mutations rather than just stops in sequencing data to identify pseudouridine sites. Here, we identify reverse transcription conditions that allow read-through of carbodiimide-modified pseudouridine (CMC-Ψ), and we show that pseudouridines in carbodiimide-treated human ribosomal RNA have context-dependent mutation and stop rates in high-throughput sequencing libraries prepared under these conditions. Furthermore, accounting for the context-dependence of mutation and stop rates can enhance the detection of pseudouridine sites. Similar approaches could contribute to the sequencing-based detection of many RNA modifications.

overall_design: HEK293T rRNA was treated with CMC or mock-treated, then reverse transcribed under 3 different conditions (HIV RT; SIII, Mn; SIII, Mg) for a total of 6 samples.

first: Katherine

middle: I

last: Zhou

first: Wesley

middle: C

last: Clark

first: Matthew

last: Eckwahl

first: Qing

last: Dai


title: Transcriptome sequencing after MAGOHB knockdown in MAGOH-deleted or non-deleted cancer cells

city: Boston

first: Srinivas

middle: Raghavan

last: Viswanathan

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Transcriptome profiling was performed after knocking down MAGOHB in ChagoK1 cells or ChagoK1 cells with ectopic re-expression of MAGOH-V5

overall_design: Knockdown of MAGOHB in either a hemizygous MAGOH-deleted or MAGOH-reconstituted context

last: Meyerson


title: CTLA4-Ig changed the gene expression associated with cellular movement in osteoclast precursors

status: Public on May 06 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To explore comprehensive gene expression changes, we performed an RNA sequence analysis of CX3CR1-EGFP+ cells from calvaria in mice treated with CTLA4-Ig or control IgG.

overall_design: CX3CR1-EGFP+ cells were isolated from calvaria in CX3CR1-EGFP mice injected LPS into periosteal endosteum, together with treated with CTLA4-Ig or control IgG using a cell sorter (n = 3, for each).

first: Yoshinobu

last: Matsuura

first: Junichi

last: Kikuta


title: RNA sequencing of control and raptor-knockout mouse sciatic nerves after crush injury

city: Zurich

first: Gianluca

last: Figlia

address: Otto-Stern-Weg 7

department: Institute for Molecular Health Sciences

country: Switzerland

institute: ETH Zurich

summary: In this study, we analyzed the transcriptome profiles of mouse sciatic nerves subjected to crush injuries after inducible deletion of Raptor conditionally in Schwann cells (using a PLPCreERT2-driven recombination of floxed alleles) as compared to controls (floxed Raptor homozygous, PLPCreERT2-negative). The transcriptome profiles of the contralateral uninjured nerves were also analyzed. Differentially expressed genes, defined as genes with a fold change>1.2 and fold discovery rate <0.05, in injured and contralateral nerves of mutants compared to controls were subjected to gene ontology analysis. Additionally, differentially expressed genes in injured mutants nerves as compared to injured control nerves were further analyzed for enrichment of transcription factor binding motifs in the corresponding promoter regions using the bioinformatic tool Homer version 4.9 (Heinz et al., Molecular Cell, 2010)

overall_design: mRNA profiles from injured and contralateral sciatic nerves of controls and mutants collected 5 days after injury, in triplicate, except for mutant contralateral nerves, which were in quadruplicate

first: Ueli

last: Suter


title: Tissue tuft cell mRNA sequencing

status: Public on May 05 2018

city: San Francisco

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

summary: The goal of the study was to sequence mRNA from tuft cells (identified as CD45-;EpCAM+;IL-25+ using Flare25 reporter mice) in the epithelia of 5 different murine tissues: trachea, thymus, colon, gall baldder, small intestine. As a control, non-tuft epithelial cells (CD45-;EpCAM+;IL-25-) were also isolated. The data were used to identify differentially expressed genes across tuft cells from different tissues and to define a transcriptional tuft cell "signature" that is common to all tissues analyzed but absent in the non-tuft epithelial cells.

overall_design: Four replicates of tuft cells were sorted from each of the 5 tissues. As a reference, four replicates of non-tuft cells were also sorted from the small intestine. One tuft replicate from the small intestine and one from the gall bladder were discarded because they failed QC. One non-tuft replicate was also discarded because of failed QC

first: Jakob

last: von Moltke

first: Christoph

last: Schneider

first: Corey

last: Miller

middle: L

first: David

last: Erle

first: Mark

last: Anderson

first: Richard

middle: M

last: Locksley


title: Boosting ATM activity alleviates ageing and extends lifespan in a mouse model of progeria.

city: Shenzhen

first: Min

middle: Xian

last: Qian

address: 3688 Nanhai Ave

department: Health Science Center

institute: Shenzhen University

summary: Protein deacetylase SIRT6 and protein kinase ATM  both decline during aging, which are of importance in regualtion of glucose metabolism . To explore the mechnisms of SIRT6 and ATM in glycolysis, we analysed the gene expressions in murine embryonic fibroblast cells generated from wildtype, Sirt6-/-, or Atm-/- mice.

overall_design: The mRNA profiles of MEF cells from wildtype, Sirt6-/-, or Atm-/- not were generated by deep sequencing using Illumina HiSeq x ten

first: Minxian

first: Baohua

last: Liu


title: Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis

status: Public on May 04 2018

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary:
Objective:Osteoarthritis (OA) is the most prevalent joint disease. As disease-modifying therapies are not available, novel therapeutic targets need to be discovered and prioritized for their importance in mediating the abnormal phenotype of cells in OA-affected joints. Here, we generated a genome-wide molecular profile of OA to elucidate regulatory mechanisms of OA pathogenesis and to identify possible therapeutic targets using integrative analysis of mRNA-sequencing data obtained from human knee cartilage.
Methods:RNA-sequencing (RNA-seq) was performed on 18 normal and 20 OA human knee cartilage tissues. RNA-seq datasets were analysed to identify genes, pathways and regulatory networks that were dysregulated in OA.
Results:RNA-seq data analysis revealed 1332 differentially expressed (DE) genes between OA and non-OA samples, including known and novel transcription factors (TFs). Pathway analysis identified 15 significantly perturbed pathways in OA with ECM-related, PI3K-Akt, HIF-1, FoxO and circadian rhythm pathways being the most significantly dysregulated. We selected differentially expressed TFs that are enriched for regulating DE genes in OA and prioritized these transcription factors by creating a cartilage-specific interaction subnetwork. This analysis revealed 8 TFs, including JUN, EGR1, JUND, FOSL2, MYC, KLF4, RELA, and FOS that both target large numbers of dysregulated genes in OA and are themselves suppressed in OA.
Conclusion:We identified a novel subnetwork of dysregulated TFs that represent new mediators of abnormal gene expression and promising therapeutic targets in OA.

first: Kathleen

last: Fisch

first: Ramya

last: Gamini

first: Oscar

last: Alvarez-Garcia

first: Ryuichiro

last: Akagi

first: Masahiko

last: Saito

first: Yuta

last: Muramatsu

first: Takahisa

last: Sasho

first: Andrew

last: Su

first: Martin

middle: K

last: Lotz


title: Differential gene expression in murine bone marrow-derived macrophages upon GABA treatment

city: Daejeon

first: Jin Kyung

last: Kim

address: Jungku 6

country: South Korea

institute: Chungnam National University School of Medicine

summary: We investigated the molecular mechanisms by which GABA regulates host defense in macrophages. To examine this, we performed global gene expression analysis of bone marrow-derived macrophages (BMDMs) after GABA treatment.

overall_design: Bone marrow-derived macrophages were isolated in 6~8 week old female C57BL6 mice and then divided into 6 groups 1) Solvent control-treated wild type BMDM  2) GABA-treated (6 h) wild type BMDM 3) GABA-treated (18 h) wild type BMDM 4) Solvent control-treated GABA BMDM 5) GABA-treated (6 h) wild type BMDM 6) GABA-treated (18 h) wild type BMDM

first: Yi Sak

first: Eun-Kyeong

last: Jo


title: An internal nutrient sensor detects specific dietary amino acids and promotes food consumption in Drosophila

city: hangzhou

first: Rui

last: Huang

address: Yu-hang-tang road 866

institute: Zhejiang University

summary: Adequate protein intake is crucial for animals. Despite the recent progress in understanding protein hunger and satiety in the fruit fly Drosophila melanogaster, how fruit flies assess prospective dietary protein sources and ensure protein consumption remains elusive. We show here that three specific amino acids, L-glutamate (L-Glu), L-alanine (L-Ala), and L-aspartate (L-Asp), but not the D-enantiomers, rapidly promote food consumption in fruit flies when present in food. The effect of dietary amino acids to promote food consumption is independent of mating experience and internal nutritional status. Calcium imaging experiments show that six brain neurons expressing diuretic hormone 44 (DH44) can be rapidly and directly activated by these three amino acids during feeding. Genetic analysis shows that DH44+ neurons are both necessary and sufficient for dietary amino acids to promote food consumption. By conducting single cell RNAseq analysis, we also identify a amino acid transporter, CG13248, which is highly expressed in DH44+ neurons and is required for dietary amino acids to promote food consumption. Therefore, these data suggest that dietary amino acids may enter DH44+ neurons via CG13248 and modulate their activity and hence food consumption. Taken together, these data identify an internal amino acid sensor in the fly brain that evaluate food sources post-ingestively and facilitates adequate protein intake. These results shed critical light on the regulation of protein homeostasis at organismal levels by the nervous system.

overall_design: As described previously (Yu et al., 2016), individual DH44+ cells (visualized by GFP experession) were harvested from dissected fly brain under a fluorescence microscope with a glass micropipette pulled from thick-walled borosilicate capillaries (BF120-69-10, Sutter Instruments).  Individual cells were immediately transferred to lysate buffer and underwent reverse transcription and cDNA amplification (SMARTer Ultra Low RNA Kit for Sequencing, Clonetech). The amplified cDNA were sonicated to ~250 bp fragments by the Covaris S2 system and then subjected to end-repair, dA-tail, adaptor ligation, and 12 cycles of PCR amplification using the library preparation kit (NEBNext Ultra II DNA Library Prep Kit, NEB). The cDNA libraries were sequenced by Illumina Hiseq 2500 platform. The sequenced raw data were first pre-processed to remove low-quality reads, adaptor sequences and amplification primer. Reads were mapped to Drosophila genome and mapped reads were selected for further analysis. FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) was used to quantify gene expression.

first: Liming

last: Wang


title: Re-evaluating Microglia Expression Profiles Using RiboTag and Cell Isolation Strategies

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Transcriptome profiling is widely used to infer functional states of specific cell types, as well as their responses to stimuli, to define contributions to physiology and pathophysiology. Focusing on microglia, the brain macrophages, we report here a side-by-side comparison of classical cell sort-based transcriptome sequencing and the ‘RiboTag’ method that avoids cell retrieval from tissue context and yields translatome sequencing information. Conventional whole cell microglia transcriptomes were found to be significantly tainted by artifacts induced by tissue-dissociation, cargo contaminations and transcripts sequestered from ribosomes. Conversely, our data highlight the added value of RiboTag profiling to assess the accuracy of Cre transgenic mice. Collectively, this study indicates method-based biases, reveals observer effects and establishes RiboTag-based translatome profiling as a valuable complement to standard sort-based profiling strategies.

overall_design: overall there are 67 samples, from total of 3 experiments. in each experiment there were at least 3 biological repeats (3 individual mice). sorting and IP were performed from the same animal. Controls  include isotype control for IP, PBS injection as control for LPS, and non tamoxifent treated animals as another IP contorl.

first: Zhana

last: Haimon

first: Alon

last: Volaski

first: Johannes

last: Orthgiess

first: Sigalit

last: Boura-Halfon

first: Diana

last: Varol

first: Anat

last: Shemer

first: Simon

last: Yona

first: Binyamin

last: Zuckerman

first: Eyal

last: David

first: Louise

last: Chappell-Maor

first: Ingo

last: Bechmann

last: Gericke

first: Igor

last: Ulitsky


title: Activity-dependent LoNA Regulates Translation by Coordinating rRNA Transcription and Methylation

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

institute: University of Science and Technology of China

summary: We report the high-throughput sequencing of LncRNA expression in nucleoli

overall_design: Examination of lncRNA expression pattern in N2a cells

first: Juan

last: Zhang


title: exRNA reference profiling of 13 individuals addressing the effect of biofluid (serum vs. EDTA plasma), individual, gender, fasting and female hormonal cycle

first: Thomas

last: Tuschl

address: 1230 York Avenue

institute: The Rockefeller University

summary: Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using novel combinations of denaturants, reducing agents, proteolysis and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and extracellular DNA (exDNA) from the same biofluid sample. We applied the method to characterize exRNAs from 312 plasma and serum samples collected from thirteen healthy volunteers at twelve time points over a two-month period.

overall_design: sRNA-derived cDNA profiling of exRNA isolated from cell-free serum and EDTA plasma, using novel automated RNA isolation and multiplexed library preparation protocols. Biofluid samples were collected from 13 healthy individuals at 12 intervals over a period of two months.

first: Klaas

last: Max

first: Zev

last: Williams

first: Kimberly

last: Bogardus


title: Serum miRNA expression in 25 oral squamous cell cancer patients with different five years survival status and 15 healthy controls

status: Public on May 03 2018

first: Shi

last: Jianbo

state: Shanghai

address: 639, ZhiZaoJu Road, Shanghai

department: Department of Oral & Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: The purpose of this study is to profile miRNA expression in serum from patients with OSCC (n=25) and healthy controls (n=15).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was isolated using TRlzolTM LS Reagent (Invitrogen life technologies) from 40 individuals’ serum. RNA samples were analyzed by Exiqon A/S using miRCURYTM Hy3TM/Hy5TM power labeling kit and the miRCURYTM Array. Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner (Axon Instruments, Foster city, CA).

first: Qin

last: Xu

first: Jianbo

last: Shi


title: Functional characterization of enhancer evolution in the primate lineage

city: Seattle

first: Jason

last: Klein

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: STARR-seq assay tiling across putative hominoid-specific enhancers and for orthologs from 11 primates and 9 ancestral reconstructions of each active tile

overall_design: Three 60mm plates, each with about 1.5 million HepG2 cells, were transfected with 5ug of either our tiling library or ortholog library and 2.5ug of a puromycin expressing palsmid. Cells were selected with 1ng/mL puromycin for 24 hours and then harvested for RNA and DNA extraciton.

first: Jay

last: Shendure


title: Regulation of pathogenic T helper 17 cell differentiation by steroid receptor coactivator-3

status: Public on May 02 2018

first: Raymond

last: Doty

department: Division of Hematology

summary:
T helper 17 (Th17) cell development is programmed by the orphan nuclear receptor RORgt, but the underlying mechanism is not well understood. Nuclear receptor-mediated transcriptional activation depends on coactivators. Here we show that the steroid receptor coactivator-3 (SRC-3) critically regulates Th17 cell differentiation. Reduced incidence of experimental autoimmune encephalitis (EAE) associated with decreased Th17 cell generation in vivo was observed in mice with SRC-3 deletion specifically in T cells. In vitro, SRC-3 deficiency did not affect TGF-/IL-6-induced Th17 cell generation but severely impaired pathogenic Th17 differentiation induced by IL-1/IL-6/IL-23.
Microarrays were used to showed that SRC-3 not only regulates IL-17A but also IL-1R1 expression. SRC-3 bound to Il17a and Il1r1 loci in a RORtdependent manner and was required for recruitment of the p300 acetyltransferase. Thus, SRC-3 is critical in RORt-dependent gene expression during Th17 cell-driven autoimmune diseases.

overall_design: Both WT and SRC-3 deficient naive CD4+ T cells were stimulated with anti-CD3 and anti-CD28 antibodies in the absence of exogenous cytokines (Th 0 cells), or differentiated with IL-1, IL-6 plus IL-23 (pathogenic Th17 cells).

first: Tanaka

last: Kentaro

first: Dong

last: Chen


title: Identification of covalent small-molecule inhibitors of STING

city: Lausanne

first: Muhammet

middle: Fatih

last: Gulen

state: VD

address: Station 19

department: GHI

institute: EPFL

overall_design: Primary wild-type Bone Marrow Derived Macrophages were treated either with Sting inhibitor or Sting agonist (CMA) or inhibitor and CMA together for 2h.

first: Simone

last: Haag

middle: F

first: Luc

last: Reymond

first: Antoine

last: Gibelin

first: Laurence

last: Abrami

first: Alexiane

last: Decou

first: Michael

last: Heymann

first: Gisou

last: van der Goot

first: Gerardo

last: Turcatti

first: Rayk

last: Behrendt

first: Andrea

last: Ablasser


title: Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a [RNA-Seq]

city: New Haven

first: Kun-Yong

last: Kim

state: CT

address: 10 Amistad Street

department: Genetics

institute: Yale University

summary: Embryonic stem cells (ESCs) maintain pluripotency through unique epigenetic states. When ESCs commit to a specific cell lineage, changes in histone modifications and DNA methylation accompany the transition to more specialized cell types. Investigating how epigenetic regulation maintains pluripotency is a critical component in order to generate the required cell types for future clinical application. Uhrf1 is a widely known hemi-methylated DNA binding protein, playing a role in heterochromatin formation alongside G9a, Trim28 and HDACs. In addition, it has been demonstrated that Uhrf1 functions to maintain DNA methylation through the recruitment of Dnmt1. Although Uhrf1 is not essential in ESC self-renewal, it still remains elusive how Uhrf1 regulates pluripotency. Here, we set out to elucidate the role of Uhrf1 in pluripotent stem cells. We found that Uhrf1 forms a complex with the active trithorax group of transcriptional regulators, in particular the Setd1a/COMPASS complex. Our data show that loss of Uhrf1 causes a dramatic reduction of bivalent histone marks, in particular those associated with neuroectoderm and mesoderm specification. Overall, our data demonstrate that Uhrf1 safeguards the balance between pluripotency and differentiation via the Setd1a/COMPASSS complex, through which Uhrf1 mediates bivalent histone modifications.

overall_design: mRNA profiles of WT and Uhrf1 KO mESCs and EBs

first: Yoshiaki

last: Tanaka

first: In-Hyun

last: Park


title: Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a [ChIP-Seq]

overall_design: Genome-wide distribution of Uhrf1, histone modifications and core pluripotent factors of WT and Uhrf1 KO mESCs and EBs


title: RNA-Sequencing analysis of differential gene transcription profiles induced by the prenatal/maternal broccoli sprout (BSp) diet

city: Columbia

first: Yuanyuan

middle: R

last: Li

state: MO

address: University of Missouri School of Medicine, One Hospital Dr., Medical Sciences Building, NW508, Medical Sciences Building, NW508, Medical Sciences Building, M659

department: Ob&Gyn

institute: University of Missouri

summary:
Purpose: We tested global gene transcriptome changes by RNA-sequencing analysis in the offspring breast tumors of SV40 transgenic mice to further identify key epigenetic-controlled genes in regulation of the prenatal/maternal BSp diet-mediated early breast cancer prevention.
Method: Mouse offspring mammary tumor mRNA from control and maternal BSp treatment were generated by deep sequencing, in duplicate or triplicate, using Illumina NextSeq500 platform (GPL19057). The sequence reads that passed quality filters were analyzed. We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distributio. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: Our data showed differential transcriptome distribution in the breast tumors of mouse offspring between the control and prenatal/maternal BSp treatment groups.

overall_design: Total RNA obtained from the offspring breast tumors of SV40 transgenic mice with mothers fed either control or BSp diets, and analyzed by Illumina NextSeq500 platform (GPL19057).

first: Phillip

last: Buckhaults


title: Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a [ATAC-Seq]

overall_design: Chromatin accessibility profile of WT and Uhrf1 KO mESCs


title: Tripartite motif-containing 33 (Trim33) determines the pathogenic function of Th17 cells

city: Osaka

first: Shinya

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

institute: Osaka University

summary:
We report that Tripartite motif-containing 33 (Trim33), a protein that was previously associated with TGF-beta signaling, determines the pathogenic function of Th17 cells. Trim33 deficiency in T cells resulted in resistance to an autoimmune disease model. Lack of Trim33 did not impact TGF-beta signaling in mediating Foxp3 gene expression but greatly reduced TGF-beta induction of IL-17 production during Th17 cell differentiation. Importantly, we found TGF-beta not only increased IL-17 but also suppressed IL-10 expression; absence of Trim33 or Smad2 but not Smad4 in T cells enhanced IL-10 expression. In a Smad2-dependent manner, Trim33 was recruited to Il17 and Il10 gene loci and was crucial in appropriate histone modification accompanying Th17 differentiation.
Our study thus demonstrates that Trim33, a non-canonical branch of TGF-beta signaling, programs the pro-inflammatory function of Th17 differentiation by promoting IL-17 and suppressing IL-10 expression. As a critical switch of pathogenic versus regulatory phenotype of T cells, Trim33 may be targeted in treating human autoimmune diseases.

overall_design: WT and Trim33 KO CD4+ T cells were cultured under Th17-skewing condition. Comparison was made based on these two types of Th17 cells.

first: Tanaka

last: Shinya

first: Dong

last: Chen


title: A novel role of Tet1/2 proteins in cell cycle progression of trophoblast stem cells

city: Babraham

first: Myriam

last: Hemberger

state: Cambridgeshire

address: Babraham Hall

department: Epigenetics

institute: Babraham Institute

summary: The ten-eleven translocation (Tet) proteins are well known for their role in maintaining naive pluripotency of embryonic stem cells. Here, we demonstrate that jointly, Tet1 and Tet2 also safeguard the self-renewal potential of trophoblast stem cells (TSCs) and have partially redundant roles in maintaining their epithelial integrity. For the more abundantly expressed Tet1, we demonstrate that this is achieved by binding to critical epithelial genes, notably E-Cadherin, which becomes hyper-methylated and down-regulated in the absence of Tet1. This epithelial-to-mesenchymal transition phenotype is accompanied by centrosome duplication and separation defects. Moreover, we identify a novel role of Tet1 in stabilizing Cyclin B1, thereby acting as a facilitator of mitotic cell cycle progression. As a result, Tet1/2 mutant TSCs are prone to undergo endoreduplicative cell cycles leading to the formation of polyploid trophoblast giant cells. Taken together, our data reveal essential functions of Tet proteins in the trophoblast lineage.

overall_design: ChIP-seq with 1 antibody (anti-Tet1) in one cell type (mouse trophoblast stem cells); RNA-seq of wild-type, Tet1 single knockout and Tet1/2 double knockout trophoblast stem cells, Bisulfite-seq of wild-type and Tet1 single knockout trophoblast stem cells.

first: Stephanie

last: Chrysanthou

first: Claire

middle: E

last: Senner

first: Sarah

last: Burge

first: Elena

last: Fineberg

first: Hanneke

last: Okkenhaug

first: Laura

last: Woods

first: Vicente

last: Perez-Garcia


title: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [5C]

city: Worcester

first: Lucio

last: Castilla

state: MA

address: 364 Plantation Street

department: MCCB

institute: University of Massachusetts

summary: We demonstrate that CBFb-SMMHCmaintains leukemia viability by inhibiting RUNX1 repression of MYC expression. Upon pharmacologic inhibition of CBF-SMMHC/RUNX1 binding, RUNX1 increases its association with three MYC distal downstream enhancers and represses MYC expression.

overall_design: 5C Chromosome Conformation Capture Carbon Copy

first: John

middle: A

last: Pulikkan

first: Mahesh

last: Hegde

first: A

last: Ahmad

first: Houda

last: Belaghzal

first: Anuradha

last: Illendula

first: Jun

last: Yu

first: Kelsey

last: O’Hagan

first: J

last: Ou

first: C

last: Muller-Tidow

first: Scot

last: Wolfe

first: Lihua

middle: J

last: Zhu

first: Job

last: Dekker

last: Bushweller