title: Parkinson’s Disease Genetic Risk in a Midbrain Neuronal Cell Line

city: Grand Rapids

first: Gerry

middle: A.

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: In genome-wide association studies of complex diseases, many risk polymorphisms are found to lie in non-coding DNA and likely confer risk through allele-dependent differences in gene regulatory elements. However, because distal regulatory elements can alter gene expression at various distances on linear DNA, the identity of relevant genes is unknown for most risk loci. In Parkinson’s disease, at least some genetic risk is likely intrinsic to a neuronal subpopulation of cells in the brain regions affected. In order to compare neuron-relevant methods of pairing risk polymorphisms to target genes as well as to further characterize a single-cell model of a neurodegenerative disease, we used the portionally-dopaminergic, neuronal, mesencephalic-derived cell line LUHMES to dissect differentiation-specific mechanisms of gene expression. We compared genome-wide gene expression in undifferentiated and differentiated cells with genome-wide histone H3K27ac and CTCF-bound regions. Whereas promoters and CTCF binding were largely consistent between differentiated and undifferentiated cells, enhancers were mostly unique. We matched the differentiation-specific appearance or disappearance of enhancers with changes in gene expression and identified 22,057 enhancers paired with 6,388 differentially expressed genes by proximity. These enhancers are enriched with at least 13 transcription factor response elements, driving a cluster of genes involved in neurogenesis. We show that differentiated LUHMES cells, but not undifferentiated cells, show enrichment for PD-risk SNPs. Candidate genes for these loci are largely unrelated, though a subset is linked to synaptic vesicle cycling and transport, implying that PD-related disruption of these pathways is intrinsic to dopaminergic neurons.

overall_design: Lund human mesencephalic cells (LUHMES) can be propagated as cycling undifferentiated neural progenitor cells or induced to differentiate into dopaminergic neurons. We cultured and propagated LUHMES cells (undifferentiated cells) and induced differentiation for 6 days (differentiated cells). We isolated RNA from undifferentiated and differentiated cells in order to compare gene expression (RNA-seq), CTCF binding location (ChIP-seq), and enhancer/promoter (H3K27Ac ChIP-seq) activity in the two states.

first: Steven

last: Pierce

first: Trevor

last: Tyson


title: Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following anti-angiogenic treatment

status: Public on Feb 28 2018

city: Tarrytown

first: Qi

last: Zhao

address: 777 Old Saw Mill River Road

country: USA

institute: Regeneron Pharmaceuticals Inc

type: Expression profiling by high throughput sequencing

summary: To understand tumor stromal cell heterogeneity focusing on tumor endothelial cells and tumor-associated fibroblasts, we isolated single cells from COLO205 tumor xenograft grown sub-cutaneously in SCID mice. To enrich stromal cell content, we removed vast majority of tumor cells by a depletion protocol using anti-CD24 and anti-E-Cadherin antibodies. The remaining single cells were profiled by single cell RNAseq

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Tumors were dissociated, sorted into single cells, and profiled by 1 chromium. Single cell 3' library, Gelbeads and multiplex kit were made by using 10x Genomics platform.

first: Gavin

last: Thurston


title: Gene expression profiles of murine fibroblasts and iPS

status: Public on Mar 01 2018

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

summary: We reprogrammed adult murine fibroblasts obtained from p14f/f (wt version of conditional loxP-flanked p14 knockout (KO); C57/Bl6) by transduction of a lentiviral vector (pRRL.PPT.SF.hOKSMco.idTom.PRE)  overexpressing the four Yamanaka factors (c-Myc, Klf-4, Oct-4, Sox-2). After successful reprogramming and establishment of stable iPS clones we performed gene expression profiling of three different murine iPS clones (#2, #2EX, #3) and their parental fibroblasts.

overall_design: murine adult fibroblasts from ear were isolated, taken into culture and transduced  with pRRL.PPT.SF.hOKSMco.idTom.PRE After successful reprogramming  total RNA from three independent iPS clone and their parental fibroblast was extracted and subjected to Microarray Analysis on Affymetrix Mouse GeneChip1.0 ST Arrays.

first: Franziska

last: Geis


title: A mouse model of miR-96, miR-182 and miR-183 misexpression implicates miRNAs in cochlear cell fate and homeostasis

city: Omaha

first: Michael

middle: D

last: Weston

state: Nebraska

address: 780729 California Plaza

department: Oral Biology

institute: Creighton University

summary:
Transgenic FVB/NCrl-Tg(GFAP-Mir183,Mir96,Mir182)MDW1 mice (Tg1MDW) overexpress this neurosensory-specific miRNA cluster in the inner ear and were developed as a model system to identify target genes and biologic processes regulated by the miR-183 cluster.
Affymetrix mRNA microarray data analysis revealed that downregulated genes in P5 Tg1MDW/1MDW cochlea are statistically enriched for evolutionarily conserved predicted miR-96, miR-182 or miR-183 target sites.

overall_design: Inner ear tissue total RNA extraction and cRNA hybridization to Affymetrix microarrays.  At postnatal age P5, ears microdissected to obtain the coclear sensory epithelium (organ or Corti, or OC).  At P18, ears were microdissected to obtain total cochlear tissue minus the vestibular labyrinth.

first: Shikha

last: Tarang

first: Marsha

middle: L

first: Umesh

last: Pyakurel

first: Sonia

last: Rocha-Sanchez

first: JoAnn

last: McGee

first: Edward

middle: J

last: Walsh

first: Garrett

middle: A

last: Soukup


title: Gene-specific mechanisms dictate glucocorticoid receptor-mediated repression of inflammatory response genes in macrophages [RNA-seq]

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: The Glucocorticoid Receptor (GR) potently represses macrophage-elicited inflammation, however, the underlying mechanisms remain obscure. Our genome-wide analysis reveals that pro-inflammatory paused genes, activated via global negative elongation factor (NELF) dissociation and RNA Polymerase (Pol)2 release from early elongation arrest, and non-paused genes, induced by de novo Pol2 recruitment, are equally susceptible to acute glucocorticoid repression. Moreover, in both cases the dominant mechanism involves rapid GR tethering to p65 at NF-kB binding sites. Yet, specifically at paused genes, GR activation triggers widespread promoter accumulation of NELF, with myeloid cell-specific NELF deletion conferring glucocorticoid resistance. Conversely, at non-paused genes, GR attenuates the recruitment of p300 and histone acetylation, leading to a failure to assemble BRD4 and Mediator at promoters and enhancers, ultimately blocking Pol2 initiation. Thus, GR displays no preference for a specific pro-inflammatory gene class, however, it effects repression by targeting distinct temporal events and components of transcriptional machinery

overall_design: BMDM from LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) mice were treated as indicated in individual figure legends (vehicle, LPS, LPS+Dex for 1 h) and RNA was isolated using Qiagen RNA-easy kit. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina). Quality control of RNA and libraries was performed using the BioAnalyzer 2100. Pair-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.

first: Maria

last: Sacta

first: Bowranigan

last: Tharmalingam

first: Maddalena

last: Coppo

first: David

last: Rollins

first: Dinesh

middle: K

last: Deochand

first: Bradley

last: Benjamin

first: Li

last: Yu

first: Bin

last: Zhang

first: Xiaoyu

last: Hu

first: Rong

last: Li

first: Inez

last: Rogatsky


title: Gene-specific mechanisms dictate glucocorticoid receptor-mediated repression of inflammatory response genes in macrophages [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
ChIPSeq experiments in primarry mouse bone marrow derived macrophages (BMMF) from the wild-type (C57BL/6 mice (NCI, Charles River Laboratories)) mice treated with LPS,Dex or LPS+Dex in comparision with untreated control to determine  genome-wide distribution of RNA polymerase II, Glucocorticoid receptors (GR), transcription factor NFkB, NELFE and BRD4.
Please note that 32_p65_Input.bam was used as an input in the Brd4 experiment


title: Single cell profiling of mouse blood cells using CEL-seq2

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Gene expression in mouse blood cells from sorted via FACS analysis into a 384-well plate were profiled using a modified CEL-seq2 protocol.

overall_design: B lymphocytes (B220+ FSC-Alow), erythroblasts (Ter119+ CD44+, FSC-Amid/high), granulocytes (Mac1+ Gr1+) and high-end progenitor/stem (Lin- Kit+ Sca1+) were sorted from the bone marrow of a C57BL/6 10-13 week old female. T cells (CD3+ FSC-Alow) were isolated from the thymus of the same mouse. Bone marrow and thymus were dissociated mechanically, washed and stained with antibodies for 1hr on ice. Single cells were deposited on a 384 well plate using an Aria cell sorter (Beckman). Index data was collected and an adapted CEL-seq2 protocol used to generate a library for sequencing. The reads were sequenced by Illumina Nextseq and preprocessed by the scPipe R/Bioconductor software.

first: Christine

last: Biben

first: Daniela

last: Amann-Zalcenstein

first: Luyi

last: Tian

first: Shalin

middle: H

last: Naik

first: Douglas

last: Hilton


title: Genome-wide methylation analysis of esophageal mucosa using Infinium HumanMethylation 450 BeadChip

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

type: Methylation profiling by genome tiling array

summary: DNA methylation in esophageal mucosae with cancer risk

overall_design: Differentially methylated regions between esophageal mucosae with low (or intermediate) risk and those with high risk to isolate candidates of cancer risk markers, which can measure DNA methylation accumulated in a normal tissue and has strong association with cancer risk.

first: Takamasa

last: Takahashi

first: Takayoshi

last: Kishino

first: Yasunori

last: Matsuda

first: Toshikazu

last: Ushijima


title: transcriptional profiling of kidney of PPARgamma null and AZIP mice

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne

summary: PPARgamma null (PpargΔ/Δ) mice and AZIP mice present a generalized lipodystrophy, accompanied by strong hyperlipidemia and hyperglycemia. Both mouse model develop progressive nephropathy. To shed ligh on the molecular mechanisms underlying the early kidney damage induced by lipodystrophy, we used microarrays to detail the global program of gene expression in whole kidney of PpargΔ/Δ mice and AZIP mice with their respective control mice at 3 weeks of age.

overall_design: We examined 4 experimental groups: PpargΔ/Δ and control mice at 3 weeks; AZIP and FVB control mice at 3 weeks. For each experimental group we analysed the transcriptional profile of 3 RNAs, each consisting of a pool of 3 individual RNAs from whole kidney.

first: Barbara

last: Toffoli

first: Carine

last: Winkler

first: Greta

middle: G

last: Attianese

first: Béatrice

last: Desvergne


title: Tissue-specific features of oxidative stress-associated gene expression in a healthy mouse model

status: Public on Feb 27 2018

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary:
Oxidative stress is a common phenomenon and is linked to a wide range of diseases and pathological processes. Tissue-specific variation in redox signaling and cellular responses to oxidative stress may be associated with vulnerability to toxic agents and carcinogenic exposures. In order to provide a basis for tissue-specific difference, we examined the tissue-specific transcriptional features of 101 oxidative stress-associated genes in 10 different tissues and organs of healthy mice under physiological conditions.
Microarray analysis results, which were consistent with qPCR results, showed that catalase, Gpx3 and Gpx4 were most highly regulated in the liver, kidney and testes. We also found the tissue-specific gene expression of SOD1 (liver and kidney), SOD2 (heart and muscle) and SOD3 (lung and kidney). The current results will serve as a reference for animal models and help advance our understanding of tissue-specific variability in oxidative stress-associated pathogenesis.

overall_design: 10 different tissues collected from the five mice: Sp, spleen; Th, thymus; Lu, lung; St, stomach; He, heart; Mu, muscle; Li, liver; Ki, kidney; Ce, cerebrum; and Te, testis.

first: Jung

middle: M

first: Hyeong-Geug

first: Chang-Gue

last: Son


title: Gene-specific mechanisms dictate glucocorticoid receptor-mediated repression of inflammatory response genes in macrophages

first: Yurii

last: Chinenov

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

overall_design: Refer to individual Series


title: The Polycomb-dependent epigenome controls β-cell dysfunction, dedifferentiation and diabetes

status: Public on Feb 26 2018

city: Freiburg

first: Steffen

last: Heyne

address: Stübeweg 51

department: Epigenetic Focus

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: To date, it remains largely unclear to what extent chromatin machinery contributes to the susceptibility and progression of complex diseases. Here, we combine deep epigenome mapping with single cell transcriptomics to mine for evidence of chromatin dysregulation in type-2 diabetes. We find two chromatin-state signatures that track β-cell dysfunction in mice and humans: ectopic activation of bivalent Polycomb-silenced domains and loss of expression at an epigenomically unique class of lineage-defining genes. β-cell specific Polycomb (Eed/PRC2) loss of function in mice triggers diabetes-mimicking transcriptional signatures and highly penetrant, hyperglycemia-independent, dedifferentiation, indicating that PRC2 dysregulation contributes to disease. The work provides novel resources for exploring β-cell transcriptional regulation and identifies PRC2 as necessary for long-term maintenance of β-cell identity. Importantly, the data suggest a two-hit (chromatin and hyperglycemia) model for loss of β-cell identity in diabetes.

overall_design:
Whole islet mRNA profiles of 8-week and 25-week old wild type (WT) and Eed -/- mice (βEedKO) were generated (in triplicates, two replicates for 25-week βEedKO samples). Whole islet ChIP-seq profiles of young mice (8-16 week old) for several histone marks and Pol-II were generated. H3K27ac ChIP was also done in Eed-knockout mice.

Please note that the 'wt_mouse_ilets_chromatin_states.paper_colors.bed' file with chromatin states output from EpicSeg (Mammana and Chung, 2015) combining the ChIP-seq data for H3K4me3, H3K27ac, H3K27me3, H3K27me2, H3K27me1, H3K36me3, H2AK119Ub, H3K9me3 and Pol2 together with external available data for H3K4me1, H3K27me3 and H3K9me3 marks [Hoffman et al., 2010; Tennant et al., 2013] and methylation data from young islets [Avrahami et al., 2015]; binSize=200bp

first: John

last: Pospisilik

first: Tess

middle: T

last: Lu


title: Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells.

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University Medical School

summary: The epithelial layer lining the airways has a central role in maintaining lung health, particularly serving as a barrier to prevent infection and delivery of harmful particles, which are cleared from the lung on the mucociliary escalator driven by the epithelium. Robust methods to culture primary airway epithelial cells were developed several decades ago and these cells provide the model of choice to investigate many diseases of the human lung. However, to date the molecular signature of cells from different regions of the airway epithelium has not been well characterized.  Here we examine primary cells derived from human tracheal and bronchial tissues and perform genome-wide analysis of their active regulatory elements and gene expression profiles. We also compare cells from healthy and diseased (cystic fibrosis) donor lung tissue.  Our data reveal an airway cell signature that is divergent from other epithelial cell types and from immortalized or transformed airway epithelial cell lines.  The differences between tracheal and bronchial cells are clearly evident as are common regulatory features between the cell types of two different origins.  Only minor variation is seen between cells from healthy or CF bronchial cells.  These data are a valuable resource for functional genomics analysis of airway epithelial tissues in human health and disease.

overall_design: Examination of open chromatin regions by DNase-seq and gene expression by RNA-seq in HBE (primary human bronchial epithelial cells from healthy donors), CFHBE (primary human bronchial epithelial cells from donors with Cystic Fibrosis), HTE (primary human tracheal epithelial cells from healthy donors) and NHBE (Lonza CC-2451 primary human bronchial and tracheal epithelial cells from healthy donors)

first: Gillen

last: Austin E


title: SOX7 Target Genes and their Contribution to its Tumor Suppressive Function

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary: As a transcription factor, SOX7 suppresses cancer development. However, only a few genes were demonstrated as SOX7-activated targets in cancer-irrelevant contexts. We used microarray chips to determine SOX7 target genes in breast cancer cells and discovered multiple signaling pathways altered by ectopic SOX7. We also investigated several genes for their roles in SOX7-mediated tumor suppression. Our study innovatively revealed SOX7 target gene profile in a cancer-relevant context and identified several SOX7-repressed target genes.

overall_design: Special MDA-MB-231 cells were generated that could inducibly express ectopic SOX7 with doxycycline (DOX) addition. When DOX was added to the medium, cells were collected at the time points of 6, 12 and 24 h. The cells of the control group were cultured for 24 h without treatment of DOX. Therefore, we totally collected 4 samples with each sample triplicated. Total RNA was isolated from each sample and gene expression levels were profiled on the Affymetrix Gene Atlas U219 array strips.

first: Yumeng

last: Zhang

first: Daniel

middle: B

last: Stovall

first: Meimei

last: Wan

first: Qiang

middle: W

first: Dangdang

last: Li

first: Guangchao

last: Sui


title: Expression data of the human colorectal cancer cell line HCT116 in response to MS-275 and hydroxyurea treatment

city: Mainz

first: Oliver

middle: H.

last: Krämer

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

institute: University Medical Center

summary:
MS-275 and hydroxyurea treatment influences whole gene expression including DNA damage response and cell cycle checkpoint signaling.
We used microarray to gain detailed insight into the expression of relevant proteins regulating cell cycle checkpoint signaling.

overall_design: HCT116 cells were treated with MS-275 and/or hydroxyurea and subjected to RNA extraction and hybridization on Affymetrix microarrays.


title: Hominin-specific NOTCH2NL genes affect Notch signaling and cortical neurogenesis

city: Santa Cruz

first: David

last: Haussler

state: California

address: 1156 High St

institute: UC Santa Cruz

summary: Genetic changes causing brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and a determinant of neuronal number in the mammalian cortex. We find three paralogs of human-specific NOTCH2NL are highly expressed in radial glia. Functional analysis reveals different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation. Furthermore, NOTCH2NL genes provide the breakpoints in typical cases of 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism, and deletions with microcephaly and schizophrenia. Thus, the emergence of hominin-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger hominin neocortex accompanied by loss of genomic stability at the 1q21.1 locus and a resulting recurrent neurodevelopmental disorder.

overall_design: H9 embryonic stem cells were used for directed differentiation towards cortical organoids. Using the CRISPR/Cas9 system, H9 control and H9 NOTCH2NL knockout lines were generated. Comparative analysis of RNA-seq at week 4 of differentiation was done to assess the effect of NOTCH2NL KO on cortical neurogenesis. Mouse 46C ES cell stable lines were generated, overexpressing either EV control, or NOTCH2NL-Sh_T197I cDNA. Mouse 46C stable cell lines were differentiated into cortical organoids, and gene expression level was compared by RNA-Seq at day 6 of differentiation.

first: Ian

last: Fiddes

first: Gerrald

last: Lodewijk

first: Meghan

last: Mooring

first: Colleen

last: Bosworth

first: Adam

last: Ewing

first: Gary

last: Mantalas

last: Novak

first: Anouk

last: van den Bout

first: Alex

last: Bishara

first: Jimi

last: Rosenkrantz

first: Ryan

last: Lorig-Roach

first: Andrew

middle: R

last: Field

first: Maximilian

last: Haeussler

first: Lotte

last: Russo

first: Aparna

last: Bhaduri

first: Tomasz

last: Nowakowski

last: Pollen

first: Max

last: Dougherty

first: Xander

last: Nuttle

first: Marie

middle: C

last: Addor

first: Simon

last: Zwolinski

first: Sol

last: Katzman

first: Arnold

last: Kriegstein

first: Evan

middle: E

last: Eichler

first: Sofie

last: Salama

first: Frank

last: Jacobs


title: Gcn4 binding in coding regions can activate internal and canonical 5’ promoters in yeast [RNA-seq]

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding.  Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ~300 Gcn4-bound sites are within coding sequences (CDS), with ~75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDS, adjacent to induced TBP peaks—consistent with Gcn4 activation of cryptic, bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDS can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters.

overall_design: We analyzed the transcriptome in wild type yeast cells after induction by 3-AT and SM by RNA-seq. The ChIP-seq data is GSE107532.

first: Yashpal

last: Rawal

first: Răzvan

middle: V

first: Vishalini

last: Valabhoju

first: Hongfang

last: Qiu

first: Josefina

last: Ocampo

first: David

last: Clark

first: Alan

last: Hinnebusch


title: Id2-deficient NK cells acquire a naïve-like fate (ATAC-seq data set)

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: All innate lymphoid cells (ILC) constitutively express and require the small helix-loop-helix protein ID2 but the functions of ID2 are not well understood in these cells. Here we show that natural killer (NK) cells, the prototypic ILC, can develop in the absence of ID2 but lose their innate properties and remain as CD27+CD11b- cells that fail to mature into cytotoxic effectors. We show that ID2 broadly limited chromatin accessibility at E protein binding sites near T lymphocyte-associated genes including multiple chemokine receptors, cytokine receptors, and signaling molecules. Moreover, ID2 prevented the conversion of CD27+CD11b- NK cells from a CD8 memory precursor-like chromatin accessibility state toward a naïve-like chromatin accessibility state, and altered their functional capacity.  Finally, we demonstrate that increased expression of the naïve T cell-associated helix-loop-helix protein ID3 was required for development of ID2-deficient NK cells, indicating that completely unfettered E protein function is incompatible with NK cell development. These data solidify the roles of ID2 and ID3 as mediators of effector and naïve gene programs, respectively, and revealed a critical role for ID2 in promoting a chromatin state and transcriptional program in CD27+CD11b- NK cells that supports the innate properties of these cells and their ability to undergo cytotoxic effector differentiation.

overall_design: CD19-Ter119-CD122+NK1.1+CD27+CD11b- natural killer cells were sorted from the bone marrow of Rag1-/-Id2f/f and Rag1-/- GzmbCre Id2f/f mice (littermates), as well as from CD19-Ter119-CD122+NK1.1+CD27-CD11b+ bone marrow natural killer cells, and processed for ATAC-seq

first: Erin

last: Zook

first: Zhong-Yin

last: Li

first: Yiying

last: Xu

first: Renee

middle: F

last: de Pooter

first: Mihalis

last: Verykokakis

first: Aimee

last: Beaulieu

first: Anna

last: Lasorella

first: Mark

last: Maienschein-Cline

first: Joseph

last: Sun

first: Mikael

last: Sigvardsson


title: rGal1 transcriptional effects over RWP-1

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

summary: rGal1 (recombinant Galectin-1) vs non treated (Ctrl) pancreatic cancer cell line RWP-1

overall_design: 4 samples were analyzed: Ctrl (n=2); rGAL1 (n=2)

first: Pilar

last: Navarro

first: Pedro

last: Guerrero

last: Martínez-Bosch

first: Carlos

last: Orozco


title: Id2-deficient NK cells acquire a naïve-like fate

middle: L


title: Effects of gene scilencing of USP2 on expression profiles of HL60 cells (PMA 1day and LPS 4hrs)

status: Public on Feb 25 2018

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

summary:
So far, we have found phorbol 12-myristate 13-acetate (PMA) induced ubiquitin specific peptidase (USP) 2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937.
HL60, THP-1, and U937 undergoes differentiation into macrophage-like cells after stimulation with phorbol ester. To explore molecular function of USP2 in macrophages especially during lipopolysaccharide(LPS) response, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA.

overall_design: HL60 derivatives continuously expressing shRNA for USP2 and control shRNA were treated with PMA (30nM) for  1 day, and subsequently stimulated with E. coli LPS (10ug/mL) for 4 hrs. Total RNA was extracted from the cells and subjected to microarray experiments using Human Genome U133 GeneChips.

first: Masatoshi

last: Ito

first: Osamu

last: Ohara


title: Effects of gene scilencing of USP2 on expression profiles of HL60 cells (PMA 3days and LPS 4hrs)

overall_design: HL60 derivatives continuously expressing shRNA for USP2 and control shRNA were treated with PMA (30nM) for  3 days, and subsequently stimulated with E. coli LPS for 4 hrs. Total RNA was extracted from the cells and subjected to microarray experiments using Human Genome U133 GeneChips.

first: Chisato

last: Kikuguchi


title: p110α of PI3K is Indispensable for Quiescence Exit in Adult Muscle Satellite Cells

city: Hong Kong

first: Han

last: ZHU

address: Room 6312, Academic Building, HKUST

department: Department of Life Science

country: China

institute: HKUST

summary: Adult muscle stem cells (MuSC) are quiescent with a localization between myofibers and basal lamina. Upon injury, MuSC exit quiescence, reenter cell cycle, expand and differentiate for muscle regeneration. By using genetic mouse model, we identified p110α/mTORC1 signaling as a indispensable pathway that permits quiescence exit and cell cycle reentry. In order to dig out the downstream effectors, we compared the transcriptome of freshly isolated MuSC from Ctrl (p110α-f/+:R26-YFP/YFP:Pax7-CreER/CreER) to MuSC-specific p110α-null (iKO, p110α-f/f:R26-YFP/YFP:Pax7-CreER/CreER) mice by RNA-sequencing, and AP1 target genes were dramatically down-regulated in iKO MuSC. Restoration of Jun could significantly rescue the cell cycle reentry defect in iKO MuSC. In summary, we provided a p110α/mTORC1/Jun axis required for quiecence exit and cell cycle reentry of MuSC.

overall_design: 2-month-old Ctrl and iKO mice (n=4 in each group) were injected with 5 consecutive doses of Tamoxifen (Tmx) followed by 7 doses of Tmx every 2-3 days. Total RNAs were extracted from freshly isolated MuSC from Ctrl and iKO mice and subjected to gene expression profiling.

first: Gang

last: Wang

first: Zhenguo

last: Wu


title: Single cell transcriptomic analysis (10x Genomics) of mouse splenic CD4+ T cells

status: Public on Feb 23 2018

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (10x Genomics)

first: Evgeny

last: Kiner

first: Christophe

last: Benoist


title: IL-10 signaling remodels adipose chromatin architecture to limit thermogenesis and energy expenditure [ChIP-Seq]

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young

institute: UCLA

summary: Signaling pathways that promote adipose tissue thermogenesis are well characterized, but the physiologic limiters of energy expenditure are largely unknown. Here we show that ablation of the anti-inflammatory cytokine IL-10 improves insulin sensitivity, protects against diet-induced obesity, and elicits the browning of white adipose tissue. Mechanistic studies define bone marrow cells as the source of the IL-10 signal and mature adipocytes as the target cell type mediating these effects. IL-10 receptor alpha is highly enriched in mature adipocytes and is induced in response to cold, obesity and aging. ATAC-seq and RNA-seq reveal that IL-10 represses the transcription of thermogenic genes in adipocytes by altering chromatin accessibility and inhibiting ATF and PGC-1alpha recruitment to key enhancer regions. These findings identify the IL-10 axis as a critical and potentially targetable regulator of thermogenesis, and expand our understanding of the links between inflammatory signaling and adipose tissue function in the setting of obesity.

overall_design: D5 differentiated cells treated with and without IL10. Input served as a control for C/EBPβ enrichment. ChIP-Seq libraries were prepared using the Kapa LTP Library Preparation Kit (Kapa Biosystems). ChIP-Seq was performed as described (Tong et al., 2016).

first: Brandon

middle: J

last: Thomas

first: Prashant

last: Rajbhandari


title: The single-cell RNA sequencing of brain microglia

status: Public on Feb 24 2018

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: The RNA sequencing of brain microglia during repopulation

overall_design: Brain microglia mRNA profiles of adult wild type C57BL/6J mice, from either control diet (CD) treated group or microglial repopulation group (PLX5622 for 14 days, followed by CD treated for 5 days)

first: Guangrong

last: Qin


title: The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: The CCCTC-binding factor (CTCF) is a versatile transcriptional regulator required for embryogenesis, but its function in vascular development or in diseases with a vascular component is poorly understood. Here, we found that endothelial Ctcf is essential for mouse vascular development and limits accumulation of reactive oxygen species (ROS). Conditional knockout of Ctcf in endothelial progenitors and their descendants affected embryonic growth, and caused lethality at embryonic day 10.5 owing to defective yolk sac and placental vascular development. Analysis of global gene expression revealed Frataxin (Fxn), the gene mutated in Friedreich’s ataxia (FRDA), as the most strongly downregulated gene in Ctcfdeficient placental endothelial cells. Moreover, in vitro reporter assays showed that Ctcf activates the Fxn promoter in endothelial cells. Reactive oxygen species (ROS) are known to accumulate in the endothelium of FRDA patients. Importantly, Ctcf deficiency induced ROS-mediated DNA damage in endothelial cells in vitro, and in placental endothelium in vivo. Taken together, our findings indicate that, Ctcf promotes vascular development, and limits oxidative stress in endothelial cells, perhaps through activation of Fxn transcription. These results reveal a function for a Ctcf–Fxn transcriptional pathway in vascular development, and also suggest a potential mechanism for endothelial dysfunction in FRDA.

overall_design: Examination of transcriptome profiles of placental endothelial cells isolated from wildtype or ctcf defecient endothelial cells at E9.5

first: Anna

last: Roy

first: Abdalla

last: Ahmed

last: DiStefano

first: Lijun

last: Chi

first: Nadiya

last: Khyzha

first: Niels

last: Galjart

first: Michael

middle: D

last: Wilson

first: Jason

last: Fish


title: Transcription elongation rate affects nascent histone pre-mRNA folding and 3’ end processing

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: We report that slow transcription by mutant RNA pol II caused accumulation of polyadenylated histone mRNAs that extend past the stem loop processing site. UV irradiation, which decelerates pol II elongation, also induced long poly(A)+ histone transcripts. Inhibition of 3’ processing by slow pol II correlates with failure to recruit SLBP to histone genes. Chemical probing of nascent RNA structure showed that the stem loop fails to fold in transcripts made by slow pol II, thereby explaining the absence of SLBP and failure to process 3’ ends. These results show that regulation of transcription speed can modulate pre-mRNA processing by changing nascent RNA structure, and suggest a mechanism by which alternative processing could be controlled

overall_design: The effect of transcription elongation rate on Stem Loop Binding Protein (SLBP), Negative Elongation Factor (Nelf) and Cleavage and polyadenylation factor 77 (CSTF77)  was analyzed by ChIP-seq in isogenic human HEK293 cell lines that inducibly express alpha-amanitin resistant mutants of the RNA polymerase II large subunit with slow elongation rates. Anti-pol II total nascent RNA isolation followed by targeted structural probing with DMS and 1M7 was employed to determine the nascent structure of replicative histone 3' stem loop.   .

first: Ben

last: Erickson


title: Expression data from mir-429 transfected HEY cells in a time-point series (0hr-HEY, 24hrs, 48hrs and 144hrs)

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

institute: The Institute for Next Generation Healthcare

summary: HEY cells display a mesenchymal phenotype (elongated). After a 48hr transfection with mir-429 their phenotype changes to an epithelial-like (cuboidal)

overall_design: We transfected HEY cells with mir-429 or negative control miRNA and analyzed global changes at the mRNA level in a time-course experiment (HEY-0hrs, 24hrs, 48hrs and 144hrs)

middle: N

first: John

last: McDonald

first: Mengnan

last: Zhang

first: Lilya

last: Matyunina

first: Lijuan

last: Wang

first: Andrew

last: Huang


title: Expression in ENO2DeltaFosB mouse hypothalamus

last: Idelevich

address: 188 Longwood

institute: HSDM

summary:
Hypothalamic differential gene expression in  transgenic ENO2DeltaFosB  compaired to control (wild-type) mice
DeltaFosB is a member of AP1 transcription factors family

overall_design: Hypothalamic RNA was extracted from 12 week old male mice

first: Roland

last: Baron


title: Characterizing the epigenome of glioma stem cells (Methylation BeadChip)

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

summary: Glioma initiating cells/stem cells exist in the bulk tumor of glioblastoma. This cell population contributes to the frequent resistances toward radiation/chemotherapy, aggressiveness of adult brain cancer and increased recurrence rate. Targeting stem cell population becomes one the most promising and permissive therapeutic strategies. We isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic features, including 4 different DNA marks and 2 enhancer marks, and transcriptome in these in vitro cultured cell lines. Three fetal brain-derived neural stem/progenitors cells were used for comparing the unique and common molecular features in these glioma cancer stem cells.

overall_design: GBM PDX tumor and PDX-derived glioma stem cells were subject to Infinium 850K and 450K respectively to examine DNA methylation levels

first: Keith

last: Robertson


title: RNA sequencing of B cell subsets (CD11c hi IgD+ B cells, CD11c hi IgD- B cells, Memory B cells and Naïve B cells) from healthy subjects and subjects with Systemic lupus erythematosus (SLE) or Rheumatoid arthritis (RA)

city: Gaithersburg

first: Jingya

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

summary: CD11c+ B cells (IgD+ and IgD-) are pathogenic B cells expanded in autoimmune disease. The purpose of this study is to identify the pathways unique to IgD+ CD11c B cells and IgD- CD11c B cells.

overall_design: B cell subsets were isolated from peripheral blood and RNA sequencing was performed with Hiseq 2000 platform

first: Rachel

last: Ettinger


title: Compendium of CD8+ T cell Data

status: Public on Mar 17 2018

city: Seattle

first: Robert

middle: Anthony

last: Amezquita

state: WA

address: 1100 Fairview Ave. N.

department: Integrated Immunotherapy Research Center

institute: Fred Hutchinson Cancer Research Institute

summary:
Compendium of high-throughput sequencing datasets derived from murine CD8+ T cells responding to infection, profiled by RNA-seq, ChIP-seq, and ATAC-seq at Naïve, Effector, and Memory timepoints across the Kaech, Goldrath, and Pereira labs, and ChIP-seq of various transcription factors across several labs

Submission contains both original data from the Kaech lab and reanalysis of data from the Pereira and Goldrath labs, as well as various other labs corresponding to individual transcription factor ChIP-seq datasets, totaling to 96 reanalyzed GSM samples across several GSE series

Included GSE series are: GSE95237 (Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets), GSE95238 (Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation),   GSE88987 (Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection), GSE58075 (Genome-wide mapping of Myc, AP4, and phosphorylated RNA polymerase II binding in activated CD8 T cells by ChIP sequencing), GSE54191 (ChIP-Seq analysis of BATF, IRF4, the Jun proteins, and histone modifications in effector CD8+ T cells), GSE20898 (Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types), GSE46943 (Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [ChIP-Seq]), GSE72997 (ChIP-Seq analysis of Helios and histone modifications in CD4+ and CD8+ Tregs), GSE50128 (Genome-wide maps of Runx3 bound regions in splenic IL-2-activated CD8+ T cells), GSE72565 (Binding of STAT5 upon IL-2 treatment to genomic sites in mouse CD8 T cells costimulated in vivo through CD134 plus CD137), GSE49930 (The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells [ChIP-seq]), and GSE52070 (Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells)

overall_design:
CD8+ T cell data was combined from the Kaech, Goldrath, Pereira and various other laboratories to create a CD8+ T cell sequencing data compendium across multiple assay types. Cells were collected in the context of infection (primarily LCMV) at Naive (day 0), Effector (day 8 or day 10), or Memory (day 30+) time points, or in 'Special' culture conditions corresponding primarily to ChIP-seq of transcription factors. Additional subsetted samples from the Effector timepoint, Memory Precursors (KLRG1lo IL7Rhi) and Terminal Effectors (KLRG1hi IL7Rlo) were also collected. Samples were analyzed by using ChIP-seq, ATAC-seq, and RNA-seq specific pipelines. ChIP-seq and ATAC-seq were first trimmed for adapters and low quality sequences with cutadapt, and subsequently aligned with bowtie2 v2.3.3.1 using `--very-sensitive-local` mode, `--no-mixed --nodiscordant`. ATAC-seq data additionally used `--maxins 2000`. ATAC-seq reads were shifted per the original Buenrostro protocol by +4/-5 bases, and filtered to remove mitochondrial mapping reads. ChIP-seq and ATAC-seq data were then called for peaks using MACS2 v2.1.0. ATAC-seq peaks were called using `--nomodel --shift -100 --extsize 200 --broad`. For H3K4me1 and H3K27me3 ChIP-seq data, `--broad --nomodel --broad-cutoff 0.1` was used. For H3K27ac and H3K4me3 ChIP-seq data, default (narrowPeak) settings were used. ChIP-seq data used control (input) data as available. ChIP-seq and ATAC-seq signal tracks were made using deepTools bamCoverage with `--binSize 5 --smoothLength 15 --normalizeTo1x 2150570000 --extendReads 200` for visualization. For RNA-seq data, kallisto v0.42 was used to quantify transcript counts directly from fastq files. All data was aligned to the Ensembl GRCm38 (mm10) reference genome, appending chromosome names with 'chr' for maximal compatibility with downstream tools. Finally, all sample annotation, counts, and peak data were combined into an R package `ctlcon`, available at "https://bitbucket.com/robert_amezquita/ctlcon" with additional processed datasets and information.
contributor: Pereira & Goldrath Labs (Histone mods and ATAC)
contributor: Haining, Egawa, Li, Zhao, Cantor, Kallies, Groner, Vella, Xue Labs (ChIP-seq of TFs)

The re-analyzed data is linked as Series supplementary file and the details (including sample-to-file associations, SRR accessions of the re-analyzed raw data etc.) are included in the 'readme_re-analyzed_samples.txt'.

middle: A

first: Simon

last: Gray

first: Tianxia

last: Guan

first: Claudia

middle: X

last: Dominguez

first: Steven

middle: H

last: Kleinstein

first: Susan

last: Kaech


title: Identification of a novel role of MTF2 in the regulation of H3K27me3 by PRC2 (RNA-Seq)

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: We sequenced mRNA from F9 cells after knockdown of EZH2, SUZ12 and EED by shRNA. EZH2, SUZ12 and EED are the core componnets of PRC2 which repress its target genes by H3K27me3.

overall_design: Examination of mRNA expression treated with retinoic acid and after the knockdown of core PRC2 components by deep sequencing.

first: Abdul

last: Khan

first: Seokjin

last: Ham


title: Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots [sncRNA]

status: Public on Feb 22 2018

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Remodelling of the sperm epigenome by lifestyle factors before conception could account for altered metabolism in the next generation offspring. Here, we hypothesized that endurance training changes the epigenome of human spermatozoa. Using small RNA (sRNA) sequencing and Reduced Representation Bisulfite Sequencing (RRBS), we respectively investigated sRNA expression and DNA methylation in pure fractions of motile spermatozoa collected from young healthy individuals before, after 6 weeks of endurance training and after 3 months without exercise. Expression of 8 piwi interacting RNA were changed by exercise training. RRBS analysis revealed 330 differentially methylated regions (DMRs) after training and 303 DMRs after the detraining period which were, in both conditions, enriched at close vicinity of transcription start sites. Ontology analysis of genes located at proximity of DMRs returned terms related to neurological function at the trained state and, to a much lesser extent, at the detrained state. Our study reveal that short-term endurance training induces marked remodelling of the sperm epigenome, and identify genes related to the development of the central nervous system as potential hot spots for epigenetic variation upon environmental stress.

overall_design: Reduced representation bisulfite sequencing (RRBS) and sncRNA-Seq on the spermatozoa of 9 lean men undergoing endurance training

first: Ida

last: Donkin

first: Odile

first: Soetkin

last: Versteyhe

first: Brynjulf

last: Mortensen

first: Nikolaj

middle: T

last: Krarup

first: Romain

last: Barrès


title: Identification of a novel role of MTF2 in the regulation of H3K27me3 by PRC2

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

overall_design: Refer to individual Series


title: 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

institute: Montreal Heart Institute

summary: In humans, fetal erythropoiesis takes place in the liver whereas adult erythropoiesis occurs in the bone marrow. Fetal and adult erythroid cells are not only produced at different sites, but are also distinguished by their respective transcriptional program. In particular, whereas fetal erythroid cells express γ-globin chains to produce fetal hemoglobin (HbF), adult cells express β-globin chains to generate adult hemoglobin. Understanding the transcriptional regulation of the fetal-to-adult hemoglobin switch is clinically important as re-activation of HbF production in adult erythroid cells would represent a promising therapy for the hemoglobin disorders sickle cell disease and β-thalassemia. We used RNA-sequencing to measure global gene and microRNA (miRNA) expression in human erythroblasts derived ex vivo from fetal liver (N = 12 donors) and bone marrow (N = 12 donors) hematopoietic stem/progenitor cells. We identified 7,829 transcripts and 402 miRNA that were differentially expressed (false discovery rate (FDR) <5%). The miRNA expression patterns were replicated in an independent collection of human erythroblasts using a different technology. By combining gene and miRNA expression data, we developed transcriptional networks which show substantial differences between fetal and adult human erythroblasts. Our analyses highlighted the miRNAs at the imprinted 14q32 locus in fetal erythroblasts and the let-7 miRNA family in adult erythroblasts as key regulators of stage-specific erythroid transcriptional programs. Altogether, our results provide a comprehensive resource to prioritize genes that may modify clinical severity in red blood cell (RBC) disorders, or genes that might be implicated in erythropoiesis by genome-wide association studies of RBC traits.

overall_design: miRNA profiles of fetal (N=12) and adult (N=12) erythroblasts were generated by RNA-sequencing with an Illumina HiSeq2000 sequencer using a single end 50-bp protocol.

first: Samuel

last: Lessard

first: Mélissa

last: Beaudoin

first: Stuart

last: Orkin

first: Daniel

last: Bauer


city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

summary: To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous, genome-wide measurements of mRNA, translation and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases—or over 8% of all measured genes—involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether an mRNA is induced or not, but rather based on the type of transcript produced.

overall_design: Sequencing of mRNA molecules and ribosome footprints to identify regulated transcript isoform changes that result in apparent translational regulation. In short,two major experiments are included here, one for parallel mRNA-seq and ribosome profiling of cells progressing through meiosis. This was performed in parallel with mass spectrometry to ascertain the relationship between transcript abundance, translation, and protein abundance over time in a developmental process. The other experiment investigates the effects on transcript abundance and translation of induction of a single transcription factor (Ndt80). The results and analysis of both studies are in the publication, "Pervasive, coordinated protein level changes driven by transcript isoform switching during meiosis" by Ze Cheng*, George Maxwell Otto*, Emily Nicole Powers, Abdurrahman Keskin, Philipp Mertins, Steve Carr, Marko Jovanovic, and Gloria Ann Brar. In press, Cell.

first: Ze

last: Cheng


title: Single cell transcriptional dynamics of flavivirus infection

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

institute: University of New South Wales

summary: Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.

overall_design: Dengue and Zika virus huh7 cells were subjected to virus-inclusive single cell RNA-Seq.

first: Szu-Yuan

last: Pu

first: Elena

last: Bekerman

first: Shirit

last: Einav

first: Stephen

middle: R

last: Quake


title: Graded arrays of spinal and supraspinal V2a interneuron subtypes underlie forelimb and hindlimb motor control

city: La Jolla

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies


title: Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots [RRBS]

first: Lars

last: Ingerslev

type: Methylation profiling by high throughput sequencing

first: Ida

last: Donkin

first: Odile

last: Versteyhe


title: DNA methylation as a predictor of fetal alcohol spectrum disorder

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Background: Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD. Building on our previous work identifying distinct DNA methylation patterns in children and adolescents with FASD, we have attempted to validate these associations in a different clinical cohort and to use our DNA methylation signature to develop a possible epigenetic predictor of FASD. Methods: Genome-wide DNA methylation patterns were analyzed using the Illumina HumanMethylation450 array in the buccal epithelial cells of a cohort of 48 individuals aged 3.5-18 (24 FASD cases, 24 controls). The DNA methylation predictor of FASD was built using a stochastic gradient boosting model on our previously published dataset FASD cases and controls (GSE80261). The predictor was tested on the current dataset and an independent dataset of 48 autism spectrum disorder cases and 48 controls (GSE50759). Results: We validated findings from our previous study that identified a DNA methylation signature of FASD, replicating the altered DNA methylation levels of 161/648 CpGs in this independent cohort, which may represent a robust signature of FASD in the epigenome. We also generated a predictive model of FASD using machine learning in a subset of our previously published cohort of 179 samples (83 FASD cases, 96 controls), which was tested in this novel cohort of 48 samples and resulted in a moderately accurate predictor of FASD status. Upon testing the algorithm in an independent cohort of individuals with autism spectrum disorder, we did not detect any bias towards autism, sex, age, or ethnicity. Conclusion: These findings further support the association of FASD with distinct DNA methylation patterns, while providing a possible entry point towards the development of epigenetic biomarkers of FASD.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation levels in human buccal epithelial cells from children with fetal alcohol spectrum disorder (n=25) and controls (n=26) to validate our previously identified DNA methylation signature of FASD.

first: Alexandre

last: Lussier

first: Alexander

middle: M

last: Morin

first: Julia

last: MacIsaac

first: Jenny

last: Salmon

first: Joanne

last: Weinberg

first: Jame

last: Reynolds

first: Paul

last: Pavlidis

first: Albert

last: Chudley

middle: S


title: Edited miR-378a-3p target genes

city: Houston

first: Enrique

last: Fuentes-Mattei

state: Texas

address: 1901 East Rd., Unit Number: 1950

department: Experimental Therapeutics

institute: The University of Texas MD Anderson Cancer Center

summary:
Wild-type (WT) miR-378a-3p or edited miR-378a-3p were expressed in SB2 KD-ADAR1 cells to identify the genes regulated by edited miR-378a-3p vs WT miR-378a-3p. PARVA was one of the genes identified to be regulated by edited miR-378a-3p. We demonstrate that this regulation of PARVA is lost in highly metastatic melanoma cells.
Microarray analysis was used to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.

overall_design: SB2 KD-ADAR1 cells were used to re-express the WT or edited-miR-378a-3p.

first: Guermarie

last: Velaquez-Torres


title: Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots


title: The signature of liver cancer in host peripheral blood mononuclear cells and T cells DNA methylation

first: Moshe

last: Szyf

address: 3655 Sir William Osler Promenade

institute: McGill University

summary: We demonstrate the feasibility of developing noninvasive DNA methylation biomarkers of early stages of HCC in the host T cells. These data are consistent with involvement of epigenetic modulation of the immune system in HCC.

overall_design: Examination of DNA methylation signatures in peripheral blood mononuclear cells and T cells from liver cancer (stage 1-4),  Hepatitis and control patients

first: Yonghong

last: Zhang

first: Sophie

last: Petropoulos

first: Liu

last: Jinhua

first: Sergiy

last: Dymov

first: Ning

last: Li


title: Graded arrays of spinal and supraspinal V2a interneuron subtypes underlie forelimb and hindlimb motor control [scRNA-seq]

first: Samuel

last: Pfaff

summary: The spinal cord contains neural networks that enable regionally-distinct motor outputs along the body axis. Nevertheless, it remains unclear how segment-specific motor computations are processed because the cardinal interneuron classes that control motor neurons appear uniform at each level of the spinal cord. V2a interneurons are essential to both fore and hindlimb movements and here we identified two major types that emerge during development: Type-I neurons marked by high Chx10 form recurrent networks with neighboring spinal neurons, and Type-II that downregulate Chx10 and project to supraspinal structures. Type-I and -II V2a interneurons are arrayed in counter-gradients and this network activates different patterns of motor output at cervical and lumbar levels. Single cell RNA-seq revealed Type-I and -II V2a neurons are each comprised of multiple subtypes. Our findings uncover a molecular and anatomical organization of V2a interneurons reminiscent of the orderly way motor neurons are divided into columns and pools.

overall_design: Single-cell RNA-Seq (scRNA-Seq) conducted on cervical and lumbar spinal V2a interneurons from 2 P0 neonates. Cells were sorted via FACS and pooled as a single sample on the 10x Chromium Controller.

first: Marito

last: Hayashi

first: Shawn

last: Driscoll


title: RNA-seq profiling identifies Androgen Receptor-regulated genes in prostate cancer cells

status: Public on Feb 21 2018

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

institute: University of Michigan

summary: The goal of this analysis is to profile AR-regulated genes, especially non-coding RNAs in three androgen sensitive prostate cancer cell lines, MDA-PCA-2B, LNCaP and VCaP. The two cell lines were serum-starved first, followed by dihydrotestosterone (DHT) stimulation or treated with Enzalutamide (AR inhibitor) without starvation. Transcriptome profiling was generated by RNA-sequencing from polyA-selected RNA. These experiments are followed by knock-down experiments of AR and ARlnc1 in MDA-PCA-2B, and also Enzalutamide (anti-androgen) treatment of LNCaP cells.

overall_design: Identification of Androgen Receptor regulated transcriptome in three prostate cancer cell lines.

first: Yajia


title: Chromatine immunoprecipation of atonal binding sites in Drosophila L3 Brains

city: Leuven

first: Mark

last: Fiers

address: Herestraat 49

department: Center for Brain and Disease

country: Belgium

institute: VIB

summary: Atonal is a proneural transcription factor expressed in the Drosophila neuroblast cluster known as the inner proliferation center (IPC). To characterize the putative targes of Atonal in the IPC we have used an endogenously GFP-tagged version of atonal to immunoprecipate brain samples with anti-GFP antibodies

overall_design: L3 larvae of the Ato::GFP genotype where dissected to collect developing brains. The fixed sample was homogenized by sonication. A 10% of the sonicated volume was processed as input controls while the rest was Immunoprecipitated with antiGFP antibodies, purified and sequence.

first: Natalia

last: Mora

first: Bassem

last: Hassan


title: RNA-Guided Transcriptional Silencing In Vivo with S. aureus CRISPR-Cas9 Repressors

city: Durham

first: Charles

last: Gersbach

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

summary: CRISPR-Cas9 transcriptional repressors have emerged as robust tools for disrupting gene regulation in vitro but have not yet been adapted for delivery in adult animal models. Here we created an S. aureus Cas9-based transcriptional repressor (dSaCas9KRAB) compatible with adeno-associated viral (AAV) delivery. To evaluate dSaCas9KRAB efficacy for targeting an endogenous gene in vivo, we silenced transcription of Pcsk9, a regulator of cholesterol levels, in the liver of adult mice. Systemic administration of a dual-vector AAV8 system expressing dSaCas9KRAB and a Pcsk9-targeting guide RNA (gRNA) resulted in significant reductions of serum PCSK9 and cholesterol levels. Despite a moderate host response to dSaCas9KRAB expression, PCSK9 repression was maintained for 24 weeks after a single treatment, demonstrating the potential for long-term gene silencing in post-mitotic tissues with dSaCas9KRAB. In vivo programmable gene silencing enables studies that link gene regulation to complex phenotypes and expands the CRISPR-Cas9 genetic perturbation toolbox for basic research and gene therapy applications.

overall_design: C57Bl/6 wild-type mice were treated with AAVs expressing dSaCas9-KRAB and/or a Pcsk9-targeting gRNA by tail-vein injection. Six weeks after treatment, we harvested the livers of treated mice and performed mRNA-sequencing.

first: Pratiksha

middle: I

last: Thakore

first: Jennifer

middle: B

last: Kwon

first: Christopher

middle: E

last: Nelson

first: Douglas

middle: C

last: Rouse

first: Matthew

middle: P

last: Gemberling

last: Oliver


title: Mouse Obox and CrxOS modulate pre-implantation transcriptional profiles revealing similarity between paralogous mouse and human homeobox genes

city: Oxford

first: Amy

last: Royall

state: Oxfordshire

address: Radcliffe Observatory Quarter

department: Zoology

country: United Kingdom

institute: University of Oxford

summary: We have ectopically expressed four V5-tagged mouse homeobox genes in mouse embryonic fibroblasts with endogenous expression restricted to the preimplantation mouse embryo. Following ectopic expression we used whole transcriptome sequencing to reveal any effect of forced missed expression on the MEF transcriptome.

overall_design: Examination of the roles of 4 homeobox transcription factors

first: Ignacio

last: Maeso

first: Thomas

middle: L

last: Dunwell

first: Peter

middle: W

last: Holland


title: Transcriptional profiles of lung macrophage subsets in Mycobacterium Tuberculosis infection

city: Ithaca

first: Lu

last: Huang

department: Microbiology and Immunology

institute: Cornell University

summary: We investigated transcriptional responses of different lung macrophage lineages during M.tuberculosis infection by RNAseq. Our data revealed that different lineages of macrophages respond differentially to M.Tuberculosis infection.

overall_design: Alveolar macrophage (AM) and interstitial macrophages (IM) with or without Mtb were FACS-sorted from Mtb infected mice for RNAseq.

middle: K

last: Grenier

first: David

middle: G

last: Russell


title: RNA sequencing of sorted microglia from NEFH-tTa/tetO-hTDP43 transgenic mouse whole spinal cord

city: Cambridge

first: Chris

last: Roberts

state: Massachusetts

address: 301 Binney St.

institute: Biogen

summary: Microglia are the resident myeloid-lineage cells in the central nervous system. Despite myriad observations of microglia associated with various tissue pathologies in degenerative disease, their function in and contributions to the pathophysiological processes remain unclear. It is particularly uncertain whether microglia act harmfully to contribute to worsening of degeneration, act beneficially to combat disease-related dysfunction, or perform functions that result in both outcomes. In this dataset, we report RNA sequencing results from mice that undergo inducible ALS/FTLD-like degeneration and subsequent recovery. The goals were to identify whether microglia show transcriptional signatures commensurate with the disease stage or if they remain constant throughout. Additionally, we sought to understand whether there was a particular transcriptional or functional signature associated with functional recovery in the mice. The latter could lead to an understanding of how microglia may be targeted to combat disease and enhance recovery following or during degeneration.

overall_design: mRNA profiles from microglia sorted from whole-spinal cord taken from doxycycline (DOX) inducible NEFH-tTa/tetO-208-hTDP43 (rNLS8, (+/+)) mice. In these mice, removal of doxycycline from the diet (DOX-OFF) induces transgenic expression and degeneration and reintroduction (DOX-ON) suppresses expression and enables recovery. We report profiles from rNLS8 mice that were DOX-OFF for 2 weeks (N=8) or 6 weeks (N=7), or DOX-OFF for 6 weeks followed by DOX-ON for 1 week (N=9).  We also report profiles from control samples that include: rNLS8 mice that were DOX-ON for 6 weeks (N = 6) as asymptomatic genetic controls and WT (-/-) littermates that were DOX-OFF for 2 weeks (N=4), 6 weeks (N=1), or DOX-OFF for 6 weeks followed by 1 week DOX-ON (N=3) as asymptomatic doxycycline controls.

first: Krista

middle: J

last: Spiller

first: Terry

last: Fang

first: Rebecca

last: Canter

first: Kelly

last: Miller

first: Richard

last: Ransohoff

first: John

middle: Q

last: Trojanowski

first: Virginia

last: Lee


title: Gene expression in WT, Flt3 KO, and Flt3L KO cDC1s and cDC2s

status: Public on Feb 20 2018

city: Saint Louis

first: Vivek

last: Durai

state: MO

address: 4940 Parkview Place, Dock at CSRB, Murphy Lab 7766

department: Pathology and Immunology

institute: Washington University in St. Louis School of Medicine

summary: The goal of this study was to determine whether there are any gene expression changes in cDC1s and cDC2s from WT, Flt3 KO, or Flt3L KO mice. Specifically whether developing in the absence of Flt3 signaling had any effects on the gene expression of the cDCs

overall_design: Mature cDC1s and cDC2s were sorted from spleens of WT, Flt3 KO, and Flt3L KO mice, there were two biological replicates for each cell type from each genotype

first: Kenneth

last: Murphy


title: Gene expression in WT and Flt3 KO pDCs

summary: The goal of this study was to determine whether there are any gene expression changes in pDCs from WT and Flt3 KO mice. Specifically whether developing in the absence of Flt3 signaling had any effects on the gene expression of the pDCs

overall_design: Mature pDCs were sorted from spleens of WT and Flt3 KO mice, there were two biological replicates for each cell type from each genotype


title: Altered compensatory cytokine signaling underlies the discrepancy between Flt3-/- and Flt3l-/- mice


title: Gene Expression of Small Cell Carcinoma of the Ovary, hypercalcemic type.

city: Phoenix

first: Jessica

last: Lang

state: AZ

address: 445 N 5th St

institute: TGen (Translational Genomics Research Institute)

summary: Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of four pathologically confirmed cases of SCCOHT tumors.

overall_design:
RNA-Seq on four SCCOHT tumor tissues
NOTE: [1] the raw data for Samples TGEN-A and TGEN-B have been submitted to dbGaP (phs001528.v1.p1; https://www.ncbi.nlm.nih.gov/gap)
[2] The submitter does not have consent to submit the raw data for Samples TGEN-C and TGEN-D.

middle: D

first: William

last: Hendricks

first: Winnie

last: Liang

first: Jeffrey

last: Trent


title: Transcriptome analysis of Follicular Lymphomas from the PRIMABIO cohort

status: Public on Feb 19 2018

city: Pierre Bénite

first: Bruno

last: Tesson

address: Centre Hospitalier Lyon-Sud  Secteur Sainte Eugénie - Pavillon 6D

department: Bioinformatics

country: France

institute: Institut Carnot CALYM

summary: We investigated the biological features of FL and their relationship to patients’ outcome.  Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and  we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome.    proposition SH:  We investigated the biological features of FL and their relationship to patients’ outcome.  Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and  we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome.

overall_design: Fresh-frozen tissue tumour biopsies were prospectively obtained from untreated FL patients participating in the international phase 3 PRIMA trial that evaluated rituximab maintenance after chemotherapy and rituximab induction (NCT00140582). Gene-expression profiling was performed using Affymetrix U133 Plus 2.0 micro-array. These data were used to identify a gene expression signature predicting early relapse in a supervised analysis. An unsupervised analysis was performed to identify the main components of transcriptional heterogeneity among follicular lymphoma tumours.

first: Sarah

last: Huet

first: Gilles

last: Salles


title: Graded arrays of spinal and supraspinal V2a interneuron subtypes underlie forelimb and hindlimb motor control [RNA-seq]

first: Samuel

last: Pfaff

overall_design: Cervical and lumbar segments were dissected in aCSF, and cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical). Via FACS (FACSDIVA or Influx, BD), cells were collected directly into Trizol (Life Technologies). 5-6 neonates at P0 were used from each litter, which typically yielded ~20K cells. ~100K Tom- cells were collected. 3 litters were used to obtain biological replicates.

first: Marito

last: Hayashi

first: Shawn

last: Driscoll


title: Transcriptome profiles of liver biopsy tissues from sever alcoholic hepatitis patients (validation cohort, Brussels)

status: Public on Feb 18 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Corticosteroids are the current standard of care to improve short_term mortality in severe alcoholic hepatitis (AH), although nearly 40% of the patients do not respond and accurate pre_treatment predictors are lacking. We developed 123_gene prognostic score based on molecular and clinical variables before initiation of corticosteroids. Furthermore, The gene signature was implemented in an FDA_approved platform (NanoString), and verified for technical validity and prognostic capability. Here we demonstrated that a Nanostring_based gene expressoin risk classificatoin is useful to predict mortality in  patients with severe alcoholic hepatitis who were treated by corticosteroid

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment.

first: Eric

last: Trépo

first: Nicolas

last: Goossens

first: Naoto

last: Fujiwara

first: Denis

last: Franchimont


title: Transcriptomic Analysis of Rev-erba Knockout vs. Wildtype Primary Myoblast

status: Public on Feb 17 2018

city: Duarte

first: Ke

last: Ma

address: 1500 E Duarte Road

department: Diabetes Complications & Metabolism

institute: City of Hope

summary: Identify signaling pathways that are differentially regulated by Rev-erba in myogenic prcursor cells

overall_design: Total RNA obtained from isolated primary myoblasts from Rev-erba Wildtype and knockout mice

first: Ma

last: Ke

first: Chatterjee

last: Somik


title: RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation [RNA-Seq]

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: Cellular response to ionizing radiation involves activation of the p53-dependent pathways and activation of the atypical NF-?B pathway. Mechanisms of the crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Novel genes potentially (co)regulated by p53 and NF-?B were found using high-throughput genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). Radiation-induced expression in cells with silenced TP53 or RELA (coding the p65 NF-?B subunit) genes was analyzed by RNA-Seq while radiation-induced binding of p53 and RelA (p65) in putative regulatory regions was analyzed by ChIP-Seq, then selected candidates were validated by qPCR. A subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA were identified. Competition for the same transcriptional coactivators of p53 and NF-?B was the most probable mechanism of a frequent antagonistic effect of the TP53 and RELA silencing. However, this mode of regulation was noted for 3 genes where radiation-induced binding of both p53 and RelA was observed, namely IL4I1, SERPINE1, and CDKN1A. This suggested a possibility of a direct antagonistic (co)regulation by both factors: activation by NF-?B and inhibition by p53 of IL4I1, and activation by p53 and inhibition by NF-?B of CDKN1A and SERPINE1. On the other hand, radiation-induced binding of both p53 and RelA was observed in a putative regulatory region of RRAD gene whose expression was downregulated both by TP53 and RELA silencing, which suggested a possibility of direct (co)activation by both factors.

overall_design: We sequenced mRNA from wild type U2OS cells and cells transiently transfected using siRNA specific for RELA gene, TP53 gene, or control siRNA. Cells were untreated (control) or subjected to ionizing radiation with subsequent recovery. Three biological replicates were performed and sequenced.

first: Patryk

last: Janus

first: Katarzyna

last: Szołtysek

first: Piotr

last: Widłak


title: Parallel-factor ER ChIP-seq of Breast Cancer PDX Material

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

summary: To demonstrate the versatility of parallel-factor ChIP-seq, we applied our method to the analysis of ER binding in five patient-derived xenograft (PDX) samples.

overall_design: Parallel-factor ChIP-seq makes use of a second antibody to provide an internal normalisation. Five samples were analysed using a combined ER/CTCF pull down. Pull down efficiency was normalised to CTCF.

first: Alejandra

last: Bruna

first: Florian

last: Markowetz

first: Carlos

last: Caldas

middle: N


title: RNA-seq of GSK-J4 Treated Neuroblastoma Cell Lines

city: Richmond

first: Timothy

last: Lochmann

state: VA

address: 521 N 11th St

department: OCMB

institute: Virginia Commonwealth University

summary: High-risk neuroblastoma is often distinguished by amplification of MYCN and loss of differentiation potential with tumors refractory to retinoic acid differentiation based therapies. Here, we leverage high-throughput drug screening of epigenetic targeted therapies across a large and diverse tumor cell line panel to uncover the hypersensitivity of neuroblastoma cells to GSK-J4, a small molecule dual inhibitor of H3K27 demethylases UTX and JMJD3. Mechanistically, GSK-J4 induced neuroblastoma differentiation and ER stress with accompanying upregulation of PUMA and apoptosis induction. Retinoic acid (RA)-resistant neuroblastoma cells were sensitive to GSK-J4. Additionally, GSK-J4 was effective at blocking the growth of chemorefractory and patient-derived xenograft models of high-risk neuroblastoma in vivo. Further, GSK-J4 and RA combined to induce differentiation, ER-stress and limit the growth of neuroblastomas resistant to either drug alone. In MYCN-amplified neuroblastoma, which is the most prevalent driver gene alteration in the refractory population, PUMA induction by GSK-J4 sensitized tumors to the BCL-2 inhibitor venetoclax, demonstrating that epigenetic targeted therapies and BH3 mimetics can be rationally combined to treat high-risk subset of neuroblastoma. Therefore, H3K27 demethylation inhibition is a promising therapeutic target to treat high-risk neuroblastoma, and H3K27 demethylation can be part of rational combination therapies to induce robust anti-neuroblastoma activity.

overall_design: Four neuroblastoma cell lines were untreated or treated with GSK-J4 for 72 hours. Each cell line and condition was performed in triplicate.

first: Anthony

last: Faber


title: Androgen Receptor-regulated genes in prostate cancer cells

first: Marcin

last: Cieslik

department: Pathology

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

overall_design: Refer to individual Series


title: Translatome of developing drosophila t4/t5 neurons in wildtype versus atonal loss of function genotypes

status: Public on Feb 16 2018

first: Mark

last: Fiers

summary: Atonal is a proneural transcription factor expressed in the Drosophila neuroblast cluster known as the inner proliferation center (IPC). The t4/t5 neurons that derived from the IPC require atonal for their normal development. To characterize the role of Atonal in t4/t5 development we have sequenced the translated RNA in t4/t5 neurons in wild type and ato loss of function flies.

overall_design: To sequence the translated RNA in wild type and ato loss of function t4/t5 neurons we have collected brains from transgenic larvae that in t4/t5 neurons express the ribosomal protein Rbp10Ab tagged with GFP. A 10% of the brain homogenates was used as input, the rest was immunuprecipated with anti-GFP antibodies to isolate t4/t5 ribosomes. The RNA bound to the ribosomes was later purified sonicated and sequenced.

first: Natalia

last: Mora

first: Bassem

last: Hassan


title: Estrogen Receptor α Drives Pro-Resilient Transcription in Mouse Models of Depression

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Most people exposed to stress do not develop depression. Animal models have shown that stress resilience is an active state that requires broad transcriptional adaptations, but how this homeostatic process is regulated remains poorly understood. In this study, we analyze upstream regulators of genes differentially expressed after chronic social defeat stress. We identify estrogen receptor α (ERα) as the top regulator of pro-resilient transcriptional changes in the nucleus accumbens (NAc), a key brain reward region implicated in depression. In accordance with these findings, nuclear ERα protein levels are altered by stress in male and female mice. Further, overexpression of ERα in the NAc promotes stress resilience in both sexes. Subsequent RNA sequencing reveals that ERα overexpression in NAc reproduces the transcriptional signature of resilience in male, but not female, mice. These results indicate that NAc ERα is an important regulator of pro-resilient transcriptional changes, but with sex-specific downstream targets.

overall_design: Understanding changes in gene expression upon ESR1 overexpression in males and females

first: Zachary

last: Lorsch

first: Yong-Hwee

last: Loh

first: Immanuel

last: Purushothaman

first: Deena

middle: M

last: Walker

first: Li

last: Shen

first: Eric

last: Nestler


title: Transcriptome profiles of liver biopsy tissues from sever alcoholic hepatitis patients (derivation cohort)

first: Yujin

last: Hoshida

summary: Corticosteroids are the current standard of care to improve short-term mortality in severe alcoholic hepatitis (AH), although nearly 40% of the patients do not respond and accurate pre-treatment predictors are lacking. We developed 123-gene prognostic score based on molecular and clinical variables before initiation of corticosteroids. Furthermore, The gene signature was implemented in an FDA-approved platform (NanoString), and verified for technical validity and prognostic capability. Here we demonstrated that a Nanostring-based gene expressoin risk classificatoin is useful to predict mortality in  patients with severe alcoholic hepatitis who were treated by corticosteroid

last: Trépo

first: Nicolas

last: Goossens

first: Naoto

last: Fujiwara

first: Denis

last: Franchimont


title: Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene [RNA-seq]

city: CAMBRIDGE

first: Shawn

last: Liu

state: MA

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

summary: Fragile X syndrome (FXS), the most common genetic form of intellectual disability in male, is caused by silencing of the FMR1 gene by hypermethylation of the CGG expansion mutation in the 5’UTR region of FMR1 in FXS patients. Here, we applied recently developed DNA methylation editing tools to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/sgRNA switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state restoring a persistent expression of FMR1 in FXS iPSCs. Neurons derived from methylation edited FXS iPSCs rescued the electrophysiological abnormalities and restored a wild-type phenotype upon the mutant neurons. FMR1 expression in edited neurons was maintained in vivo after engrafting into the mouse brain. Finally, demethylation of the CGG repeats in post-mitotic FXS neurons also reactivated FMR1. Our data establish demethylation of the CGG expansion is sufficient for FMR1 reactivation, suggesting potential therapeutic strategies for FXS.

overall_design: RNA-seq of FXS iPSC and neurons derived from FXS iPSC infected with lentiviruses expressing dCas9-Tet1-P2A-tBFP (dC-T) and a mCherry-expressing sgRNA targeting CGG repeats.

first: X

middle: S


title: Genome-wide DNA methylation study of Parkinson's disease in saliva samples

status: Public on Mar 02 2018

city: Los Angeles

first: Ritz

last: Beate

state: California

address: 650 Charles E Young Dr. South

department: Epidemiology

institute: UCLA Fielding School of Public Health

summary: Genome wide DNA methylation profiling of saliva samples in Parkinson's disease (PD) patients and PD-free controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles. Samples included 128 PD patients and 131 controls with saliva DNA.

overall_design: Bisulphite converted DNA from the 259 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Beate

last: Ritz

first: Steve

last: Horvath


title: The MHC class II transactivator Ciita has a highly restricted transcriptional footprint in murine classical dendritic cells

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

institute: Washington University School of Medicine

summary:
Ciita has been suggested to control the expression of a number of genes based on ChIP-Seq or reporter anaysis but in vivo regulation beyong MHC class II has largely not been confirmed. We crossed Ciita knock out mice to Zbtb46 GFP knock-in knock out mice to identify classical dendritic cells in vivo in a Ciita deficient background.
Expression microarray analysis of CD24+ and CD172a+ DCs from homeostatic spleen or activated BM Flt3l cultures show a highly resitrcited transcriptional footprint of Ciita. These findings underscore the fact that canonical binding sites active in transient expression assays may not always be functional in vivo. In addition, ChIP-Seq alone is not sufficient to discriminate binding from control of expression of a nearby gene.

overall_design: CD24+ and CD172a+ DCs were sorted from the spleens Ciita -/- Zbtb46 GFP/+ and Ciita +/+ Zbtb46 GFP/+ mice. Alternatively, CD24+ and CD172a+ DCs were sorted from the BM cultures of Ciita -/- Zbtb46 GFP/+ and Ciita +/+ Zbtb46 GFP/+ mice after 9 days in Flt3l followed by activation with gamma interferon for 16 hours and LPS for 4 hours. Total RNA was extracted from cells and used for hybridization on Affymetrix Mouse Gene 1.0 ST microarrays.

middle: A

first: Gary

last: Grajales-Reyes

first: Carlos

last: Vasquez Hueichucura

first: Theresa

last: Murphy

first: Kenneth


title: Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

status: Public on Feb 15 2018

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Breast cancer metastasis remains a deadly disease with poorly understood clonal evolution and the timing with which drivers are acquired. Here, we present the RNA sequencing data as the RSEM upper quantile normalized data.

overall_design: Raw data are not publicly available for this series due to patient privacy concerns. The raw data have been deposited at dbGaP for controlled access under accession ID:  phs000676.v2.p1

first: Marni

last: Siegel


title: Gene expression profile of in vitro differentiated mouse bone marrow-derived dendritic cells.

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Mouse BMDCs were differentiated from bone marrow by GM-CSF and IL-4 for 9 days.
We used microarray to obtain global mRNA expression data of the differentiated mouse BMDCs.

overall_design: Mouse BMDCs were differentiated by GM-CSF and IL-4. The global mRNA expression profile were analyzed on Affymetrix microarrays.

first: Zsolt

last: Czimmerer

first: Attila

last: Pap

first: Laszlo

last: Nagy


title: Single-Cell RNA Sequencing Reveals Metallothionein Heterogeneity during hESC Differentiation to Definitive Endoderm

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic


title: Insm1 induces neural progenitor delamination in developing neocortex via down-regulation of the adherens junction belt-specific protein Plekha7

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: Delamination of neural progenitor cells (NPCs) from the ventricular surface is a crucial prerequisite to form the subventricular zone, the germinal layer linked to the expansion of the mammalian neocortex in development and evolution. Here, we dissect the molecular mechanism by which the transcription factor Insm1 promotes the generation of basal progenitors (BPs). Insm1 protein is most highly expressed in newborn BPs in mouse and human developing neocortex. Forced Insm1 expression in embryonic mouse neocortex causes NPC delamination, converting apical to basal radial glia. Insm1 represses the expression of the apical adherens junction belt-specific protein Plekha7. CRISPR/Cas9-mediated disruption of Plekha7 expression suffices to cause NPC delamination. Plekha7 overexpression impedes the intrinsic, and counteracts the Insm1-induced, NPC delamination. Our findings uncover a novel molecular mechanism underlying NPC delamination in which a BP-genic transcription factor specifically targets the integrity of the apical adherens junction belt, rather than adherens junction components as such.

overall_design: Gene expression profiles of mCherry+ neocortical cells 24h after in utero electroporation of either control or Insm1-overexpressing plasmids were generated by RNA-seq and analyzed. mCherry+ cells were isolated using FACS.

first: Tavano

last: Stefania

first: Wieland

middle: B

last: Huttner


title: Single-Cell RNA Sequencing Reveals Metallothionein Heterogeneity during hESC Differentiation to Definitive Endoderm [scRNA-Seq]

summary: Differentiation of human pluripotent stem cells toward definitive endoderm (DE) is the critical first step for generating cells comprising organs such as the gut, liver, pancreas and lung. This in-vitro differentiation process generates a heterogeneous population with a proportion of cells failing to differentiate properly and maintaining expression of pluripotency factors such as Oct4. RNA-sequencing of single cells collected at four time points during a 4-day DE differentiation identified high expression of metallothionein genes in the residual Oct4-positive cells that failed to differentiate to DE. Using X-ray fluorescence microscopy and multi-isotope mass spectrometry, we discovered that high intracellular zinc level corresponds with persistent Oct4 expression and failure to differentiate. We further show that differentiation-arrested phenotype is inversely correlated with zinc concentration in the differentiation media. This study improves our understanding of in-vitro DE differentiation and provides actionable options to improve DE differentiation efficiency.

overall_design: RNA-sequencing of 329 single cells collected at four time points during a 4-day DE differentiation to identify mechanisms leading to cellular heterogeneity during differentiation

first: Junjie

last: Lu

first: Paul

last: Lerou


title: RNAseq of cortex of 6-month old APPPS1 and APPPS1;Apoe-/- mice

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

summary: One of the hallmarks of Alzheimer’s disease is the presence of extracellular diffuse and fibrillar plaques predominantly consisting of the amyloid-β (Aβ) peptide. ApoE influences the deposition of amyloid pathology through affecting the clearance and aggregation of monomeric Aβ in the brain. In addition to influencing Aβ metabolism, increasing evidence suggests that apoE influences microglial function in neurodegenerative diseases. Here, we characterize the impact that apoE has on amyloid pathology and the innate immune response in APPPS1∆E9 and APPPS1-21 transgenic mice. We report that Apoe deficiency reduced fibrillar plaque deposition consistent with previous studies. However, fibrillar plaques in Apoe-deficient mice exhibited a striking reduction in plaque compaction. Hyperspectral fluorescent imaging using luminescent conjugated oligothiophenes identified distinct Aβ morphotypes in Apoe-deficient mice. We also observed a significant reduction in fibrillar plaque-associated microgliosis and activated microglial gene expression in Apoe-deficient mice, along with significant increases in dystrophic neurites around fibrillar plaques. Our results suggest that apoE is critical in stimulating the innate immune response to amyloid pathology.

overall_design: Assessed the cortical gene expression of 6-month old APPPS1-21;ApoE-/- (n=7) and  APPPS1-21 mice (n=6).

first: Ulrich

last: Jason

first: Holtzman

last: David


title: Maternal transmission of anti-miRs into offspring

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

summary: Pregnant mice were administered anti-miR specific to miR-29a-3p or scrambled control at embryonic day E17 and expression levels of miRNAs were assessed in offspring.

overall_design: Impact of anti-miR-29a-3p on miRNA expression was investigated in liver homogenates of mouse pups (postnatal day 7) either directly injected by anti-miR-29a-3p (25mg/kg, via i.p. route) on postnatal day 1, or born to dams previously injected by anti-miR-29a-3p (100mg/kg; via i.v. route) on gestational day 17.

middle: E

first: Ivana

last: Mizikova


title: The interplay of MMP-8, TGF-β1 and VEGF-C cooperatively contributes to the aggressiveness of oral tongue squamous cell carcinoma

city: Oulu

first: Pirjo

last: Åström

address: Aapistie 5A

country: Finland

institute: University of Oulu

summary:
The study aimed to resolve the mechanisms of protective actions of MMP-8 in oral tongue squamous cell carcinoma.
The experiment compares the gene expression levels of control and MMP-8 overexpressing human oral tongue squamous cell carcinoma cells (HSC-3) in stationary and migrating phenotype.

overall_design: 90 000 HSC-3 cells were cultured in 6-well plates (three replicates) with and without wounding the cell layer. The RNA samples from three different plates of each cell lines (wounded +/-) were pooled and the changes in gene expressions were analyzed.

first: Krista

last: Juurikka

first: Elin

last: Hadler-Olsen

first: Gunbjørg

last: Svineng

first: Nilva

last: Cervigne

first: Ricardo

last: Coletta

first: Juha

last: Risteli

first: Joonas

middle: H

last: Kauppila

first: Sini

last: Skarp

first: Samuel

last: Kuttner

first: Ana

last: Oteiza

first: Meeri

last: Sutinen

first: Tuula

last: Salo


title: Hepatic loss of Lis1 leads to fatty liver and predisposes to tumorigenesis in mice

city: hangzhou

first: Xiaoling

last: Li

state: Zhejiang

department: Life Sciences Institute

institute: Zhejiang University

summary: We found that genetic deletion of Lis1 (also known as Pafah1b1) in mouse liver led to increased lipid accumulation and inflammation in the liver. Further analysis revealed that loss of Lis1 led to endoplasmic reticulum (ER) stress and reduced triglyceride secretion. Attenuation of ER stress by tauroursodeoxycholic acid (TUDCA) diminished lipid accumulation in the Lis1 defecient hepatocytes. In addition, Golgi was disorganized in Lis1 deficient livers. These mutants exhibited increased hepatocyte ploidy and accelerated development of liver cancer when treated with DEN. Taken together, these findings suggest that Lis1 is involved in the development and progression of liver diseases from steatosis to liver cancer and provide a useful model for delineating the molecular pathways that lead to these diseases.

overall_design: Gene expression in 4 control livers (CT)  and 4 Lis1 knockout livers (KO) at 2 months was analyzed by RNA-Seq.

first: Hai

last: Song


title: mRNA profiles in PAF KO intestinal adenoma

city: Houston

first: Bo

last: Xia

address: 6670 Bertner Ave, R10-414D

institute: Houston Methodist

overall_design: Examination of mRNA profiles level between APC Min adenoma versus PAF KO; APC Min adenoma

first: Moon

last: Kim

first: Jae-II

last: Park

first: Kaifu

last: Chen