title: Functional and genomic characterization of a xenograft model system for the study of metastasis in triple-negative breast cancer.

city: Melbourne

last: Pattison

state: Vic

address: Wellington Rd

institute: Monash University

summary: To define the molecular regulators of metastasis of triple-negative breast cancer, we conducted a rigorous characterization of four isogenic populations of MDA-MB-231 human triple-negative breast cancer cells that display a range of intrinsic spontaneous metastatic capacities in immuno-deficient mice, from non-metastatic to highly metastatic to lung, liver, spleen and spine. PAT-Seq gene expression profiling of primary tumor cells identified the fibroblast growth factor homologous factor, FGF13, as a candidate metastatic virulence gene highly upregulated in aggressively metastatic MDA-MB-231HM tumors.

overall_design: Gene expression analysis from PAT-Seq of 4 increasingly metastatic breast cancer xenograft tumours

middle: F

last: Harrison

last: Powell

first: Traude

last: Beilharz


title: Transcriptional regulatory networks underlying gene expression changes in Huntington's disease

status: Public on Feb 01 2018

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional changes occur presymptomatically and throughout Huntington’s disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and CAG repeat length-dependent gene expression changes in Htt CAG knock-in mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. 13 of 48 of these predicted TF-target gene modules were also differentially expressed in striatal tissue from human disease. We experimentally validated a specific model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum.  We found CAG repeat length-dependent changes in the genomic occupancy of SMAD3 and confirmed our model’s prediction that many SMAD3 target genes are down-regulated early in HD.

overall_design: Duplicate ChIP samples for each antibody from four-month-old HttQ111/+  and from age-matched wildtype mice. For each ChIP preparation, chromatin DNA was prepared using the combined striatal tissue from both hemispheres of three mice. IPs were performed using Abcam Anti-SMAD3 antibody ab28379 [ChIP grade] or Anti-RNA polymerase II CTD repeat YSPTSPS antibody [8WG16] [ChIP Grade] ab817. Sequencing libraries were prepared from the isolated ChIP DNA and from input DNA controls. Libraries were sequenced on an Illumina HiSeq 2500 sequencer to a depth of ~17-25 million paired-end 25 bp reads per sample

first: Seth

middle: A

last: Ament

middle: R

first: Nathan

middle: D

last: Price


title: Mitotically associated long non-coding RNA, MANCR regulates cell cycle in triple negative breast cancer cells

status: Public on Jan 31 2018

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

type: Expression profiling by high throughput sequencing

summary: Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that is difficult to treat as it is unresponsive to hormone-therapy; therefore, it is imperative to identify novel, targetable regulators of progression in TNBC. Long non-coding RNAs (lncRNAs) are important regulators in breast cancer and have great potential as therapeutic targets; however, little is known about how the majority of lncRNAs function within TNBC cells. In this study, we identify a novel lncRNA, MANCR (LINC00704), which is upregulated in TNBC cells and breast cancer patient samples. Depletion of MANCR in TNBC cells results in a significant decrease in cell proliferation and viability with a concomitant increase in DNA damage. Transcriptome-wide sequencing following MANCR knockdown reveals significant differences in the expression of >2000 genes, and gene set enrichment analysis identifies changes in multiple categories related to cell cycle regulation. Furthermore, MANCR expression is highest in mitotic cells by both RT-qPCR and RNA in situ hybridization. Consistent with a possible role in cell cycle regulation, MANCR-depleted cells have a lower mitotic index and a higher incidence of defective cytokinesis. Taken together, our data reveal a role for the novel lncRNA, MANCR (mitotically-associated long non-coding RNA), in cell cycle regulation of aggressive breast cancer, and identify it as a potential therapeutic target.

first: Kirsten

last: Tracy

first: Coralee

last: Tye

first: Joseph

last: Boyd

first: Jane

last: Lian

first: Gary

last: Stein


title: Insights into gene expression profiles induced by Socs3 depletion in Keratinocytes

city: Tsurumi-ku, Yokohama City,

first: Archana

last: Bajpai

state: Kanagawa,

address: 1-7-22 Suehiro-cho,

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: Specific deletion of suppressor of cytokine signaling 3 (Socs3) in keratinocytes can cause severe skin inflammation with infiltration of immune cells, however the molecular mechanisms and key regulatory pathways involved remains poorly understood. To investigate the role of Socs3 in keratinocytes, we generated and analyzed global RNA-Seq profiles in Socs3 conditional knockout (cKO) mice at two different stages (2- and 10- weeks). Over 400 shared genes were found to be significantly regulated at both time points. Two week samples were marked by initial skin barrier dysfunction established by the downregulation of keratin associated genes and upregulation of genes regulating lipid metabolism. Subsequent increase in expression level of multiple chemokines and cytokines at 10 week were observed representing response to skin inflammation caused by the disruption of skin barrier function. A group of activator protein-1 related genes were to found to be highly elevated in Socs3 cKO mice at both time points. This observation was duly validated using qRT-PCR in Socs3 depleted human keratinocyte–derived HaCaT cells. Overall this study reveals an important regulatory dynamics of Socs3 in skin barrier dysfunction.

overall_design: Socs3 cKO mice mRNA profiles of 2  and 10 week wild type (WT)  C57BL/6 mice were generated by sequencing using HiSeq 1000 system (Illumina) machine  which could read a 50 bp sequence.

first: Vipul

last: Gupta

first: Takashi

last: Ishii

first: Kosuke

last: Miyauchi

first: Yuki

last: Shimizu-Yoshida

first: Masato

last: Kubo

first: Hiroaki

last: Kitano


title: Transcriptome profiling of two inbred lines with distinct responses to Gibberella ear rot disease identified candidate genes for resistance in maize

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

summary:
Purpose: Breeding for gibberella ear rot resistance have been challenging due to the high complexity of the trait. The current study attempts to characterize defence responses to Fusarium graminearum infection in two maize inbred lines with different levels of resistance to the pathogen.
Methods: RNA was extracted from developing kernels of two inbred lines, which had been either fungal (F. graminearum DAOM180378) or mock inoculated 11 days post sibcrossing, using a guanidine isothiocyanate method and ultra-centrifugation with cesium chloride. Isolated RNA was used to quantify whole genome gene expression using RNA-seq (Illumina TruSeq RNA library prep kit v2, Illumina HiSeq 2000). Paired end reads generated from RNA-seq were trimmed of adaptors and low quality reads, aligned with the B73 reference genome sequence version 2, expression levels (TPM) were computed and differential gene expression analysis were performed using CLC Genomics Workbench version 9.
Results: Gene transcripts responding to fungal infection were captured by comparing gene expression levels in mock and fungal inoculated maize ears and gene ontology terms associated with significantly up-regulated gene transcripts were determined for each inbred. More genes were up regulated in the susceptible inbred relative to the resistant inbred, many of which are associated with oxidation-reduction processes potentially causing earlier programmed cell death in the susceptible inbred.
Conclusions: This information helped to identify gene transcripts that were relevant in defense responses with potential applicability in routine breeding efforts and to propose an effective GER resistance mechanism.

overall_design: The experiment consisted of 16 RNA samples from two inbreds (B73 and CO441) tested over two years (2004 and 2006), two treatments (mock and fungal) and two sampling times (1 and 2 days after inoculation).

first: Aida

middle: Z

last: Kebede


title: Defining the responses governing disease tolerance during Citrobacter rodentium infection of mice by deep RNA sequencing

city: Montreal

first: Samantha

last: Gruenheid

state: Quebec

address: 3649 Promenade Sir-William-Osler, Room 365

department: Microbiology and Immunology

institute: McGill University

summary: We performed deep RNA sequencing and systematically analyzed the global gene expression profiles of C. rodentium-infected colon tissues from both susceptible and resistant congenic mice strains to determine the common transcriptomic responses to infection and the Rspo2-mediated dysregulated pathway signatures associated with the loss of disease tolerance.

overall_design: C. rodentium infection in OuJ and O.B6 mice strains

first: Eugene

last: Kang

first: Guangyan

last: Zhou


title: Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from Danio embryo cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Examination of gene expressive levels in embryo development of Danio

first: Baofa

first: Yun-Gui

last: Yang


title: Rhizophagus irregularis gene regulation in early steps of AMF-plant symbiosis

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

summary:
Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here adress the gene regulation of R. irregularis in response to plant signals in the switch from asymbiotic to presymbiotic growth
Methods: Spores of R. irregularis were treated with GR24 (strigolactone synthetic analog) and collected at 1 hour, 2 days, 7 days and 14 days after induction. To stimulate the fungus with root exudates, a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 14 days after. To monitor fungal gene regulation, control conditions were also prepared and mRNA were sequenced by HiSeq Illumina. Read were mapped on the genome assembly with CLCworkbench
Results: At 1 hour, GR24 triggered the overexpression (fold change >2; FDR<0,05) of 123 genes and the repression (fold change < -2; FDR<0,05) of 17 genes. At 2 days, 33 genes were induced, 13 repressed ; at 7 days 106 genes were induced and 13 repressed and at 14 days 19 genes were induced and 10 repressed. Few genes overlap between the different time point. Root exudates induced 251 genes and repressed 63 genes. Few genes were regulated by both GR24 and root exudates.
Conclusions:  GR24 kinetic showed that fungal gene regulation is sequential, quick and involves hundreds of genes. Among those genes, a chitin synthase, involved either in fungal growth either in symbiotic signal production was strongly induced at 1hour, 7 days and 14 days. As few genes are regulated in response to root exudates and GR24, we propose that other plant signals play a role in ealy steps and trigger fungal gene regulation. Several genes coding for putative secreted peptides were induced in response to these plant signals. These genes might be effectors involved in early plant defense manipulation, then facilitating root entry. Thus, they are good candidates to investigate early steps of plant penetration.

sample_organism: Rhizophagus irregularis DAOM 181602=DAOM 197198

overall_design: mRNA profiles spores treated with strigolactone or root exudates were generated by deep sequencing, in triplicate, using Illumina.

first: Mathilde

last: Malbreil


title: Genetic, Biochemical, and Molecular Characterization of Methanosarcina barkeri Mutants Lacking Three Distinct Classes of Hydrogenase

city: Urbana

first: William

middle: W

last: Metcalf

state: Illinois

address: 601 South Goodwin Avenue

department: Microbiology

institute: University of Illinois - Urbana-Champaign

summary: Hydrogenases are a critical component of H2-dependent energy-conservation pathways in Methanosarcina barkeri. To allow phenotypic analysis of the hydrogenases, we constructed mutants lacking the frhADGB, freAEGB, vhtGACD, vhxGAC and echABCDEF operons, individually and in all possible combinations. In addition to measuring the effect of each deletion on growth, methane production, and hydrogenase activity, the effect on gene expression was measured by RNA sequencing to detect potential transcriptional regulation by the hydrogenases.

overall_design: The parental strain of M. barkeri and strains in which the hydrogenases were removed in various combinations were grown to mid-exponential phase on media containing methanol as the growth substrate. RNA was extracted, sequenced, and mapped to the M. barkeri genome. Pairwise comparisons of transcript levels were made for each strain against all other strains.

first: Thomas

last: Mand

first: Gargi

last: Kulkarni


title: PKCα-LSD1-NF-κB Signaling Cascade Is Crucial for Epigenetic Control of the Inflammatory Response

city: Seoul

first: Dongha

last: Kim

address: 599 Gwanak-ro

country: South Korea

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Expression profiles of restoration of BAP1 in a BAP1 deficient cell line

city: New York

first: Yu

last: Chen

state: NY

address: 1237 York Ave.

institute: Memorial Sloan Kettering Cance

summary: RNA-seq of UPMM3 with restoration of BAP1 and BAP1 mutant proteins. Cell line UPMM3 contains a frameshift mutation in BAP1.

first: Amanda

last: Moore


title: Transcriptome analysis of BAP1 knockout and restoration

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Hepatocyte maturation

city: Madison

first: Srikumar

last: Sengupta

state: WI

address: 330 N Orchard St

department: Regenerative Biology

institute: Morgridge Institute for Research

summary: We report the maintenance of mature metabolic function and their induction in primary and hepatic cell lines respectivvely

overall_design: Screening of small molecule pathway inhibitors for hepatic maturation

first: Scott

last: Swanson


title: Next generation sequencing analysis of potential target genes of lncRNA BLACAT2

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

institute: Sun Yat-sen Memorial Hospital

summary: Next generation sequencing analysis was performed to identify potential target genes of lncRNA BLACAT2.  Purified total RNA (3 μg) was used to deplete ribosomal RNA with Ribo-Zero rRNA Removal Kits (MRZMB126,Epicentre). Poly(A)+ RNA was purified with oligo(dT) magnetic beads and fragmented into short sequences. The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions. Each library was sequenced on an Illumina Hiseq2500 in 125PE mode (Illumina, San Diego, CA, USA). These data provided transcriptional changes in bladder cancer cell line UM-UC-3 after BLACAT2 depletion.

overall_design: BLACAT2 was depleted with lentiviral vectors expressing two independent short hairpin RNA specifically targeting BLACAT2 in human bladder cancer cell line UM-UC-3, and knockdown efficiency was quantified by quantitative RT-PCR before library construction. A scramble shRNA sequence was used as a negative control.

first: Tianxin

last: Lin


title: PKCα-LSD1-NF-κB Signaling Cascade Is Crucial for Epigenetic Control of the Inflammatory Response [ChIP-Seq]

summary: The inflammatory response mediated by NF-κB signaling is essential for host defense against pathogens. Although the components and regulatory mechanism of NF-κB signaling have been well-studied, molecular basis for the epigenetic regulation of the inflammatory response is poorly understood. Here, we identify a new signaling axis of PKCα- LSD1-NF-κB p65 which is critical for activation and amplification of the inflammatory response and triggering systemic inflammatory diseases. In response to excessive inflammatory stimuli, PKCα translocates to the nucleus and phosphorylates LSD1. Phosphorylation of LSD1 is required for its interaction with p65 and facilitates demethylation of p65 leading to enhanced protein stability. Genome-wide analysis reveals a critical role of LPS-induced LSD1 phosphorylation in the transcriptional activation of NF-κB target genes. Together, we demonstrate that PKCα-LSD1-NF-κB signaling cascade is crucial for epigenetic control of the inflammatory response.

overall_design: Examination of LSD1 and p65 in WT BMDMs upon LPS

first: Kyoung-Jae

last: Won

first: Sung

last: Baek


title: Genome-wide investigation of pentatricopeptide repeat (PPR) gene family in poplar and their expression analysis in response to biotic and abiotic stresses

city: Chongqing

first: Haitao

last: Xing

address: No.2 Tiansheng Road ,Beibei district

department: School of Life Sciences

institute: Southwest University

summary: Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships, gene duplication. Transcriptomic analyses identified that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), wounding, cold and salinity. Quantitative RT-PCR analysis further confirmed the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a more comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.

overall_design: Purpose: The goal of this study is to compare the PPR genes profile in Wild Type with biotic and abiotic treatment of P. trichocarpa. Treatment including M. brunnea, SA and MeJA, wound, low temperature, and salinity. Plant material treatment: Hormone treatments: SA (5 mM in water) and MeJA [1mM in 0.1% (v/v) ethanol] were applied at the different concentrations as 5 ml droplets on each plant. The treated plants were immediately covered with a transparent lid. Fungal inoculation: The leaves were collected after 24 h. Leaves of three-month-old plants were inoculated with M. brunnea f.sp. multigermtubi. Mycelial plugs (6 mm) were placed on excised leaves (at least three leaves for each plant). These leaves were incubated in Petri dishes with humid filter paper in a humid chamber for 3 d. Low temperature stress: The healthy, well-hydrated plants were transferred to a growth chamber at 4°C under the same light and photoperiodic conditions for 1 h. After cold treatment, plants were allowed to recover at 20°C for 1 h. Wounding stress: For the wounding treatment, the young leaves of poplar plants were harvested after being punctured with sterile needles and placed at 20°C for 2 h. Salinity stress: The four-week-old seedlings were subjected to salt stress. Saline treatments had the NaCl concentrations of 100 mM added to full-strength Hoagland’s solution for 2 d. Wild type plant were grown in a greenhouse at 25°C under a 14/10 h light/dark cycle. Additionally, the leaves applied for all stress treatments, pathogen infection, CK and DGE analysis were excised from the second and third internodes.

first: Keming

last: Luo


title: Regeneration of functional human respiratory epithelium by transplantation of expandable Sox9+ Basal Cell

city: shanghai

first: wei

last: zuo

state: shanghai

address: chifeng road #50

department: medicine

institute: tongji university

summary: We sequenced mRNA from 4 lung epithelium samples (2 brush samples and 2 clone samples) taken from chinese male person.

overall_design: Examination of mRNA levels in brushed lung sample and its corresponding clone sample

first: qiwang

last: ma

first: yu

first: ting

last: zhang


title: SILAC identifies LAD1 as an oncogenic filamin binder regulating actin dynamics in response to EGF and marking aggressive breast tumors

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: Mutations mimicking growth factor-induced proliferation and motility characterize some aggressive subtypes of mammary tumors. To unravel novel players, we applied phosphoproteomics on untransformed mammary cells, which were pre-stimulated with the epidermal growth factor (EGF). This analysis identified ladinin-1 (LAD1), a hitherto poorly characterized protein, as a phosphor-effector of the EGF-to-ERK pathway. We report that LAD1 is essential for mammary cell proliferation and migration. LAD1 is transcriptionally induced, undergoes phosphorylation by EGF and co-localizes with actin stress fibers. Yeast 2-hybrids and co-immunoprecipitation screens revealed that LAD1 binds with filamins, actin cross-linking proteins. Co-sedimentation analyses attribute to LAD1 a role in actin treadmilling, probably in conjuction with SFN/14-3-3sigma. Depletion of LAD1 led to a decrease in viability related transcripts, and inhibited growth of mammary xenografts in an animal model. Furthermore, LAD1 is highly expressed in two aggressive subtypes of breast cancer, as well as predicts poor patient prognosis. These studies identify a new cytoskeletal component essential for signal transduction and for the acquisition of oncogenic attributes by human mammary tumors.

overall_design: RNA-Seq – EGF treatemnt for 0, 40 and 240 minutes of HCC70 cell-line stably expressing LAD1 targeting shRNA (or scrambled control)


title: mRNA expression profile of Lymphocytes by high-throuput sequencing

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: The activation of CD4+ T helper (Th) cells is crucial for the induction of cytotoxic T lymphocyte (CTL) responses against malignancy. We reprogrammed a Th clone specific for chronic myelogenous leukemia (CML)-derived b3a2 peptide to pluripotency and re-differentiated the cells into T-lineage cells (iPS-T cells). Although iPS-T cells retained the same T-cell receptor (TCR) as the original Th clone, their gene expression patterns resembled those of group 1 innate lymphoid cells, and CD4 molecule, an essential co-receptor in TCR-mediated Th responses, was not expressed. The transduction of CD4 genes into iPS-T cells enhanced b3a2 peptide–specific responses. iPS-T cells contained a subpopulation that up-regulates CD40 ligand (CD40L) in response to IL-2 and IL-15. Besides CD4 expression, CD40Lhigh iPS-T cells induced antigen-specific DC maturation characterized by enhanced CD83, CD86, and CCR7. In the presence of Wilms tumor 1 (WT1) peptide, DCs conditioned by CD4-modified CD40Lhigh iPS-T cells stimulated the priming of WT1-specific CTLs. These CTLs eliminated WT1 peptide-expressing CML cell lines in vitro and in vivo. Our findings indicate CD4 modification and purification of CD40Lhigh iPS-T cells generates T helper-like cells that induce effective anti-leukemic CTL responses via DC maturation and suggest feasibility of the cells for adoptive immunotherapy against leukemia.

overall_design: Expression profile of the lymphocytes (n = 18) by high-throuput sequencing

first: Ueda

last: Norihiro

first: Mizoro

last: Yasutaka

first: Watanabe

last: Akira

first: Kaneko

last: Shin


title: A regulatory circuitry between the Gria2 mRNA and miR-409/miR-495 is altered in mESC-derived motor neurons carrying an ALS-associated FUS mutation

city: Rome

first: Pietro

last: Laneve

state: RM

address: Viale Regina Elena 291

department: Center for Life Nano Science@Sapienza

country: Italy

institute: Istituto Italiano di Tecnologia

type: Non-coding RNA profiling by high throughput sequencing

summary: Mutations in FUS/TLS have been genetically associated to Amyotrophic Lateral Sclerosis (ALS).  Since FUS is a multifunctional protein involved in the biogenesis and activity of several types of RNAs, the understanding of the molecular basis of ALS pathogenesis should take into account both direct effects of FUS mutation through gain- and loss-of function mechanisms as well as indirect effects due to the crosstalk between different classes of RNAs.   To identify how FUS alterations impinge on MN-specific RNA-based circuitries, we performed a transcriptome profiling of small- and long- RNAs of motor neurons derived in vitro from differentiation of mouse Embryonic Stem Cells carrying a knock-in FUS-P517L mutation, corresponding to the human FUS-P525L. Combining ontological, predictive and molecular analyses we found an interesting inverse correlation between several classes of deregulated miRNAs and their corresponding mRNA targets. Among them we validated a circuitry in which the up-regulation of miR-409-3p and miR-495-3p produced the down-regulation of the Gria2 mRNA. This cross-talk is relevant for the ALS pathogenesis since Gria2, encoding for a subunit of the glutamate AMPA receptor, has been already linked to ALS through an excitotoxicity mechanism. Notably, this circuitry resulted deregulated also in heterozygous conditions, which match the genetic background of the human pathology.

overall_design:
High-throughput sequencing of total RNA from FUS-P517L/P517L  mutant mESCs-derived Hb9::GFP-positive motoneurons, 3 replicates. High-throughput sequencing of small RNA from  FUS-WT mESCs-derived Hb9::GFP-positive motoneurons, 2 replicates; FUS-KO mESCs-derived Hb9::GFP-positive motoneurons, 2 replicates; FUS-P517L/P517L mESCs-derived Hb9::GFP-positive motoneurons, 2 replicates.

This series includes the re-analysis of all samples in GSE83226.

first: Irene

last: Bozzoni

first: Davide

last: Capauto

first: Alessio

last: Colantoni

first: Lei

last: Lu

first: Tiziana

last: Santini

first: Silvia

last: Biscarini

first: Giovanna

last: Peruzzi

first: Beatriz

last: Blanco Redondo

first: Neil

last: Shneider

first: Elisa

last: Caffarelli


title: Next-gen RNA sequencing of human osteosarcoma tumors

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Trascriptome analysis of osteosarcoma samples were performed

overall_design: Tumor samples were obtained from UMN BioNet or HTCC, cell lines were purchased from ATCC and sequenced using Illumina HiSeq 2000

first: David

last: Largaespada

first: Jaime

last: Modiano

first: Subbaya

last: Subramanian

first: Logan

middle: G

last: Spector

first: Aaron

middle: L

last: Sarver


title: Alternative classification of glioblastoma based on BUB1B-inhibition sensitivity

first: Jun

last: Zhu

address: 1 Gustave L. Levy Pl

department: Genetics and genomic sciences

institute: Icahn school of medicine at mount sinai

summary: We created a computational framework with which to predict BUB1B-GLEBS sensitivity based on gene expression data from BUB1B-inhibition sensitive (BUB1BS) or resistant (BUB1BR) GBM stem cells (GSCs), astrocytes, and neural progenitors. Our classifier examines the expression of 838 genes comprising the BUB1BS signature. Applying this scheme to GBM patient tumor data stratified tumors into BUB1BS and BUB1BR subtypes, revealing that BUB1BS patients have a significantly worse prognosis regardless of their tumor's development subtype (i.e., classical, mesenchymal, neural, proneural). Applying the same scheme to drug sensitivity profiles predicts that BUB1BS cells to be more sensitive to Raf inhibitors as well as other drugs such as type I and II topoisomerase inhibitors among other drugs. Functional genomic profiling of BUB1BR versus BUB1BS GBM isolates revealed differentially reliance of genes enriched in the BUB1BS classifier, including those involved in mitotic cell cycle, microtubule organization, and chromosome segregation. Taken together, our results show that BUB1BR/S classification of GBM tumors, in addition to predicting BUB1B-inhibition sensitivity, may help predict cancer aggressiveness and sensitivity to multiple anti-cancer drugs.

overall_design: Examination of 9 GBM tumor tissue and the corresponding GSC.

first: Eunjee

last: Lee


title: Becoming monogamous quickly: Adaptive evolution of a pallidal enhancer at the prairie vole Avpr1a locus

city: DURHAM

first: Alejandro

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

summary: We use ChIP-seq targeting histone 3 lysine 27-acetylation (H3K27ac) to identify putative enhancer sites genome-wide in the ventral pallidum cortex of adult prairie voles

overall_design: ChIP samples were generated by targeting an active enhancer mark (H3K27ac) in chromatin extracted from the ventral pallidum of nine individuals pooled in batches of three individuals each. Illumina libraries were prepared from ChIP and INPUT DNA and sequenced on Illimuna NextSeq platform.

first: Berrio

last: Alejandro

first: Phelps

last: Steve


title: Cross species transcriptome analysis of osteosarcoma


title: Next-gen RNA sequencing of mouse osteosarcoma tumors

overall_design: Tumor samples were obtained from a previously published Sleeping Beauty forward genetic screen,  cell lines were derived from previous primary tumors and sequenced using Illumina HiSeq 2000


title: mRNA sequencing in cde-1 mutants versus WT C. elegans infected by the Orsay virus

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary:
Aim: We question relative mRNA levels in cde-1 mutants versus WT C. elegans (N2 strain) infected by the Orsay virus
Methods: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological triplicates. Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. mRNA libraries were prepared using the NEBNext Ultra directional RNA library kit (NEB) with poly(A) selection and deep sequencing was produced with an Illumina HiSeq machine (single read 50). For differential expression analysis, genes were only included in the analysis if they had at least 1 count per million in all of the control samples or all of the experiment samples. After applying this filter, differentially expressed genes were then called using EdgeR (Robinson, et al. 2010). For the correlation matrix, Pairwise Pearson correlation values were calculated between all samples.

overall_design: Examination of mRNA profiles in Orsay virus infected animals from two different genetic backgrounds

first: Jeremie

last: Le Pen

first: George

middle: E

last: Allen

first: Eric

last: Miska


title: Allergic Airway Disease is Dependent on Methylene-Tetrahydrofolate Reductase

city: Aurora

first: Kenneth

last: Eyring

state: CO

address: 12700 East 19th Avernue, 8611

department: Department of Medicine

institute: University of Colorado School of Medicine

type: Methylation profiling by high throughput sequencing


title: Allergic Airway Disease is Dependent on Methylene-Tetrahydrofolate Reductase (Bisulfite-Seq)

summary:
RATIONALE: The development and progression of asthma are strongly influenced by environmental exposures.  We have demonstrated that mice exposed to a diet enriched with methyl donors during vulnerable periods of fetal development can enhance the heritable risk of allergic airway disease through epigenetic changes.
OBJECTIVES: Since there is conflicting evidence on the role of folate in modifying allergic airway disease risk, we hypothesized that blocking folate metabolism through the loss of methylene-tetrahydrofolate reductase (MTHFR) activity would reduce the allergic airway disease phenotype.
METHODS: Using a house dust mite (HDM) induced model of allergic airway disease, we tested the effect of MTHFR on disease severity.
MEASUREMENTS AND MAIN RESULTS: Loss of MTHFR alters single carbon metabolite levels in the lung and serum including elevated homocysteine and cystathionine and reduced methionine.  HDM-treated C57BL/6MTHFR-/- mice demonstrate significantly less airway hyerreactivity (AHR) compared to HDM-treated C57BL/6 mice.  Furthermore, HDM-treated C57BL/6MTHFR-/- mice compared to HDM-treated C57BL/6 mice have reduced whole lung lavage (WLL) cellularity, eosinophilia, and IL-4/IL-5 cytokine concentrations.  The effect of MTHFR loss on HDM-induced allergic airway disease was reversed by betaine supplementation. 737 genes are differentially expressed and 146 regions are differentially methylated in lung tissue from HDM-treated C57BL/6MTHFR-/- mice and HDM-treated C57BL/6 mice.  Additionally, analysis of methylation/expression relationships identified 503 significant correlations.
CONCLUSION: Collectively, these findings indicate that single carbon metabolism warrants further investigation as a disease modifier in allergic airway disease.

overall_design: Lung DNA methylation profiles of MTHFR-/- mice treated with house dust mite (HDM, n = 9) or saline (n = 5) or wild-type (WT) mice treated with house dust mite (HDM, n = 9) or saline (n = 6)

first: Brent

middle: S

last: Pedersen

middle: N

last: Maclean

first: Sally

middle: P

last: Stabler

first: Ivana

middle: V

last: Yang

last: Schwartz


title: RNA-Sequencing experiment for effects of PKF115-584 treatment on four T-ALL cell lines (RPMI8402, HPB-ALL, Jurkat, CCRF-CEM).

city: Barcelona

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Notch activation is instrumental in the development of most T-cell acute lymphoblastic leukemia (T-ALL) cases, yet Notch mutations alone are not sufficient to recapitulate the full human disease in animal models. We here found that Notch1 activation at the fetal liver (FL) stage expanded the hematopoietic progenitor population and conferred it transplantable leukemic-initiating capacity. However, leukemogenesis and leukemic-initiating cell capacity induced by Notch1 was critically dependent on the levels of β-Catenin in both FL and adult bone marrow contexts. In addition, inhibition of β-Catenin compromised survival and proliferation of human T-ALL cell lines carrying activated Notch1. By transcriptome analyses, we identified the MYC pathway as a crucial element downstream of β-Catenin in these T-ALL cells and demonstrate that the MYC 3' enhancer required β-Catenin and Notch1 recruitment to induce transcription. Finally, PKF115-584 treatment prevented and partially reverted leukemogenesis induced by active Notch1.

overall_design: Four T-ALL cell lines (RPMI8402, HPB-ALL, Jurkat, CCRF-CEM)  were treated with DMSO (control) or PKF115-584 (310nM) for 3hrs. Gene expression changes were measured with Cufflinks comparing the 4 control with the 4 treated samples.

first: Anna

last: Bigas


title: PKCα-LSD1-NF-κB Signaling Cascade Is Crucial for Epigenetic Control of the Inflammatory Response [RNA-Seq]

first: Dongha

last: Kim

overall_design: Gene expression profiling of WT and phosphorylation-defective Lsd1SA/SA knock-in bone marrow-derived macrophages (BMDMs) untreated or treated with LPS for 2 hours.

first: Kyoung-Jae

last: Won

first: Sung

middle: H

last: Baek


title: Transcriptome study of A. fumigatus hyphae and human neutrophils

city: Jena

first: Jörg

last: Linde

address: Naumburger Str. 96 a

department: Institute for Bacterial Infections and Zoonoses

country: Germany

institute: Federal Research Institute for Animal Health - Friedrich-Loeffler-Institute

summary: The infections with the human pathogenic fungus A. fumigatus is an emerging problem. The infections process and the reaction of the immune systeme to the infection is still not complete understood. So we analyzed the response of A. fumigatus to human neutrophils to get insights of these interaction.

overall_design: Examination of whole RNA of human neutrophils and the fungus A. fumigatus. Different donors (D1-D6), treatment protocols (C,T) and time-points (0,30,90,180 minutes) have been used.

first: Katrin

last: Lapp

first: Martin

last: Vödisch

first: Kristin

last: Kroll

first: Vera

last: Pähtz

first: Sandra

last: Bruns

first: Maria

last: Strassburger

first: Reinhard

last: Guthke

first: Olaf

last: Kniemeyer

first: Vito

last: Valiante

first: Thorsten

last: Heinekamp

first: Axel

last: Brakhage


title: RNA-sequencing of bulk CD19+ Thymic B cells from young (5 week) and aged (10-24 month) mice

status: Public on Jan 30 2018

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Thymic B cells have been recently shown the ability to be licensed to express Aire, a critical transcription factor involved in the expression of self-antigens in the thymus which are critical for clonal deletion of autoreactive T cells and maintenance of self-tolerance. Mutations in AIRE cause systemic autoimmunity in humans and autoimmunity with varying degrees of severity in different mouse strains. Thymic B cells have been studied in young animals, but studies of this population with age are lacking. Given the thymus undergoes age-associated atrophy in its stromal compartment, we hypothesized that aged thymic B cells may under go changes with age which may impact their ability to mediate clonal deletion of autoreactive T cells and may contribute to age-associated increases in autoimmune prevalence. By comparing the transcriptome of young and aged thymic B cells we find that Aire and transcriptional activators of Aire are signficantly decreased with age.

overall_design: Thymic B cells were enriched by incubating total thymocytes with CD19-APC (Clone: MB19-1) followed by incubation with anti-APC magnetic beads (Miltenyi Biotec). Enriched cells were then sorted using a BD FACS ARIA to a minimum purity of 98.5%, RNA extracted and analyzed

first: Sergio

last: Cepeda

first: Carolina

last: Cantu

first: Stephanie

last: Orozco

first: Yangming

last: Xiao

first: Zoe

last: Brown

first: Manpreet

middle: K

last: Semwal

first: Thomas

last: Venables

first: Mark

last: Anderson

first: Ann

last: Griffith


title: Root hair-expressed genes in rice

city: Yongin-si

first: Moon

last: Sunok

state: Gyeonggi-do

address: 1732, Deogyeong-daero

department: genetic engineering

institute: kyung hee university

summary: To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar

overall_design: After sterilizing, seeds of rice were placed on an MSO medium during 3 day. The seminal roots were detached and submerged in liquid nitrogen and then gently were rubbed to purify root hairs

first: Sunok

last: Moon

first: Ki-Hong

last: Jung


title: Transcriptional change of HTR8/Svneo cells over expressed with PLAC8-EGFP

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The goal of this this project was to study the transcriptional change when PLAC8-EGFP was over expressed in the trophoblast cell line, HTR8/Svneo.

overall_design: HTR8/Svneo cells which were stably over expressed with PLAC8-EGFP and EGFP were established.Then trancriptional sequencing experiment was performed to explore the effect of PLAC8 on trophoblast cells.

first: Wenlin

last: Chang

first: Yawei

last: liu

first: Yanli

last: Dang

first: Hongmei

last: Wang


title: Investigate A2M treatment in liver of mice

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat’s cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumour development. Here we found that A2M modulates tumour cell adhesion, migration and growth by inhibition of tumour promoting signalling pathways, e.g. PI3K / AKT, SMAD and up-regulated PTEN via down-regulation of miR-21, in vitro and in tumour xenografts. A2M increases the expression of CD29 and CD44 but did not evoke EMT. Transcriptome analysis of A2M-treated tumour cells, xenografts and mouse liver demonstrated a multifaceted regulation of tumour promoting signalling pathways indicating a less tumorigenic environment mediated by A2M. By virtue of these multiple actions the naturally occurring A2M has strong potential as a novel therapeutic agent.

overall_design: 11 samples: 5 treated with PBS, 6 treated with A2M

first: Gerd

last: Birkenmeier

first: Ronny

last: Amberg

first: Rene

last: Thieme


title: Expression profiles of genetically engineered mouse model tumors (GNA11 Q209L and GNA11 Q209L Bap1 KO)

city: New York

first: Yu

last: Chen

address: 1237 York Ave.

institute: Memorial Sloan Kettering Cance

overall_design: RNA-seq of end-point tumors harvested from genetically engineered mouse melanoma model with genotypes GNA11 Q209L, GNA11 Q209L Bap1 KO and BRAF V600E Bap1 KO.

first: Amanda

last: Moore


title: De novo assembly and transcriptome analysis of two different starch content Ipomoea batatas cultivars

city: Nanchang

first: Dong

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: In this study, we compared the root transcriptomes between high and low starch content species in three different growth and development periods.This provided a new perspective and resources for the molecular mechanisms study of storage root formation and development process.

overall_design: Compare the transcriptome of high starch content sweetpotato cultivar Chuanshu 218 (H) and low starch content cultivar 15-94 (L) in three different periods.

first: Lan

last: Yang

first: Songtao


title: Variation of genome-wide NF-kappa B RELA binding sites in response to different microbial stimuli

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

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

overall_design: Refer to individual Series


title: MYC favors the onset of tumorigenesis by inducing epigenetic reprogramming of mammary epithelial cells towards a stem cell-like state [ChIP-seq]

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento

summary: We address the molecular mechanisms through which MYC promotes loss of cell identity and acquisition of stem cell-like traits, favouring the onset of tumorigenesis, by performing epigenetic profile analyses in a transition from WT IMEC, IMEC over-expressing MYC and mammospeheres formed from IMEC-MYC (named M2).

overall_design: ChIP-seq for H3K4me3, H3K4me1, H3K27ac and MYC binding in WT IMEC, IMEC-MYC and M2 mammospheres

first: Luca

last: Fagnocchi

first: Vittoria

last: Poli

first: Alessio


title: Gene expression response to 5 microbial stimuli in Detroit562 cells [RNA-seq]

summary: NFKB is a family of transcription factors (TF), which are master regulators of the innate immune system. It is activated downstream of pathogen recognition receptors after ligand binding and regulates the expression of antimicrobials, cytokines and chemokines, thus helping to fight infections as well as recruiting the adaptive immune system. Although NFKB responds to a wide variety of signals, the processes in which stimulus-specificity is attained are still unclear. We characterized the response of one of the NFKB members, RELA, to five stimuli mimicking infection in nasopharyngeal epithelial cells. We wanted to investigate gene expression in response to these stimuli as well, in order to relate RELA binding to differences to expression regulation. Although most RELA binding sites where common among stimulation, we distinguished a minority of stimulus-specific RELA binding sites. Interestingly, some of these seemed to have a biological effect as they correlated with corresponding gene expression. Especially, the response to Poly I:C mimicking viral dsRNA gave a distinct RELA profile binding the vicinity of antiviral genes. Some of which were overexpressed under Poly I:C stimulation specifically.

overall_design: Treatment of Detroit 562 cells with 5 stimuli: LPS, TNFα, Pam2CSK4, Poly I:C or M tri-DAP followed by gene expression analysis by RNA-seq. Two biological duplicates were analyzed for each condition.


title: Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [RNA-seq]

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates1,2. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models3. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness4,5 and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation6-9. MYCN down-regulation broadly reverses these oncogenic phenotypes in a variety of neuroblastoma models10-12 and recent thereapeutic strategies to indirectly target MYCN production or protein stability have reduced tumor growth in vivo13-15. These observations motivate an investigation of MYCN binding in MYCN amplified tumors as it remains fundamentally unclear how elevated levels of the factor occupy the genome and alter transcriptional programs in neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of direct MYCN perturbation in neuroblastoma. We find that at oncogenic levels, MYCN associates with E-box (CANNTG) binding motifs in an affinity dependent manner across most active cis-regulatory promoters and enhancers. MYCN shutdown globally reduces histone acetylation and transcription, consistent with prior descriptions of MYC proteins as non-linear amplifiers of gene expression. We establish that MYCN load at the promoter and proximal enhancers predicts transcriptional responsiveness to MYCN shutdown and that MYCN enhancer binding occurs prominently at the most strongly occupied and down-regulated genes, suggesting a role for these tissue specific elements in predicating MYCN responsive “target” genes. At these invaded enhancers, we identify the lineage specific bHLH TWIST1 as a key collaborator and dependency of oncogenic MYCN. These data suggest that MYCN enhancer invasion helps shape transcriptional amplification of the neuroblastoma gene expression program to promote tumorigenesis.

overall_design: RNA-Seq in SHEP-21 DOX treated time course. RNA-Seq in BE2C cells

first: Rhamy

last: Zeid

first: Charles

middle: Y

last: Lin


title: Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ChIP_RX]

summary: In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation. MYCN down-regulation broadly reverses these oncogenic phenotypes in a variety of neuroblastoma models and recent thereapeutic strategies to indirectly target MYCN production or protein stability have reduced tumor growth in vivo. These observations motivate an investigation of MYCN binding in MYCN amplified tumors as it remains fundamentally unclear how elevated levels of the factor occupy the genome and alter transcriptional programs in neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of direct MYCN perturbation in neuroblastoma. We find that at oncogenic levels, MYCN associates with E-box (CANNTG) binding motifs in an affinity dependent manner across most active cis-regulatory promoters and enhancers. MYCN shutdown globally reduces histone acetylation and transcription, consistent with prior descriptions of MYC proteins as non-linear amplifiers of gene expression. We establish that MYCN load at the promoter and proximal enhancers predicts transcriptional responsiveness to MYCN shutdown and that MYCN enhancer binding occurs prominently at the most strongly occupied and down-regulated genes, suggesting a role for these tissue specific elements in predicating MYCN responsive “target” genes. At these invaded enhancers, we identify the lineage specific bHLH TWIST1 as a key collaborator and dependency of oncogenic MYCN. These data suggest that MYCN enhancer invasion helps shape transcriptional amplification of the neuroblastoma gene expression program to promote tumorigenesis.

overall_design: ChIP-Rx in the SHEP21 neuroblastoma cell lines for H3K27ac, RNA PolII, and MYCN. ChIP-Rx in the SHEP21 neuroblastoma cell lines for H3K4me3 and CTCF.


title: Genome-wide RELA binding sites in response to 5 microbial stimuli in Detroit562 cells [ChIP-seq]

summary: NFKB is a family of transcription factors (TF), which are master regulators of the innate immune system. It is activated downstream of pathogen recognition receptors after ligand binding and regulates the expression of antimicrobials, cytokines and chemokines, thus helping to fight infections as well as recruiting the adaptive immune system. Although NFKB responds to a wide variety of signals, the processes in which stimulus-specificity is attained are still unclear. Here, we characterized the response of one of the NFKB members, RELA, to five stimuli mimicking infection in nasopharyngeal epithelial cells. When comparing RELA genome-wide binding sites , we detected most of them to be overlapping among the different stimulations. Yet, we distinguished a minority of stimulus-specific RELA binding sites. Interestingly, some of these seemed to have a biological effect as they correlated with corresponding gene expression. Specifically, the response to Poly I:C mimicking viral dsRNA gave a distinct RELA profile binding the vicinity of antiviral genes. This group of binding sites was also enriched in Interferon Regulatory Factor motifs indicating that the interaction with more specialized TFs could contribute to stimulus-specific RELA activity. Furthermore, motif analysis revealed differences in the sequence of the NFKB motifs between certain stimulus-specific sets of peaks suggesting preferences for particular NFKB dimers in response to defined signals.

overall_design:
Treatment of Detroit 562 cells with 5 stimuli: LPS, TNFα, Pam2CSK4, Poly I:C or M tri-DAP. Examination of RELA genome-wide binding sites by ChIP-seq after the 5 stimulations. Two biological duplicates were analyzed for each condition.
Please note that the 'Input' and 'No Treatment' samples were used as background to call the peaks and generate the wig files for the processed data of Treatment RELA ChIP-seq (each treatment RELA ChIP-seq samples was processed against Input DNA + No Treatment RELA ChIP-seq (of the same batch) so the wig files generated are normalized ).


title: Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ATAC-seq]

overall_design: ATAC-Seq in SHEP21, BE2C, KELLY, NGP, and MM1S cell lines


title: Identification of differentially expressed genes between senescence and senescence bypass cells

status: Public on Jan 29 2018

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

summary: We applied RNA-seq analysis to control and senescent human primary BJ fibroblast cells (senescence induced by activation of the oncogenic RASG12V gene), as well as in BJ cells that fully or partially bypass oncogene-idnuced senescence (OIS) due to knock-down of either p53 or BRD7 or LncRNA-OIS1 (using 4 different shRNAs).

overall_design: RNA-seq was applied to untreated and RASG12V-activated BJ cells. RASG12V was activated in unmanipulated cells or in cells knocked-down for p53 or BRD7 or LncRNA-OIS1.

first: Li

last: Li

first: Rani

first: Reuven

last: Agami


title: Genetic determinants and epigenetic effects of pioneer factor binding [ChIP-BS-seq]

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

summary: Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of two distinct TFs, the pioneer factor FOXA2 and the pluripotency-associated factor OCT4 (POU5F1), in both endogenous and ectopic settings. We find that, while stable binding of FOXA2 is highly cell type specific and similar to what is observed for most TFs including OCT4, pioneer activity can be distinguished by notable sampling of additional loci that are occupied in alternative lineages. In our ectopic system, FOXA2 binding can be selectively stabilized at previously sampled sites by co-expressing the lineage specific regulator GATA4. Alternatively, we observe minimal influence of chromatin state on discrete, stabilized binding choices for FOXA2 but a strong bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 binding and nucleosome remodeling at silent loci can occur when the cell cycle is halted in G1, but surprisingly subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming.

overall_design:
FOXA2 ChIP bisulfite sequencing
FOXA2 ChIP bisulfite sequencing on cells halted in G1 with Mimosine treatment
FOXA2 ChIP bisulfite sequencing in FOXA2-CDT1 fusion cells

first: Julie

last: Donaghey

first: Alexander

last: Meissner


title: RNA-sequencing of bulk CD19+ Thymic B cells from young (3 month - 4 year) and old (42 - 61 years) humans

first: Yidong

overall_design: Thymic B cells were enriched by staining total thymocytes with CD19-APC (Clone: HIB19) followed by incubation with anti-APC magnetic beads (Miltenyi Biotec). Enriched cells were then sorted using a BD FACS ARIA to a minimum purity of at least 98.5% or better, then total RNA was isolated and analyzed.

first: Sergio

last: Cepeda

first: Carolina

last: Cantu

first: Stephanie

last: Orozco

first: Yangming

last: Xiao

first: Zoe

last: Brown

first: Manpreet

last: Semwal

first: Thomas

last: Venables

first: Mark

last: Anderson

first: Ann

last: Griffith


title: Specific labeling of stem cell activity in human colorectal organoids using an ASCL2-responsive minigene

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: Organoid technology provides the possibility to culture human colon tissue and patient-derived colorectal cancers (CRC) while maintaining all functional and phenotypic characteristics. Labeling of human colon stem cells (CoSCs), especially in normal and benign tumor organoids, is challenging and therefore limits usability of multi-patient organoid libraries for CoSC research. Here, we developed STAR (STem cell Ascl2 Reporter), a minimal enhancer/promoter element that reports transcriptional activity of ASCL2, a master regulator of LGR5+ CoSC fate. Among others via lentiviral infection, STAR minigene labels stem cells in normal as well as in multiple engineered and patient-derived CRC organoids of different stage and genetic make-up. STAR revealed that stem cell driven differentiation hierarchies and the capacity of cell fate plasticity (de-differentiation) are present at all stages of human CRC development. The flexible and user-friendly nature of STAR applications in combination with organoid technology will facilitate basic research on human adult stem cell biology.

overall_design: Cells from different colon organoid types were FACS sorted for stem STemness Ascl2 Reporter activity for transcriptome profiling by RNA-seq.

first: Koen

last: Oost

first: Hugo

last: Snippert


title: ZFR coordinates crosstalk between RNA decay and transcription in innate immunity

city: Bethesda

first: J

middle: Robert

last: Hogg

state: MD

address: 50 South Drive, #2239

department: Biochemistry and Biophysics Center

institute: National Heart, Lung and Blood Institute

summary: Identification of RNAs differentially expressed upon ZFR knockdown in THP1 and HEK-293TO cells.

overall_design: Paired-end RNA-Seq on THP1 cells treated with ZFR-specific or control shRNAs and HEK-293TO cells treated with ZFR-specific or control siRNAs.

first: Nazmul

last: Haque

middle: R


title: Genetic determinants and epigenetic effects of pioneer factor binding [ChIP-seq 2]

first: Sudhir

last: Thakurela

overall_design:
In order to understand the binding dynamics of a pioneer transcription factor and its underlying chromatin environment, we performed high through-put sequencing for FOXA1 ChIP along with several histone marks. Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and quenched with 125mM glycine at room temperature.  Chips were performed as previously described(Gifford et al., 2013) by isolating nuclei and shearing DNA to 200-600 basepair fragments using Branson sonicator.Antibody incubation with chromatin was performed overnight.  ~10 million cells were used per FOXA2 ChIP with 1ug of antibody/ million cells.  ~1 million cells were used for each histone ChIP.  Following an overnight incubation, antibody-protein complexes were isolated using Protein G/A beads (Life Technologies) and sequencing libraries were generated.  Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90453 records.

first: Julie


title: Genetic determinants and epigenetic effects of pioneer factor binding [ATAC-seq 2]

overall_design:
To combine the dynamics of FOXA2 binding with the accessibility of DNA, we assessed the chromatin accessibility using ATAC-seq. Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013).DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions.  The rest of the DNA was then amplified using the chosen cycle number and PCR libraries were purified using double sided Ampure clean up to remove high molecular weight fragments. .55x Ampure volume was added to the PCR, mixed and incubated. Supernatant was removed following magnet separation and cleaned-up with a 1X Ampure volume.  Libraries were sequenced on a HiSeq 2500 at 8pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90453 records.^SERIES = GSE92491

last: Donaghey

first: Alexander


title: Genetic determinants and epigenetic effects of pioneer factor binding


title: Integrated transcriptional analysis unveils the dynamics of cellular differentiation in the developing mouse hippocampus

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: The ability to assign expression patterns to individual cell types that constitute a tissue is a major challenge in RNA expression analysis. This especially applies to brain given the plethora of different cells coexisting in that tissue. Here, we derived cell-type specific transcriptome signatures from existing single cell RNA data and integrated these signatures with a newly generated dataset of expression (bulk RNA-seq) of the postnatal developing hippocampus. This integrated analysis allowed us to provide a comprehensive and unbiased prediction of the differentiation drivers for 10 different hippocampal cell types and describe how the different cell types interact to support crucial developmental stages. Our integrated analysis provides a reliable resource of predicted differentiation drivers and insight into the multifaceted aspects of the cells in hippocampus during development.

overall_design: 21 RNA-seq samples. For the stages E15, P1, P7, P15, and P30, there are respectively 3, 4, 3, 3, and 6 RNA-seq biological replica (total 19). One RNA-seq sample has two technical replica.

first: Giovanni

last: Iacono

first: Marco

last: Benevento

first: Yann

last: Herault

first: Aline

last: Dubos

first: Hans

last: van Bokhoven

first: Nael

last: Kasri

first: Henk

last: Stunnenberg


title: Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors [repli-seq]

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

institute: Florida State University

summary: The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system consisting of ~200kb human bacteria artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) replication origin elements (E-BACs). E-BACs were stably maintained as autonomous mini-chromosomes in both HeLa and human induced pluripotent stem cells (hiPSCs) and established their RT de novo. We applied repli-seq to evaluate E-BACs' replication timing.

overall_design: Genome-wide replication timing profiles of E-BAC transfected HeLa-EBNA1 and K3-EBNA1 cells

first: Jiao

last: Sima


title: Genetic determinants and epigenetic effects of pioneer factor binding [RNA-seq]

overall_design: To understand the effect of FOXA2 induction on expressed we profiled genowide-wide abundance of RNA using RNA-seq. RNA was isolated with RNeasy columns (Qiagen) and non-stranded libraries were performed using Illumina’s standard Tru-Seq kit.  Libraries were sequenced on a HiSeq 2500 at 11pmol.

last: Meissner


title: Genetic determinants and epigenetic effects of pioneer factor binding [ATAC-seq]

type:
Other
Third-party reanalysis

overall_design:
To combine the dynamics of FOXA2 binding with the accessibility of DNA, we assessed the chromatin accessibility using ATAC-seq. Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013).DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions.  The rest of the DNA was then amplified using the chosen cycle number and PCR libraries were purified using double sided Ampure clean up to remove high molecular weight fragments. .55x Ampure volume was added to the PCR, mixed and incubated. Supernatant was removed following magnet separation and cleaned-up with a 1X Ampure volume.  Libraries were sequenced on a HiSeq 2500 at 8pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90454 records.


title: RNA-sequencing of bulk CD19+ Thymic B cells from mice and humans

first: Yidong

last: Chen

overall_design: Refer to individual Series


title: Transcriptional regulation by NR5A2 couples cell differentiation

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: Tissue-specific differentiation and inflammatory programmes are thought to independently contribute to disease. The orphan nuclear receptor NR5A2 is a key regulator of pancreas differentiation, and SNPs in and near the human gene are associated with risk of pancreatic cancer. In mice, Nr5a2 heterozygosity sensitizes the pancreas to damage, impairs regeneration, and cooperates with mutant Kras in tumor progression. Through transcriptomic analysis, we uncovered a basal pre-inflammatory state in the pancreas of heterozygous mice that is reminiscent of pancreatitis-induced inflammation and is conserved in histologically normal human pancreata with reduced Nr5a2 mRNA expression. In mice, Nr5a2 undergoes a dramatic transcriptional switch from tissue-specific to inflammatory loci, which promotes AP-1-dependent inflammatory gene transcription. Deletion of c-Jun in the pancreas of Nr5a2+/- mice rescues the pre-inflammatory phenotype and the defective regenerative response to damage. These findings provide compelling evidence that the same transcriptional networks supporting homeostasis in normal tissue can be subverted to foster inflammation upon genetic or environmental constraints.

overall_design: A  mild  acute  pancreatitis  was  induced  by  seven  hourly  injections  of  the  CCK analog  caerulein  (Bachem)  at  50 ug/kg.  Briefly,  animals  were  weighted  before  the beginning of the procedure and caerulein was administered i.p. Mice were sacrificed by cervical dislocation 8h, 24h,and 48h after the first injection. Three animals of each genotype and timepoint were analysed.

first: Marta

last: Flández

first: Isidoro

last: Cobo

first: Paola

last: Martinelli

first: Francisco

middle: X

last: Real


title: Streptococcus pneumoniae. Two-color microarray bases Gene Expression Analysis v.6.5

status: Public on Jan 27 2018

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

institute: Universidad de Córdoba

summary: TIGR4 and R6 bacterial strains of Streptococcus pneumoniae treated and not treated with the iron chelator deferoxamine mesylate (DFO)

overall_design: Bacteria subject to two conditions. Control and those treated with the iron chelator DFO (deferoxamine). Microarray experimental design done according to the loop approach. 4 biological replicates

first: Irene

last: Jiménez-Munguía

last: Rodríguez-Franco

first: Manuel

middle: J

last: Rodriguez-Ortega


city: Daejeon

first: Chan Soon

last: Park

address: 291 Daehak-ro, Yu-seong gu

department: graduate school of medical science and engineering

institute: KAIST

summary: Glioblastoma multiforme (GBM) is a highly aggressive and vascularized malignant brain tumor. SoxF transcription factors consisting of Sox7, Sox17, and Sox18 are expressed specifically in endothelial cells (ECs) and contribute to vascular morphogenesis. While the role of Sox17 was found in subcutaneous ectopic tumors, Sox7 has not been studied in the context of tumor angiogenesis. Here, we investigated gene expression profile of RNA analysis of Sox7- and Sox17-deficient mouse endothelial cells from high grade glioma using RNA sequencing to validate molecular characteristics of Sox7 and Sox17 in high grade glioma.

overall_design: To reveal molecular characteristics of Sox7 and Sox17 in high-grade glioma endothelial cells, we established mouse orthotopic glioma model by intracranially injecting GL26l glioma cells into congenic B6 genetic background mice. To excise Sox7 and Sox17 in ECs, the Cdh5(BAC)-CreERT2 driver line was bred with Sox7fl/fl and Sox17fl/fl mice and experimental mice intraperitoneally administered 20 mg/kg tamoxifen. For in-depth understanding of different gene expression of Sox7- and Sox17- deficient vessels, we purified endothelial population and performed RNA-sequencing analysis. There are two independent sets of Sox7-deficient and control group, and three independent sets of Sox17-deficient and control group.

first: Il-Kug

last: Kim

first: Kangsan

first: ChanSoon

first: Injune


title: Next Generation Sequencing Facilitates Quantitative Analysis of MiRNAs in fetal Keratinocytes at different gestational ages

city: Shenyang City

first: Xining

last: Pang

address: 77 Puhe Street, Shenbei New District

department: Department of Stem Cells and Regenerative Medicine

institute: China Medical University

summary:
Purpose: Next-generation sequencing technologies allow miRNA detection at an unprecedented sensitivity.Early- to mid-gestational fetal mammalian skin wounds heal rapidly and without scarring. The goals of this study are to obtain the differently expressed miRNAs between late- and mid-gestational fetal Keratinocytes for further studies.
Methods: Keratinocytes were obtained from six fetal skin samples dividied into two groups: a mid-gestation group and a late-gestation group. RNA extracted from Keratinocytes was used to prepare a small RNA library for next-generation sequencing (NGS) using an Illumina Genome Analyzer IIx. To uncover potentially novel microRNA (miRNAs), the mirTools 2.0 web server was used to identify candidate novel human miRNAs from the NGS data.UCSC Genome Browser and the Vienna RNAfold web server were used to further validate the novel miRNA candidates. The repeatability of the expression levels detected by NGS was confirmed by real-time quantitative RT-PCR.
Results: Using an optimized data analysis workflow, we detected a total of 99,354,224 raw reads from the six samples, 85,252,341 (85.81%) were high-quality reads (≥ 18nt). After alignment to the human genome (GRCH38), the number of genome-aligned reads was 74,678,115 (87.60% of the high-quality reads). The number of sequence reads that correspond to known miRNAs was 61,587,749 (82.47% of the genome-matching reads), as was determined by perfect sequence matching to the database of known miRNAs (miRBase release 18). After removing the matched non-coding RNAs (Release 10), 8,755,258 reads remained for identification of novel miRNA candidates by mirTools 2.0. The results revealed the existence of 202 novel miRNA candidates and 29 known miRNAs that were not listed in miRBase release 18. Of the 202 potential novel miRNAs, 106 candidates were detected by at least 10 counts, by NGS, indicating that they have a higher probability of being novel human miRNAs. Using Student's t-test, 173 known miRNAs and 23 novel miRNA candidates were found to be statistically significant (P values < 0.05). The expression of 22 novel miRNA candidates and 88 known miRNAs was changed by more than 2.0-fold (known: 15 up-regulated and 73 down-regulated; novel: two up-regulated and 20 down-regulated).
Conclusions: Our study represents the first detailed analysis of human miRNAs in fetal Keratinocytes. Using mirTools 2.0 web server, we have revealed the existence of 202 novel miRNA candidates. Of the 202 potential novel miRNAs, 106 candidates were detected by at least 10 counts, by NGS, indicating that they have a higher probability of being novel human miRNAs. Taken together, our results provide compelling evidence that dynamic expression of miRNAs in fetal Keratinocytes at different gestational ages. MiRNAs presenting altered expression at different gestational ages in fetal Keratinocytes may contribute to scarless wound healing in early- to mid-gestational fetal Keratinocytes, and thus may be new targets for potential scar prevention and reduction therapies.

overall_design: small RNA profiles of human fetal Keratinocytes at different gestational ages were generated by next-generation sequencing on a Genome Analyzer (GA) (Illumina) IIx platform

first: Feng

last: Zhao

first: Zhe

last: Wang


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

status: Public on Jan 28 2018

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young

department: Pathology

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: Immortalized brown/beige-like preadipocyte cell line(iBAd Cells) was used for ATAC-Seq and mRNA-Seq. For RNA-Seq, triplicate experiments were performed, for ATAC-Seq individual samples were sequenced after 5 days of differentiation with either control treatment, or including IL-10 overnight prior to addition of Isoproterenol for 5-6 hours.  Inguinal White adipose tissue was used for RNA-Seq from either WT or IL-10-/- animals, where 11 IL10-/- mice and 9 WT mice were seperately pooled for library construction and sequencing.

first: Brandon

last: Thomas

first: Prashant

last: Rajbhandari


title: Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA

status: Public on Jan 26 2018

first: David

last: Casero

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

summary: Nuclear receptors are important conduits between environmental cues and gene expression, but the molecular events governing spatial variation in their responses remain poorly understood. Here we outline an important role for a non-coding RNA in modulating the cell type-specific actions of the cholesterol-activated nuclear receptor LXR. LXR regulates the expression of genes involved in responses to excess cholesterol and has been causally linked to the pathogenesis and treatment of prevention and atherosclerosis in animals. We identify the lncRNA MeXis as an amplifier of LXRdependent transcription of the critical cholesterol efflux gene Abca1. MeXis interacts with and guides the promoter binding of the nuclear receptor transcriptional coactivator DDX17. Loss of MeXis in murine immune cells has a marked impact on chromosome architecture at the Abca1 locus, impairs cellular responses to cholesterol overload, and accelerates the development of atherosclerosis. Our findings define MeXis as a lncRNA gatekeeper that modifies the actions of LXR in lipid-dependent control of macrophage gene expression. This has important implications for mechanisms that underlie spatial activation patterns of nuclear receptors. Our work opens a new gateway to targeting reverse cholesterol transport since it is conceivable that therapeutic approaches that enhance MeXis activity might reduce foam cell formation and atherogenesis

overall_design: The experiments compare gene expression in mouse macrophages treated with DMSO or the LXR agonist GW3965

first: Tamer

last: Sallam

first: Marius

last: Jones

first: Xiaohui

last: Wu

first: Thomas

last: Gilliland

first: Kevin

last: Qian

first: Ascia

last: Eskin

first: Cynthia

last: Hong

first: Ayaka

last: Ito

first: Bence

last: Daniel

first: Julian

last: Whitelegge

first: Laszlo

last: Nagy

last: Castrillo

first: Stephen

last: Smale


title: Regulation of the positive transcriptional effect of PLZF through a non-canonical EZH2 activity

city: Marseille

first: Estelle

last: Duprez

address: 27 boulevard Lei Roure

department: Centre de Recherche en Cancérologie de Marseille

institute: INSERM

summary: The transcription factor PLZF (promyelocytic leukemia zinc finger protein) acts as an epigenetic regulator balancing self-renewal and differentiation of hematopoietic cells through binding to various chromatin-modifying factors. First described as a transcriptional repressor, PLZF is also associated with active transcription, although the molecular bases underlying the differences are unknown. Here, we reveal that, in a hematopoietic cell line, PLZF is predominantly associated with transcribed genes. Additionally, we identify a new association between PLZF and the histone methyltransferase, EZH2 at the genomic level. We find that co-occupancy of PLZF and EZH2 on chromatin at PLZF target genes is not associated with SUZ12 or trimethylated lysine 27 of histone H3 (H3K27me3) but with the active histone mark H3K4me3 and active transcription. Removal of EZH2 leads to an increase of PLZF binding and increased in gene expression. Our results suggest a new role of EZH2 in restricting PLZF positive transcriptional activity independently of its canonical PRC2 activity.

overall_design: PLZF, EZH2, SUZ12 and histone marks (H3K27me3, H3K4me3, H3K36me3) were analyzed using ChIPseq in human myeloblastic cell line (KG1) in wild-type (WT), shPLZF or shEZH2 conditions.  Each condition represents a merge of two biological replicates.

first: Myriam

last: Koubi

first: Mathilde

last: Poplineau

first: Julien

last: Vernerey

first: Lia

last: Nguyen

first: Guillaume

last: Tiberi

first: Abdessamad

last: El-Kaoutari

first: Sylvain

last: Garciaz

first: Jean-Christophe

last: Andrau

first: Muhammad

last: Maqbool

first: Christel

last: Guillouf

first: Andrew

last: Saurin


title: The investigation of target gene of antisense oligonucleotides (ASOs) against microRNA-21 in colorectal carcinoma cells in vivo

status: Public on Jan 25 2018

city: Zunyi

first: Tao

last: Ding

state: Guizhou Province

address: Xuefu Road, Honghuagang District

institute: Zunyi medical college

summary: To further elucidate the potential molecular mechanism through which down-regulated the expression level of miR-21 affected the growth of colorectal carcinoma cells, we used TargetScan and MIRDB software to screen out 16 genes, and 5 genes were up-regulated, putative target genes of miR-21 including PDZD2, DUSP8, B3GAT2, STAG2 and CCL1, which were closely correlated with proliferation, apoptosis and metastasis in tumor cells according to previous literatures.

overall_design: ASOs against miR-21 in CRC cells in vivo altered the expression of target gene, for preparation of subcutaneous xenograft model, cells were subcutaneously implanted into the right flanks of nude mice at 3.5×10e6 SW620 cells density (n=20). Then 7 days after tumor cells inoculation with confirmation of successful maturation of tumors, 20 mice were divided randomly into two groups (10 mice per group). The 100μg plasmid of p-miR-21-ASOs or p-Cont was given locally by direct injection into the tumor tissues of nude mice at four times every three days.

first: Panpan

last: Cui


title: Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice transcriptome [RNA-seq]

city: Seoul

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

institute: Sookmyung Women's university

summary:
Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD mouse models.
Method (mRNA-seq): In order to construct cDNA libraries with the TruSeq RNA library kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2000. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer.  The transcript counts in isoform level and gene level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Method (common): Both miRNA-seq and RNA-seq were carried out using the kidney tissues from two mouse models at postnatal day 1, 3 and 7 in triplicate samples. Total RNA was isolated using TRIzol method according to manufacturer’s protocol (Invitrogen Life Technologies).
Result: UIn RNA-seq analysis, total 3,040 transcripts in Pkd1f/f:HoxB7-cre mice and 2,470 transcripts in Pkd2f/f:HoxB7-cre mice were differentially expressed at indicated time points (FDR<0.05). In addition, we also identified 1,297 common transcripts in both mouse models. In miRNA analysis, total 243 of miRNAs were identified as differentially expressed genes while 130 miRNAs were common in both mouse models. Among common miRNAs, total 13 miRNAs including 11 upregulated and 2 downregulated miRNAs were selected based on comparison of expression patterns at each time point.
Conclusion: Our study described the parallel integrated analysis of miRNA-seq and RNA-seq data and validated the expression, direct interaction and cystogenesis-related functions of key miRNAs and mRNA targets.

overall_design: miRNA and mRNA profiles according to cystogenesis of postnatal day 1, 3 and 7 in two representative ADPKD mouse models were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Jong

first: Yu

last: Woo

first: Do

last: Kim

first: Nam

last: Koo


title: Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice smallRNA [miRNA-seq]

summary:
Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD mouse models.
Method(miRNA-seq):  Small RNA sample preparation was done according to Illumina’s protocol. In brief, 5’ and 3’ adapters were sequentially ligated to small RNA of 18–30 bases gel purified from 5–10 µ total RNA. Adapter-ligated small RNA was reverse transcribed, amplified and sequenced on a HiSeq2000 (Illumina) following manufacturer's instructions. Raw data (the reads for each miRNA) were normalized to the total reads of each individual sample as the standardized to reads per (RPM; miRNA counts / total count of each sample x 1 million).
Method(common): Both miRNA-seq and RNA-seq were carried out using the kidney tissues from two mouse models at postnatal day 1, 3 and 7 in triplicate samples. Total RNA was isolated using TRIzol method according to manufacturer’s protocol (Invitrogen Life Technologies).
Result: UIn RNA-seq analysis, total 3,040 transcripts in Pkd1f/f:HoxB7-cre mice and 2,470 transcripts in Pkd2f/f:HoxB7-cre mice were differentially expressed at indicated time points (FDR<0.05). In addition, we also identified 1,297 common transcripts in both mouse models. In miRNA analysis, total 243 of miRNAs were identified as differentially expressed genes while 130 miRNAs were common in both mouse models. Among common miRNAs, total 13 miRNAs including 11 upregulated and 2 downregulated miRNAs were selected based on comparison of expression patterns at each time point.
Conclusion: Our study described the parallel integrated analysis of miRNA-seq and RNA-seq data and validated the expression, direct interaction and cystogenesis-related functions of key miRNAs and mRNA targets.


title: The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings

city: Salt Lake City

first: Leslie

middle: Ellen

last: Sieburth

state: UT

address: 257 South 1400 East

department: Biology

institute: University of Utah

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


title: Genetic determinants and epigenetic effects of pioneer factor binding [ChIP-seq]

city: Cambridge

first: Sudhir

last: Thakurela

overall_design:
In order to understand the binding dynamics of a pioneer transcription factor and its underlying chromatin environment, we performed high through-put sequencing for FOXA1 ChIP along with several histone marks. Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and quenched with 125mM glycine at room temperature.  Chips were performed as previously described(Gifford et al., 2013) by isolating nuclei and shearing DNA to 200-600 basepair fragments using Branson sonicator.Antibody incubation with chromatin was performed overnight.  ~10 million cells were used per FOXA2 ChIP with 1ug of antibody/ million cells.  ~1 million cells were used for each histone ChIP.  Following an overnight incubation, antibody-protein complexes were isolated using Protein G/A beads (Life Technologies) and sequencing libraries were generated.  Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90454 records.

The file MatchingSampleTable.xlsx includes a key to the column headers in RPKM_Table.txt and the sample titles from all the above-listed ATAC-seq and ChIP-seq studies. The RPKM table includes re-analyzed data and these samples are listed in Re-AnalysisTable.xlsx.  Links to the re-analyzed samples can be found below.

first: Julie

last: Donaghey

first: Alexander

last: Meissner


title: Investigate A2M treatment on human prostate cancer and mouse liver

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - FLI


title: Small RNA-seq of adult male and female mouse liver

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Total RNA-seq analysis of mouse liver RNA following locked nucleic acids (LNAs) treatment to identify mRNA targets of mmu-miR-802-5p and mmu-miR-1948-5p in vivo. These datasets are part of a study where we used small RNA sequencing to discover 24 sex-biased mouse liver miRNAs, and then investigated the roles of two of these miRNAs in GH-regulated liver sex differences. Studies in pre-pubertal and young adult mice, and in mice where pituitary hormones are ablated or where sex-specific hepatic GH signaling is dysregulated, demonstrated that the male-biased miR-1948 and the female-biased miR-802 are both regulated by sex-specific pituitary GH secretory patterns, acquire sex specificity at puberty, and are dependent on the GH-activated transcription factor STAT5 for their sex-specific expression. Both miRNAs are within genomic regions characterized by sex-biased chromatin accessibility. miR-1948, a novel, uncharacterized miRNA, has essential features for correct Drosha/Dicer processing, generates a bona fide mature miRNA with strong strand bias for the 5p arm, and is bound by Argonaute in liver tissue, as is miR-802. In vivo studies using inhibitory locked nucleic acid sequences revealed that miR-1948-5p preferentially represses female-biased mRNAs and induces male-biased mRNAs in male liver, and conversely, miR-802-5p preferentially represses male-biased mRNAs and increases levels of female-biased mRNAs in female liver. Cytochrome P450 mRNAs were strongly enriched as targets of both miRNAs. Thus, miR-1948-5p and miR-802-5p are functional components of the GH regulatory network that shapes sex-differential gene expression in mouse liver.

overall_design: Small RNA-seq libraries were generated from total liver RNA isolated from 8 week old male and female mice.  Differential analysis between male and female small RNA-seq datasets identified sex-differential microRNAs.

first: Pengying

last: Hao


title: RNA-seq expression analysis of mouse liver treated with locked nucleic acids (LNAs) that inhibit mmu-miR-802-5p and mmu-miR-1948-5p

summary: Total RNA-seq analysis of mouse liver following LNA treatment in vivo to identify mRNA targets of mmu-miR-802-5p and mmu-miR-1948-5p.

overall_design: Male and female 9-wk ICR mice were injected with LNAs complementary to mmu-miR-1948-5p and mmu-miR-802-5p, respectively.  Liver RNA was analyzed by RNA-seq 3 days or 6 days after LNA treatment.


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [RNA-Seq]

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: The adult brain is composed of hundreds of different neuronal subtypes, which retain their differentiated traits and identity throughout the lifespan of the organism. Nevertheless, in part due to technical limitations, the mechanisms governing this stability are not fully understood. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in sparse neuronal populations in vivo, we present, to our knowledge, the first comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons and embryonic neural progenitors. Our results support a model wherein a sequential deposition of the repressive modifications H3K27me3 and H3K9me3 occur on developmental genes in a neuronal subtype specific manner. We furthermore show that aberrant gene expression during dopaminergic stress in a mouse model of Parkinson’s disease, or after methamphetamine injection, is characterized by the de-repression of genes with promoter regions that are dually marked by H3K4me3 and H3K27me3, whereas the induction of genes with promoter regions marked by any other combination of H3K27me3 and H3K9me3 occur less frequently. Our study provides to our knowledge the first genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare but clinically relevant neuronal subtypes. This strategy can be generalized for the identification and functional characterization of molecular determinants involved in the maintenance of gene expression in other classes of neurons.

overall_design: 10 samples of 1000 neuronal nuclei were analyzed in total, 4 samples of adult mDA nuclei, 3 samples of adult SER nuclei and 3 samples of E11.5 Sox2 positive NPC nuclei. Each sample originate from individual mice. Nuclei from these samples were also used for ChIP-seq.

first: Erik

last: Södersten

first: Konstantinos

last: Toskas

first: Vilma

last: Rrakli

first: Katarina

last: Tiklova

first: Åsa

last: Björklund

last: Ringnér

first: Thomas

last: Perlmann

first: Johan

last: Holmberg


title: Investigate A2M treatment on human prostate cancer xenograft in mice

department: Core Facility - Next Generation Sequencing

summary: Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat’s cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumor development. Here we found that A2M modulates tumor cell adhesion, migration and growth by inhibition of tumor promoting signalling pathways, e.g. PI3K / AKT, SMAD and up-regulated PTEN via down-regulation of miR-21, in vitro and in tumor xenografts. A2M increases the expression of CD29 and CD44 but did not evoke EMT. Transcriptome analysis of A2M-treated tumor cells, xenografts and mouse liver demonstrated a multifaceted regulation of tumor promoting signalling pathways indicating a less tumorigenic environment mediated by A2M. By virtue of these multiple actions the naturally occurring A2M has strong potential as a novel therapeutic agent.

overall_design: 11 samples: 5 treated with PBS, 6 treated with A2M

first: Gerd

last: Birkenmeier

first: Ronny

last: Amberg

first: Rene

last: Thieme


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [ChIP-Seq]

overall_design: 52 samples of ChIP-seq libraries. Up to 2 batches with 1000-nuclei ChIP-seq libraries for input, H3K9me3, H3K27me3 and H3K4me3 in 3 biological replicates originating from FACS sorted cell type specific nuclei from individual mice. Samples from batch I were also used for RNA-seq.


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [scRNA-Seq]

overall_design: Single nuclei RNA-seq on 98 FACS sorted nuclei from adult mouse midbrain based on mCherry expression driven by the Slc6a3 promoter. Pooled nuclei from one male and one female mouse were sorted.


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

overall_design: Refer to individual Series


title: Epigenetic regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA

first: Peter

last: Tontonoz

summary: Nuclear receptors are important conduits between environmental cues and gene expression, but the molecular events governing spatial variation in their responses remain poorly understood. Here we outline an important role for a non-coding RNA in modulating the cell type-specific actions of the cholesterol-activated nuclear receptor LXR. LXR regulates the expression of genes involved in responses to excess cholesterol and has been causally linked to the pathogenesis and treatment of prevention and atherosclerosis in animals. We identify the lncRNA MeXis as an amplifier of LXR-dependent transcription of the critical cholesterol efflux gene Abca1. MeXis interacts with and guides the promoter binding of the nuclear receptor transcriptional coactivator DDX17. Loss of MeXis in murine immune cells has a marked impact on chromosome architecture at the Abca1 locus, impairs cellular responses to cholesterol overload, and accelerates the development of atherosclerosis. Our findings define MeXis as a lncRNA gatekeeper that modifies the actions of LXR in lipid-dependent control of macrophage gene expression. This has important implications for mechanisms that underlie spatial activation patterns of nuclear receptors. Our work opens a new gateway to targeting reverse cholesterol transport since it is conceivable that therapeutic approaches that enhance MeXis activity might reduce foam cell formation and atherogenesis.

overall_design: Peritoneal macrophages were isolated from either WT or KO animals and treated for 3 hours with or without GW using DMSO as control. Using four replicates per condition libraries were prepared using the Nextera Tn5 Transposase kit (Illumina) as described by Buenrostro and colleagues with slight modifications

first: Tamer

last: Sallam

first: Brandon

last: Thomas