title: Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space [combinatorial_library_sort_seq]

status: Public on Jul 27 2019

first: Conor

last: McClune

address: 31 Ames St

institute: Massachusetts Institute of Technology

summary:
The cross compatibility of functional PhoQ-PhoP mutants with altered specificity residues was analyzed by sort seq. We cloned and combinatorially combined 79 PhoQ* and 71 PhoP* variants, producing a library with a theoretical diversity of 5,609.
The library was then subjected to Sort-Seq, using fluorescence-activated cell sorting (FACS) and deep sequencing to quantify the signal responsiveness of variants in the library. To gauge the phosphorylation of PhoP in vivo, we used a fluorescent transcriptional reporter, PmgrB-yfp. In the presence of low extracellular Mg2+, functional PhoQ promotes the phosphorylation of PhoP and the production of YFP, whereas in the presence of high concentrations of Mg2+, PhoQ drives the dephosphorylation of PhoP, limiting the accumulation of YFP). The library was grown in each condition for 6 hours before sorting and sequencing.
To identify variants that are signal responsive and drive YFP production specifically in low Mg2+, we sorted cells from each condition into 8 separate bins and deep sequenced the randomized regions of variants collected in each bin (Fig. 2b). We then calculated the frequency of each variant in each bin to yield the distributions of individual variants in low and high Mg2+, which were fit to Gaussians. From these fits, we assessed the mean level of YFP in each condition and the fold-induction, or signal responsiveness, of each variant detected in the library.

The 11 codons / amino acids listed in this dataset refer to codons 12, 14, 15, 18, and 19 in PhoP and codons 284, 288, 289, 292, 302, and 303 in PhoQ, in that order.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Compatability of PhoQ and PhoP variants were analyzed by deep sequenceing bins sorted by fluorescence under different Mg2+ conditions

first: Christopher

last: Voigt

first: Michael

last: Laub


title: Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection

status: Public on Jul 19 2019

city: Lisboa

first: Francisco

last: Caiado

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

type: Expression profiling by high throughput sequencing

summary: Chemotherapy-resistant cancer recurrence is a major cause of mortality. In acute myeloid leukemia (AML), chemorefractory relapses result from the complex interplay between altered genetic, epigenetic and transcriptional states in leukemic cells. We developed an experimental model system using in vitro lineage tracing coupled with exome, transcriptome and in vivo functional readouts to assess the AML population dynamics and associated molecular determinants underpinning chemoresistance development. We found that combining standard chemotherapeutic regimens with low doses of DNA methyltransferase inhibitors (DNMTi, hypomethylating drugs) prevents chemoresistant relapses. Mechanistically, DNMTi suppressed the outgrowth of a pre-determined set of chemoresistant AML clones with stemness properties, instead favoring the expansion of rarer and unfit chemosensitive clones. Importantly, we confirmed the capacity of DNMTi combination to suppress stemness-dependent chemoresistance development in both xenotransplantation models and primary AML patient samples. Together, these results support the potential of DNMTi combination treatment to circumvent the development of chemorefractory AML relapses.

overall_design: We preformed RNA-Seq analysis of 3 untreated HEL (AML cell line) replicates; 3 Doxorubicin treated HEL replicates; 3 Doxorubicn + Cytarabine treated HEL replicates; 4 Doxorubicin + Cytarabine + Decitabine

first: Diogo

last: Maia-Silva

first: Carolina

last: Jardim

first: Nina

last: Schmolka

first: Tânia

last: Carvalho

first: Cláudia

last: Reforço

first: Rita

last: Faria

first: Branka

last: Kolundzija

first: André

middle: E

last: Simões

last: Vakoc

first: Maria

last: Gomes da Silva

first: Markus

middle: G

last: Manz

first: Ton

middle: N

last: Schumacher

first: Håkan

last: Norell

first: Bruno

last: Silva-Santos


title: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells

status: Public on Jul 29 2019

city: La Jolla

first: Daria

last: Merkurjev

state: CA

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

country: USA

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene expression with the potential to express a different cPcdh combination in every neuron. Here, we report a limited version established during the transition from the naive to the primed states of human cell pluripotency that reduces by orders of magnitude the combinatorial potential in the cPcdh locus. It is a chromatin-based mechanism that increases the frequency of stochastic selection of a subset of cPcdh promoters upon differentiation to fetal-like neurons in monolayers, organoids, or the rat spinal cord. Signs of similar preferential selections can be observed in the brain throughout fetal development, disappearing after birth, but not in a condition of delayed maturation such as Down Syndrome. We therefore propose that pluripotent cells impose a pattern of limited cPcdh diversity on neurons that increases the likelihood of cPcdh repetition until these cells acquire adult-like maturation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Lines/sublines: The hiPSC1-8 sublines were generated from single cells of the parent CVB hiPSC line. Six of these sublines were genetically modified (hiPSC2-7) and two were cases of failed genome editing (hiPSC1 and 8); please see Supplementary Table S1 in the associated publication for more details. Initially, these modifications should be irrelevant to the study of the cPcdh locus. The. hiPSC1 1.1-6 sublines were generated from the hiPSC1 subline and all underwent a process of genome editing, which again should be irrelevant to the study of the cPcdh locus (see Supplementary Table S1 in the associated publication for more details). The hiPSC 1.7-1.9 sublines were also generated from single cells of the parent CVB hiPSC line without undergoing any genome editing protocol. The hiPSC 1.13-15 sublines were generated from single cells of the parent CVI hiPSC line also without undergoing any genome editing protocol. The parent CVB and CVI lines were generated in the same reprogramming process and corresponded to two independent colonies. The hESC 1.7-1.9 sublines were generated from single cells of the parent HUES9 hESC line without undergoing any genome editing protocol. The HUES9 hESC 1.8 1.1-8 sublines were generated from single cells of the HUES9 1.8 subline after a process of primed-to-naive-to-reprimed conversion. All hiPSC/hESC lines/sublines were cultured in the primed state unless indicated (when indicated, some lines/sublines were cultured under naive-inducing conditions (5iLA protocol, and when returned to the primed state, the conditions were referred to as 're-primed'). For mouse cells, the 46C mESC 1.1-1.6 sublines were generated from single cells of the parent 46C mESC line. The R1 mESC 1.4/1.7 and 2.10/2.13 sublines were generated from single cells of the parent R1 mESC line. The R1 EpiSC 1.1-1.15 sublines were generated from single cells of the parent R1 mESC line after conversion to EpiSCs. The parental R1 mESC and EpiSC populations have also been included here.
ChIP-seq data: All ChIP-seq experiments were performed in pluripotent stem cells (hiPSCs/hESCs/mESCs/EpiSCs). Most profiles were based on H3K4me3, but many others also on CTCF, Rad1, H3K4me2,  H3K9me3, H3K9ac, H2A.Z, REST/NRSF,  SIN3A, and JMJD2A.
RNA-seq data: triplicate differentiation replicates of neurons generated from NPCs derived from hiPSC1-8 (n=24); cortical neurons generated from hiPSC1/3/5 (n=3); 10-month-old cortical organoids generated from the CVB line (n=1, pool of organoids); and primed, naive, and re-primed HUES9 1.8 subline (n=1 each).
scRNA-seq data (SMART-seq+NEXTERA; full transcript): 79 single cells of neurons generated from NPCs of the hiPSC1 line (54 to 71), hiPSC2 (1 to 51), hiPSC6 (88 to 96), and hiPSC7 (72 to 87). The libraries were sequenced twice, in one case the libraries from all cells were pooled before cleaning and measuring DNA concentration, whereas in the other case the libraries were pooled after cleaning. and measuring DNA concentration (so equal amounts were mixed).


title: Single cell sequencing of CD11c-selected cells from the TME of PyMT C57BL/6N mice

status: Public on Jul 26 2019

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

summary: We performed single-cell sequencing on CD11c-selected cells from 20 week old PyMT mice

overall_design: 2 Samples

first: Wolfram

last: Ruf


title: RUNX1 safeguards the identity of the fetal ovary through an interplay with FOXL2

status: Public on Jul 17 2019

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We discovered that expression of the transcription factor RUNX1 is enriched in the fetal ovary in various vertebrate species. In the mouse, RUNX1 marks the supporting cell lineage and becomes granulosa cell-specific as the gonads differentiate. To understand the function of Runx1 during fetal development of the ovary, we ablated Runx1 specifically in the somatic cell lineage of the fetal ovaries using  Sf1-Cre . We compared ovarian differentiation in wild type, Runx1 and Foxl2 single knockouts, and Runx1/Foxl2 double knockout ovaries. Transcriptome comparisons of newborn ovaries revealed that loss of Runx1 or Foxl2 affected a similar set of genes: 41% of the genes affected by the loss of Runx1 were also changed by the loss of Foxl2. Despite these transcriptomic changes, granulosa cell identity was maintained during fetal life in both Runx1 or Foxl2 single knockout ovaries. However, the combined loss of Runx1/Foxl2 resulted in masculinization of the ovaries during fetal life. To further characterize the impacts of the combined loss of Runx1 and Foxl2 on ovarian differentiation, we compared the transcriptome of Runx1/Foxl2 DKO newborn ovaries with the transcriptomes of control, Runx1, or Foxl2 single KO ovaries.

overall_design: We developed mouse genetic models that lack either Runx1, Foxl2, or both specifically in the somatic cells of the fetal ovaries. All newborn mice used in this study resulted from the crossing between Runx1f/f; Foxl2+/- females with Sf1-cre+/Tg ;Runx1+/-;Foxl2+/- males.

first: Barbara

last: Nicol

first: Humphrey

last: Yao


title: The effect of H1N1 vaccination on serum miRNA expression in children: a tale of caution for microRNA microarray studies

status: Public on Jul 13 2019

city: Oxford

first: ruth

middle: Elizabeth

last: Drury

state: Oxforshire

address: Centre for Tropical Medicine and Vaccinology, Churchill Drive

department: Paediatrics

country: United Kingdom

institute: University of Oxford

summary: To describe vaccine associated changes in the expression of microRNAs 21 days after vaccination in children receiving one of two pandemic influenza (H1N1) vaccines.

overall_design: Serum samples were obtained from children aged 6 months to 12 years enrolled in an open label randomised control trial of two pandemic influenza (H1N1) vaccines, in which participants received either ASO3B adjuvanted split virion or a whole virion non-adjuvanted vaccine.  44 samples from a discovery cohort of 22 children were assayed. The microarray results revealed 19 microRNAs were differentially expressed after vaccination after adjustment for multiple testing. The microarray detected ubiquitous expression of several microRNAs which could not be validated by RT-qPCR, many of which have little evidence of existence in publicly available RNA sequencing data. Real time PCR (RT-qPCR) confirmed downregulation of miR-142-3p in the discovery cohort. These findings were not replicated in the subsequent validation cohort (n=22).

first: R

first: D

last: O'Connor

first: A

last: Pollard


title: Human pulmonary artery endothelial cells  (hPAECs) with downregulated BMPR2 signaling demonstrate a unique gene expression signature after exposure to overexpression of AdAlox5

status: Public on Jul 04 2019

city: Stanford

first: Mark

last: Nicolls

state: California

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

institute: Stanford University School of Medicine

summary: Bmpr2 mutations are critical risk factors for hereditary pulmonary arterial hypertension (hPAH) with approximately 20% of carriers developing disease. There is an unmet medical need to understand how environmental factors, such as inflammation, render Bmpr2 mutants susceptible to PAH. Overexpressing 5-lipoxygenase (5-LO) provokes lung inflammation and transient PAH in Bmpr2+/- mice. Accordingly, 5-LO and its metabolite, leukotriene B4 (LTB4), are candidates for the ‘second hit’. The purpose of this study was to determine how 5-LO-mediated pulmonary inflammation synergized with phenotypically-silent Bmpr2 defects to elicit significant pulmonary vascular disease in rats. Monoallelic Bmpr2 mutant rats were generated and found phenotypically normal for up to one year of observation. To evaluate whether a second hit would elicit disease, animals were exposed to 5-LO-expressing adenovirus (AdAlox5), monocrotaline, SU5416 or chronic hypoxia and analyzed. Bmpr2-mutant hPAH patient samples were assessed for neointimal 5-LO expression. Pulmonary artery endothelial cells (PAECs) were cultured with lentivirus expressing short hairpin RNA (shRNA) targeting Bmpr2 (shBmpr2) to model the impaired BMPR2 signaling, and were then exposed to 5-LO-expressing adenovirus (AdAlox5), and were assessed for phenotypic and transcriptomic changes. In vitro, BMPR2 deficiency, compounded by 5-LO-mediated inflammation, generated apoptosis-resistant and proliferative PAECs with mesenchymal characteristics. These transformed cells expressed nuclear envelop-localized 5-LO consistent with induced LTB4 production, as well as a transcriptomic signature similar to clinical disease, including upregulated NF-kB, IL-6 and TGF-β signaling pathways. The reversal of PAH and vasculopathy in Bmpr2 mutants by TGF-β antagonism suggests that TGF-β is critical for neointimal transformation. Thus, in a new two-hit model of disease, lung inflammation induced severe PAH pathology in Bmpr2+/- rats. Endothelial transformation required the activation of canonical and noncanonical TGF-β signaling pathways and was characterized by 5-LO nuclear envelope translocation with enhanced LTB4 production. This study offers one explanation of how an environmental injury unleashes the destructive potential of an otherwise-silent genetic mutation.

overall_design: PAECs, at passage number 3–5 from control subjects, infected by lentivirus expressing shBmpr2 to silent BMPR2 signaling were treated with AdGfp vector or AdAlox5, each condition performed in triplicate (n=3)

first: Ting-Hsuan

last: Wu

first: Peter

last: Kao

first: Wen

last: Tian

middle: R


title: DNA polymerase Δ synthesizes both strands during break-induced replication

status: Public on Jul 01 2019

city: Durham

first: Zhi-Xiong

last: Zhou

address: 111 TW Alexander Dr.

institute: National Institute of Envinromental Health Sciences

summary: We applied our ribonucleotide mapping technique HydEn-seq to study DNA polymerase usage during break-induced replication (BIR) in the budding yeast Saccharomyces cerevisiae.

overall_design:
A genetic assay of BIR was designed to induce a single break on the left arm chromosome X which triggers recombination with homology donor on Chromosome VI and leads to BIR. The BIR product (Chromosome VI/X hybrid) was isolated in polymerase mutants promiscuous for ribonucleotide incorporation. HydEn-seq was performed to map ribonucleotides in the BIR products. Data was anylzed to discern polymerase usage during BIR.

Please note that the BIR_* sample processed data was generated from both replicates (BIR_*_1 and BIR_*_2 samples) and is linked to the corresponding BIR_*_1 sample records.

first: Roberto

middle: A

last: Donnianni

first: Adam

middle: B

last: Burkholder

first: Scott

last: Lujan

first: Thomas

last: Kunkel

first: Lorraine

middle: S

last: Symington


title: A pooled single-cell genetic screen identifies regulatory barriers in the continuum of the epithelial-to-mesenchymal transition

status: Public on Jul 12 2019

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

summary: We demonstrate that progression along EMT occurs along a continuum and that interruption of key signaling events reveals regulatory “barriers” that mimic discrete stages.

overall_design: Single-cell RNA-seq experiments were performed on the 10X Genomics platform for MCF10A and HuMEC cells plated and harvested as a function of space. These experiments were repeated in MCF10A cells expressing Cas9 and transduced with a CROP-seq library targeting EMT-associated cell surface receptors and transcription factors.

first: J

first: C

last: Trapnell


title: 8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice

status: Public on Jun 30 2019

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Promoter-specific dynamics of TATA-binding protein association with the human genome

status: Public on Jul 03 2019

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: We performed a tamoxifen-inducible, time-course ChIP-seq analysis of TBP that permits the measurement of TBP binding dynamics at target sites on a genome-wide scale in human cells.

overall_design: Examination of genome-wide TBP-ERT2-3HA distribution at various time after tamoxifen induction in HEK293 cells. Spike-in control (yeast chromatin prepared from the strain expressing 3HA-TBP) was added to the sheared human chromatin lysate. We performed ChIP-seq of TBP-ERT2-3HA using single end sequencing. Reads were mapped to the custom genome containing human genome (hg38) and yeast genome (sacCer3).  SRA Study accession is SRP200890, and BioProject accession is PRJNA547816.

first: Kevin

last: Struhl


title: 8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [8oxoG-seq]

summary: We observed that transcriptional activity and the number of active genes were significantly correlated with the distribution of 8-oxoG in gene promoter regions, as determined by liquid chromatography/mass spectrometry (LC/MS), and 8-oxoG and RNA sequencing

overall_design: 8oxoG-sequencing of lung and adipose tissues isolated from two juvenile female C57BL/6 mice

first: Jong-Woo

first: Young-In

last: Han

first: Tae-Min

last: Kim

first: Jaeku

last: Kang


title: shRNA-mediated knockdown of ETV4 and MED25 in the prostate cell line PC3 reveals set of genes potentially coregulated by MED25 and ETV4

status: Public on Jun 28 2019

city: Salt Lake City

first: Kathleen

last: Clark

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Our in vitro binding studies support a model whereby MED25 exhibits multivalent interactions with a subset of related ETS factors, ETV1/4/5. We hypothesize that the interaction would allow for coregulation of genes by ETV1/4/5 and MED25, acting perhaps to link the ETVs to the Mediator complex. To explore this possibility, we compared the genome occupancy for FLAG-tagged MED25 and ETV4 in the prostate cancer cell line PC3, which overexpresses ETV4. We also tested for relevance of MED25 and ETV4 binding to for gene expression in PC3s. We found a high degree of overlap in the FLAG-MED25 and ETV4 ChIPs datasets consistent with our model, and also identified a subset of target genes co-dependent on Med25 and ETV4.

overall_design: RNAseq in PC3 cells expressing shRNA directed against MED25, or ETV4, or empty vector.

first: Barbara

last: Graves


title: Identification and Characterization of Splenic Adherent Cells forming Densely-Packed Colony

status: Public on Jun 25 2019

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

summary: As a first step for identifying hypothetical splenic stem cells for nonhematopoietic cells, densely-packed colony-forming cells were isolated from mouse spleen. Those which we designated as Splenic Adherent Colony-Forming Cells (SACCs) are positive for some of stem cell markers such as alkaline phosphatase and SSEA-1 antigen. We herewith determined global expression profiles of SACCs and control splenic adherent cells.

overall_design: SACCs were prepared form mouse spleen. Splenic adherent cells forming monolayer on culture dish were also prepared as control cells. Then, overall gene expression profiles were determined for SACCs and the control splenic cells by means of DNA microarray analyses and differentially expressed between SACCs and the control splenic cells were subjected to bioinformatics analyses.

first: Hirasaki

last: Masataka

first: Norihiro

last: Kotani


title: Genome-wide occupancy of FLAG-MED25 and ETV4 in PC3 cells

overall_design: ChIP-seq  in PC3 cells expressing FLAG-MED25 using either anti-FLAG antibody or anti-ETV4 antibody.


title: Molecular mechanisms implicated in myogenic differentiation of human alveolar mucosa derived cells

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: Different approaches of skeletal muscle cell regeneration originated from progenitor cells are extensively studied under the strategies of muscle tissue pathologies treatment. Recently it was discovered that anatomically localized alveolar mucosa multipotent mesenchymal stromal cells (AMC) are characterized by myogenic potential and high feasibility for muscle tissue recovery and regeneration. Although the resulting multinuclear myotubes are featured by expressing skeletal muscle specific markers (skeletal myosin, actin, myogenin and MyoD1) the exact molecular mechanism controlling differentiation of AMC in myogenic direction is still unclear and poorly scrutinized. In this research we used combination of large-scale transcriptome analysis and bioinformatics approach to appreciate molecular pathways and crucial nodes responsible for myogenic differentiation.

overall_design: Multipotent mesenchymal stromal cells (MMSC) were isolated from alveolar mucosa (AMC), attached gingiva (AGC) and skeletal muscle (SMC) biopsy samples, and skin fibroblasts from the skin. AMC and SMC were subjected to myogenic differentiation. High throughput transcriptional profiling of undifferentiated AMC, AGC, SMC, differentiated AMC and SMC, and skin fibroblasts was performed to elucidate molecular pathways accompanying myogenic differentiation.

first: Ilya

last: Eremin

first: Maxim

last: Sorokin

first: Anton

last: Buzdin


title: Antibody crossreactivity with mRNA cap accounts for widespread appearance of m1A throughout the transcriptome

status: Public on Jun 23 2019

first: Anya

last: Grozhik

state: New York

address: 1300 York Ave, Room LC-523

institute: Weill Cornell Medicine

summary: N1-methyladenosine (m1A) was recently identified as a new mRNA modification based on its mapping to the 5’UTRs of thousands of mRNAs with an m1A-binding antibody.  More recent studies have questioned the prevalence of m1A.  To address this discrepancy, we mapped m1A using ultra-deep RNA-Seq datasets based on m1A-induced misincorporations during reverse transcription.  Using this approach, we find m1A only in the mitochondrial MT-ND5 transcript.  In contrast, m1A mapping using an m1A-binding antibody showed binding to transcription start nucleotides in mRNA 5’UTRs.  Biochemical measurements indicate that m1A is not present at these sites.  Instead, we find that the m1A antibody exhibits m1A-independent binding to mRNA cap structures.  Our data demonstrate that high-stoichiometry m1A sites are rare in the transcriptome and that previous mapping of m1A to mRNA 5’UTRs reflect an unintended binding to mRNA caps.

overall_design:
The data for this study contains the following samples:
m1A miCLIP of HEK 293T cell poly(A) RNA: 2 biological replicates
RNA-Seq of HEK 293T cell poly(A) RNA: 1 biological replicate
m1A miCLIP in mouse brain poly(A) RNA: 6 biological replicates (3 control, 3 AlkB-treated)
Second 1mA miCLIP of HEK 293T cells poly(A) RNA: 6 samples (2 biological replicates per antibody, 3 different antibodies)

middle: V

first: Samie

last: Jaffrey

first: Anthony

middle: O

last: Olarerin-George


title: Genome-wide occupancy of FLAG-MED25 and ETV4 and expression profiling of shRNA-mediated knockdown of ETV4 and MED25 in the prostate cell line PC3


title: Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

status: Public on Jun 12 2019

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Most pancreatic neuroendocrine tumors (PNETs) do not produce symptoms of hormonal excess and are hence considered ‘non-functional’. Their clinical behaviors vary widely, emphasizing the need for a robust classification with prognostic power. Using enhancer maps to infer regulatory programs, we find that the large majority of non-functional PNETs fall into two major sub-types –A and B– that reflect alpha and beta endocrine cell ontogeny, respectively. A and B tumors have similar clinical presentations and histology, but express distinct lineage-specifying transcription factors, ARX or PDX1. In immunohistochemistry, 84% of 142 non-functional PNETs expressed one or the other factor, rarely both. Longitudinal data on 104 cases revealed markedly different outcomes, irrespective of MEN1 mutation status: relapse occurred almost exclusively in patients with type A tumors. These findings reveal a robust molecular stratification that provides insight into cellular origins of non-functional PNETs, accurately predicts disease course, and informs clinical decisions and future trial design.

overall_design:
RNA-seq, H3K27ac and H3K4me2 profiles profiling in carinoids and pancreatic neuroendocrine tumors

Due to patient privacy concerns, raw data have been submitted to dbGAP, accession phs001910.v1.p1.

first: Paloma

last: Cejas

first: Bradley

last: Bernstein

first: Ramesh

last: Shivdasani


title: Transcriptional profiling of mouse embryonic tissues with Firre deletion

status: Public on Jun 22 2019

city: Cambridge

first: Jordan

last: Lewandowski

address: 7 Divinity Ave

institute: Harvard University

summary: Firre is a long non-coding RNA expressed dynamically in a variety of tissues throughout mouse development. While it is known to play a role in chromatin organization, its physiological relevance remains unclear. In order to better understand the role of Firre in vivo, we generated Firre knockout mice and performed RNA sequencing and differential expression analysis on eight tissues from both males and females at E11.5.

overall_design: RNA sequencing in triplicate of eight E11.5 tissues from male and female mice with Firre knockout.

first: William

last: Mallard

first: Chiara

last: Gerhardinger

first: John

last: Rinn


title: 8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [RNA-Seq]

first: Joonghoon

last: Park

overall_design: RNA-sequencing of lung and adipose tissues isolated from two juvenile female C57BL/6 mice

first: Jong

middle: W

first: Young

middle: I

last: Han

first: Tae

middle: M

last: Kim

first: Jaeku

last: Kang


title: Neuropeptide CGRP limits ILC2 responses and constrains type 2 inflammation

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: Innate and adaptive lymphocytes work in concert to maintain tissue homeostasis and to mediate host defense at mucosal barriers. Herein, we used single cell analysis to show substantial diversity of gene expression in ILCs and T helper cells during a helminth infection in the lung. Notably, we found that the Calca gene, which is spliced to generate the neuropeptide CGRP, was selectively transcribed in ILC2s and Th2 cells in an activation dependent manner. The Calca locus acquired chromatin accessibility at the ILC2 precursor stage and is pre-programmed for rapid production of CGRP upon ILC2 activation. CGRP globally antagonized actions of neuromedin U (NMU) and the alarmin IL-33. However, CGRP selectively acted in concert with NMU and IL-33 to promote IL-5 expression, but not IL-13. The complex interplay among neuropeptides and alarmin fine-tunes type 2 immune responses and will undoubtedly become more relevant as therapeutic neuropeptide blockade advances in the clinic.

overall_design: Integrated analysis of transcriptome and epigenome data from ILCs and Th cells in steady or activated conditions

first: H

last: Nagashima

middle: Y

last: Shih

last: Sun

first: S

last: Brooks

first: G

last: Gutierrez-Cruz

last: Dell'Orso

first: Y

first: J

middle: J

last: O'Shea


title: Activation of P-TEFb by cAMP-PKA signaling in autosomal dominant polycystic kidney disease

status: Public on Jun 20 2019

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

country: China

institute: Tianjin Medical University


title: Genome-wide CRISPR inactivation based resistance screens using IMiDs in Primary Effusion Lymphoma (PEL) cells

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

summary: We report the application of genome-wide CRISPR-Cas9 inactivation based screening technology to identify genes whose inactivation can confer resistance to the IMiD compounds Lenalidomide, Pomalidomide and Avadomide (CC-122) in Kaposi's sarcoma-associated herpesvirus-transformed primary effusion lymphoma cell line BC-3. Cas9 expressing BC-3 cells were transduced with a lentiviral genome-wide targeting sgRNA library (Brunello, Doench et al, Nature Biotechnology, 2016) and subsequently treated with lethal concentrations (5uM Lenalidomide, 1uM Pomalidomide and 1uM CC-122) of the IMiD compounds mentioned above or DMSO vehicle. gDNA from resistant cells and matched DMSO treated control cells was harvested and the lentiviral sgRNA inserts in each sample were PCR amplified, barcoded and subjected to next gen sequencing on the Illumina HiSeq 4000 platform. This study provides a candidate list of genes whose inactivation can confer resistance to one or more IMiD compounds in BC-3 cells.

overall_design: Identification of genes whose inactivation confers resistance to IMiD compounds in PEL


title: Gene regulation by TLR2 and TLR10 in oncogene-induced senescence

status: Public on Jun 11 2019

city: Edinburgh

first: Juan

middle: Carlos

last: Acosta

address: Crewe Rd South

department: Cancer Research UK - Edinburgh Centre

institute: The University of Edinburgh

summary: In the present study, we analyse the effect of knocking down TLR2 and TLR10 during oncogene induced senescence in IMR90 cells expressing a inducible version of oncogenic RAS (ER:RAS) in the transcriptome using Ampliseq RNA sequencig. We observed that TLR2 and TLR10 regulate the expression of many pro-inflammatory cytokines and chemokines that constitute the senescence associated secretory phenotype. There is also significant regulation of genes of the acute phase response.

overall_design: IMR90 expressing ER:RAS fusion protein induced to senescence with activated oncogenic RAS by addition of 4 hydroxy-tamoxifen (4OHT), were transfected with siRNA to knockdown of TLR2 and TLR10. Total mRNA was extracted and expression profiles were analysed.

first: Priya

last: Hari

middle: C


title: Methylation analysis of Epstein-Barr virus-associated gastric cancer case

status: Public on Jun 08 2019

city: Fukuoka

first: Hirofumi

last: Ohmura

address: 3-1-1 Maidashi

institute: Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences

type: Methylation profiling by genome tiling array

summary: The comprehensive DNA methylation status of gastric cancer cells obtained from an advanced Epstein-Barr virus-associated gastric cancer case, in which complete response to S-1 plus cisplatin chemotherapy was achieved, was analyzed with DNA methylation microarray (Illumina Infinium MethylationEPIC BeadChip). DNA was extracted from metastatic lesion (lymph node).

overall_design: Bisulphite-converted DNA from one sample was hybridised to the Illumina Infinium MethylationEPIC BeadChip.


title: Gene expression analysis of jam3b mutant embryos

status: Public on Jun 01 2019

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

summary: Junctional adhesion molecule 3 (Jam3) is a cell adhesion molecule that is involved in cell-cell interaction, cell migration, and cell polarization in many tissue including the epithelium, endothelium, and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells, the role of Jam3 in hematopoietic or vascular development is still unknown. In this study, a zebrafish jam3b mutant line, jam3b-sa37, was used for the cap analysis gene expression (CAGE) sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo.

overall_design: Whole embryos mRNA profiles of wild type or jam3b-sa37 embryos at 12 or 16 hours post-fertilization were generated by CAGE sequencing using Illumina NextSeq500.


title: Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

status: Public on May 14 2019

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

type: Methylation profiling by high throughput sequencing

summary: In the study of DNA methylation, genetic variation between species, strains, or individuals can result in CpG sites that are exclusive to a subset of samples, and insertions and deletions can rearrange the spatial distribution of CpGs. How to account for this variation in an analysis of the interplay between sequence variation and DNA methylation is not well understood, especially when the number of CpG differences between samples is large. Here we use whole-genome bisulfite sequencing data on two highly divergent mouse strains to study this problem. We show that alignment to personal genomes is necessary for valid methylation quantification. We introduce a method for including strain-specific CpGs in differential analysis, and show that accounting for strain-specific CpGs increases power.  Our method uses smoothing to impute methylation levels at strain-specific sites, thereby allowing strain-specific CpGs to contribute to the analysis, and also allowing us to account for differences in the spatial occurrences of CpGs.  Our results have implications for joint analysis of genetic variation and DNA methylation using bisulfite-converted DNA, and unlocks the use of personal genomes for addressing this question.

overall_design: 4 samples each from 2 mouse strains, 8 samples total

first: Kasper

middle: D

last: Hansen

first: Andrew

middle: P

last: Feinberg


title: Global altered gene expression in  triple-negative breast cancer tumor samples treated with CDK2 and EZH2 inhibitors

status: Public on Jun 05 2019

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: Triple-negative breast cancer cell line SUM-149 xenograft mouse model was treated with CDK2 inhibitor (dinaciclib) and EZH2 inhibitor (EPZ6438) for 10 days to examine global transcriptome alternations by RNAseq. Expression levels of more than 801 and  741 gene were altered by CDK2 inhibitor and EZH2 inhibitor treatment, respectively.Among differential changed genes induced by CDK2 inhibitor and EZH2 inhibitor, we defined top 109 common up- and down-regulated gene sets in the inhibitor-treated tumors.

overall_design: Global gene changes in triple-negative breast cancer xenograft mouse model treated with CDK2 and EZH2 inhibitors was examined by RNAseq

first: Lei

last: Nie

first: Yongkun

last: Wei

first: Fei

last: Zhang

first: Yi-Hsin

last: Hsu

first: Li-Chuan

last: Chan

first: Weiya

last: Xia

first: Baozhen

last: Ke

first: Cihui

last: Zhu

first: Rong

last: Deng

first: Jun

last: Tang

last: Yao

first: Yu-Yi

last: Chu

first: Xixi

last: Zhao

first: Ye

last: Han

first: Junwei

last: Hou

first: Longfei

last: Huo

first: How-Wen

last: Ko

first: Wan-Chi

last: Lin

first: Hirohito

last: Yamaguchi

first: Jung-Mao

first: Yi

last: Yang

first: Dean

middle: N

last: Pan

first: Jennifer

last: Hus

first: Celina

middle: G

last: Kleer

first: Nancy

middle: E

last: Davidson

first: Gabriel

last: Hortobagyi

first: Mien-Chie

last: Hung


title: Transcriptome analysis of virus infected tissues

status: Public on May 18 2019

first: Yiska

last: Weisblum

address: Kiryat Hadassah

institute: Hadassah Hebrew University Medical Center

summary: We report the application of RNA sequencing for transcriptome analysis of virus infected tissues, enabling the study of tissue responses to infection

overall_design: Transcriptome analysis of 2 different tissues infected with two different viruses

first: Esther

last: Oiknine-Djian

first: Olesya

last: Vorontsov

first: Ronit

last: Haimov-Kochman

first: Zichria

last: Zakay-Rones

first: Karen

last: Meir

first: David

last: Shveiky

first: Sharona

last: Elgavish

first: Yuval

last: Nevo

first: Moshe

last: Roseman

first: Michal

last: Bronstein

first: Arbel

last: Ben David

first: Iris

last: Eisenberg

first: Simcha

last: Yagel

first: Amos

last: Panet

first: Dana

last: Wolf


title: Whole genome bisulfite genome analysis of OX40L-Jagged-1 expanded Treg and Teff cells

status: Public on May 03 2019

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

summary: NOD mice were treated with PBS or OX40L and Jagged-1 proteins once a week for three weeks. A week after final treatment CD4+CD25- Teff cells and CD4+CD25hi Treg cells were sorted by FACS. Genomic DNA isolated from sorted cells and differences in DNA methylation pattern in these cell types between PBS and OX40L-Jagged-1 treated mice was analyzed by whole genome bi-sulfite sequencing.

overall_design: Examination of methylation pattern in Teff vs Treg cells  between PBS and OX40L-JAG1 mice.

first: Mark

last: Maienschein-Cline

first: Zarema

last: Arbieva

first: Bellur

last: Prabhakar


title: Transcriptional alteration after ionizing radiation exposure in human fibroblasts, iPSCs and NPCs

city: Tokyo

first: Mikio

last: Shimada

address: 2-12-1 N1-30 Oookayama, Meouro-ku

department: Institute of Innovative Research

institute: Tokyo Institute of Technology

summary: RNA sequencing was performed to investigate ionizing radiation-dependent transcriptional change in human pluripotent cells and differentiated cells.

overall_design: Examined 3 types of cells (fibroblasts, iPS cells and neural progenitor cells) and 2 types of treatments (non IR or IR), total 6 samples were analyzed.

first: Kaima

last: Tsukada

first: Nozomi

last: Kagawa

first: Yoshihisa

last: Matsumoto


title: Rhizobial and non/mycorrhizal Medicago truncatula roots and shoots transcriptome

status: Public on Apr 21 2019

city: Prague 2

first: Jan

last: Konečný

address: Albertov 6

department: Experimental Plant Biology

country: Czech Republic

institute: Faculty of Science, Charles University

summary: Plant species posses a special set of genes functional only in arbuscular mycorrhizal symbiosis. So, the model plant Medicago truncatula (Jemalong 5) was used for transcriptome comparative analysis while infected with compatible rhizobia Sinorhizobium meliloti (strain 10) and with or without arbuscular mycorrhizal fungus Rhizophagus irregularis (SYM5). Whole shoot and whole root were used for RNA isolation and processed via one of the European certified Affymetrix core labs (http://core.img.cas.cz).

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 6 pots of Medicago truncatula (3 plants per pot processed as single unit) were harvested 35 days post planting (dpp). All rhizobial (Sinorhizobium meliloti) and half nonmycorrhizal (NM, i.e. negative control), half mycorrhizal (M) by Rhizophagus irregularis. Whole roots (3NM and 3M) and whole shoots (3NM and 3M) processed to RNA isolation.

first: Hana

last: Hršelová

last: Jansa


title: CRISPR screens are feasible in TP53 wild-type cells

status: Public on Apr 30 2019

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: CRISPR-Cas9 genome-wide screens were performed in retinal pigment epithelial cells (RPE1) with either wild-type TP53 gene, or a TP53-null background.  Results show wild-type TP53 has minimal impact on the efficiency of CRISPR dropout screens.

overall_design: Five genome-wide CRISPR dropout screens are performed independently in RPE1 cells using TKOv1 (n=1), TKOv2 (n=1) or TKOv3 (n=3) CRISPR libraries.  Screens were performed in duplicate (n=2) or triplicate (n=3).

first: Kevin

middle: R

last: Brown


title: Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

country: Germany

institute: University Freiburg Medical Center

summary: This study was conducted to investigate the effects of DN-tp63 loss-of-function on mucociliary basal stem cells in Xenopus laevis. Uninjected control embryos and DN-tp63 morpholino oligonucleotide injected embryos were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16-19, and 24-25 for total RNA extraction.

overall_design: The experiment was conducted in three biological replicates (embryos were derived from three different females and fertilizations). Control samples remained uninjected, DN-tp63 morphant samples were injected with morpholino oligonucleotides targeting the start condon of DN-tp63 and resulted in protein knockdown (loss-of-function). Sequencing was performed in two seperate paired-end runs to increase sequencing dpth, with each run containing all samples.


title: Comorbidities - microcephaly, facial dysmorphia and epilepsy - increase the risk of the pathogenic CNV finding in patients with intellectual disability and autism

city: Olomouc

first: Zuzana

last: Čapková

state: Czech Republic

address: I.P. Pavlova 6

department: Department of Medical Genetics

institute: University Hospital Olomouc

type: Genome variation profiling by genome tiling array

summary: CNV are known to be a frequent cause of the autism spectrum disorders (ASD) and intellectual disabilities (ID). However, the clinical heterogeneity of both disorders causes the diagnostic efficacy of CNV analysis to be modest. We conclude that comorbidities such as microcephaly, facial dysmorphia and epilepsy increase the risk of the pathogenic CNV finding in patients with ID and ASD. However, the significance of these comorbidities differs between both groups and shows dependency on whether the patients were primarily classified as ID or ASD. We suggest that stratification of the patients according to their comorbidities before testing can increase the yield of the detection rate of pathogenic CNV in both groups. The likelihood of pathogenic CNV detection in ASD patients without any comorbidities is low. Therefore, the effectivity of CNV analysis in these cases is modest

overall_design: 204 patients were analyzed by aCGH and MLPA proceadures. Cytoscan HD and GenomeWideSNP_6 (Affymetrix, Santa Clara, CA, USA) were used for CNV analysis of 112 patients with ID (N=29) and ASD (N=83) according to the manufacturers’ protocols.

first: Z

last: Capkova

first: P

first: J

last: Srovnal

first: K

last: Staffova


title: RNA-seq dynamic transcriptomic pipeline

status: Public on Apr 13 2019

city: Bron

first: Sally

last: Badawi

address: 59 Bd Pinel

department: Biology

country: France

institute: Université Claude Bernard Lyon1

summary:
Purpose: Develop an analytical pipeline for dynamic RNA-seq experiments and highlight the importance of considering surgery effect in MI-induced models
Methods: Mice have undergone surgery, hearts were harvested and RNA was extracted, sequenced and analyzed by DESeq2 R package. Differentially expressed transcripts were clustered by WGCNA and  then analyzed to identify enriched biological processes and transcription factors.
Results: Our pipeline enabled the detection of 1027 DETs. Enriched biological processes were mainly cell signilisation and inflammatory related. IL-6 was found as a key controller of the identified TFs and DETs. Immune cells were recruited to the myocardium later post surgery and some possessed phenotypic changes.

overall_design: 3 time points (0, 45 minutes and 24 hours) and 8 animals per time point were used to increase statistical power of the analysis.

first: Gabriel

last: Bidaux

first: Joel

last: Lachuer


title: Analysis of skin in wild-type vs. mast cell-deficient mice after allogeneic bone marrow transplant

status: Public on Apr 10 2019

city: Lexington

first: Ethan

middle: Jesse

last: Strattan

state: KY

address: 900 South Limestone Street, Wethington Building, CTW453

department: Hematology/BMT

institute: University of Kentucky

summary:
LP/J marrow and splenocytes were infused into C57BL/6 or Wsh mast cell-deficient mice after irradiation of recipients. Chronic graft-versus-host disease was observed in the skin. Skin was collected after 7 weeks and RNA was isolated.
RNA was analyzed by the NanoString Myeloid Innate Immunity panel

overall_design: 3 mice from syngeneic transplant, 3 mice from allogeneic transplant into WT mice, 5 mice from allogeneic transplant into Wsh mast cell-deficient mice

first: Senthilnathan

last: Palaniyandi

first: Reena

last: Kumari

first: Gerhard

last: Hildebrandt


title: Effects of exosomes derived from mice endothelial progenitor cells (EPCs-exo) on mice fibroblast following inducement of dexamethasone

status: Public on Apr 03 2019

city: Hefei

first: Jinsen

last: Lu

state: Anhui

address: Lujiang Road No.17

department: orthopaedics

institute: Anhui Provincial Hospital

summary: This study sought to explore the specific effects of EPCs-exos on steroid induced osteoporosis in mice, and figuring out its regulation pattern of whole transcriptomes in osteoblasts attempting to verify the role of ferroptotic pathways during steroid hormone and EPCs-exo intervention.

overall_design: EPCs were derived from mice bone marrow and the secreted exosomes were extracted. Mice fibroblasts were cultivated to appropriate amount and divided into two experimental groups receiving 10μM dexamethasone alone and combination of dexamethasone and 100μg EPCs-exo respectively for 48 hours. Then total RNA of cells in all groups were extracted and conducted all transcriptome sequencing. The results were subsequently conducted bioinformatic analysis.

first: Jiwei

last: Li


title: Differential lncRNA expression upon hypoxia affects splicing efficiency

status: Public on Apr 05 2019

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequencing was performed to identify long non-coding RNAs that are dysregulated upon hypoxia in breast cancer. Subsequently, the effect on splicing effiency (intron retention, exon skipping …) was investigated from RNA sequencing analysis upon knockdown of the candidate lncRNA and upon hypoxia.

overall_design: Cells were treated with GapmeRs or tetracycline-inducible shRNAs against the candidate lncRNA and cultured upon hypoxic conditions (1%O2). Additionally, cells were treated with shRNAs against SART3 or GFP.

first: Tibor

last: Pastor

first: Linde

last: De Troyer

first: Anna

last: Sablina


title: Genes regulated by GSK343 in HepG2 and PLC5 hepatocellular carcinoma cells

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Our previous study has found that GSK343 is a potent autophagy inducer. To further investigate the underlying mechanisms, microarray analysis was performed.

overall_design: GSK343-induced gene expression in HepG2 and PLC5 cells was measured at 16 hours after exposure to 10 uM GSK343.


title: RUNX1 safeguards the identity of the fetal ovary through an interplay with FOXL2

status: Public on Apr 02 2019

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Sex determination of the gonads begins with fate specification of gonadal supporting cells into either ovarian granulosa cells or testicular Sertoli cells. This process of fate specification hinges on a balance of transcriptional control. We discovered that the transcription factor RUNX1 is enriched in the fetal ovary in rainbow trout, turtle, mouse, and human. In the mouse, RUNX1 marks the supporting cell lineage and becomes granulosa cell-specific as the gonads differentiate. RUNX1 plays complementary/redundant roles with FOXL2 to maintain fetal granulosa cell identity, and combined loss of RUNX1 and FOXL2 results in masculinization of the fetal ovaries. To determine whether interplay between RUNX1 and FOXL2 occurs at the chromatin level, we performed genome-wide analysis of RUNX1 chromatin occupancy in E14.5 ovaries. The top de novo motif identified in RUNX1 ChIP-seq matched the RUNX motif. We found that RUNX1 chromatin occupancy was partially overlapping with FOXL2 chromatin occupancy in fetal ovaries.

overall_design: ChIP-seq for RUNX1 and input on chromatin from pools of mouse CD1 fetal ovaries (E14.5).

first: Barbara

last: Nicol

first: Sara

middle: A

last: Grimm

first: Estelle

last: Lecluze

first: Frederic

last: Chalmel

first: Maëlle

last: Pannetier

first: Eric

last: Pailhoux

first: Elodie

last: Dupin-De-Beyssat

first: Yann

last: Guiguen

first: Blanche

last: Capel

middle: H


title: Transcriptom analysis of ZFP708 loss and overexpression in preimplantation embryos and embryonic stem cells

status: Public on Mar 27 2019

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

summary: This work describes the function and targets of a maternal KRAB-Zinc finger protein, ZFP708, which specifically mediates maintenance of DNA-methylation at a subset of LTR retrotransposons during embryonic epigenetic reprogramming.

overall_design: This dataset contains RNA-seq analysis of wildtype and maternal ZFP708 knock out GV oocytes, zygotes, 2-cell stage embryos, blastocysts and embryonic stem cells derived from maternal/zygotic ZFP708 embryos. It further contains expression analysis of ZFP708 overexpressing mouse embryonic stem cells.

first: Diana

last: Loh

first: Pierre-Alexis

middle: V

last: Goy

first: Ernesto

last: Guccione


title: Effect of TGF-beta1 on the miRNome in CFBE41o- cells stably transduced with Wild Type (WT)-CFTR and F508del-CFTR

status: Public on Mar 25 2019

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: The purpose of this study was to explore miRNA mediated Transforming Growth Factor (TGF)-β1 regulation of F508del Cystic Fibrosis Transmembrane Conductance regulator (CFTR). To fulfill this goal, miRNA sequencing was done to see miRNA landscape in Cystic Fibrosis Bronchial Epithelial (CFBE) Cells with homozygous WT-CFTR and F508del mutated CFTR in response to TGFβ1 treatment.

overall_design: Sequencing microRNAs in WT-CFBE41o- and F508delCFBE41o- cells after 24hour treatment with TGFβ1.

first: Nilay

last: Mitash

first: Fangping

last: Mu

first: Agnieszka

last: Swiatecka-Urban


title: RNA sequencing of LNZ308 glioma cells treated under differential conditions including monotherapies, dual therapy and synergistic triple regimen employing γ-irradiation, temozolomide and oncolytic measles virus.

status: Public on Mar 26 2019

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary: The synergistic regimen CT-VT-RT triggers proinflammatory antiviral signalling with activation of apoptotic cascades resulting in tumor cell death.

overall_design: The experiment was designed to elicit individual treatment effects using monotherapies to understand the combinatorial sequential effect of dual and triple regimen using appropriate controls.

first: Srinath

last: Rajaraman

first: Ghazaleh

last: Tabatabai

first: Marius

last: Cosmin Codrea

first: Sven

last: Nahnsen


title: Free circular introns with an unusual branchpoint in neuronal projections

status: Public on Apr 18 2019

city: Boston

first: Harleen

last: Saini

state: MA

address: 240 Longwood Avenue

institute: Harvard Medical School

summary: In eukaryotic cells, most introns are degraded soon after splicing in the nucleus but some persist either due to lack of splicing (detained/retained introns) or because they contain important functional elements, for example, sno/scaRNAs. Few introns are detectable outside the nucleus. To hunt for interesting new phenomena in cytoplasmic introns and splicing, we conducted a multimodal study of total RNA within projections (axons, dendrites, glial projections) of rat hippocampal neurons and discovered a class of free circular introns enriched in distal projections.

overall_design: A variety of sequencing datasets from rat primary hippocampal neurons are provided: From physically separated cellular projections and whole-cell lysates, (a) rRNA-depleted total RNA-seq (5 biological replicates, each) and (b) polyA site sequencing or PAS-seq (3 biological replicates, each); from fractionated cytoplasmic lysate (c) ribosome profiling (3 biological replicates) and (d) polyA+ RNA-seq (3 biological replicates).

first: Sean

last: Eddy

first: Melissa

middle: J

last: Moore


title: The transcription factor ERG regulates super-enhancers in endothelial cells

status: Public on Mar 22 2019

city: London

first: Graeme

middle: Miles

last: Birdsey

address: Hammersmith Hospital, Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

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

overall_design: Refer to individual Series


title: The transcription factor ERG regulates super-enhancers in endothelial cells [ERG siRNA]

summary: We provide the functional and epigenomic evidence for ERG binding to super-enhancers in HUVEC and further show that loss of ERG results in inhibition of specific endothelial super-enhancers and associated target genes.

overall_design: ChIP-seq was used to determine the changes to acetylated H3K27 and the transcriptional coactivator MED1 in response to ERG siRNA.

middle: M

first: Viktoria

last: Kalna


title: Effects of OCT1 knockdown in castration-resistant prostate cancer cells

status: Public on Mar 01 2019

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Although initially hormone-deprovation therapy is effective to inhibit cancer progression, most of cancers relapse as castration-resistant prostate cancer (CRPC). Therefore, we examined the effect of AR interacting partner OCT1 in CRPC cells.
In order to investigate the OCT1 function in CRPC cells, we performed gene expression in AR-positive CRPC cell line, 22Rv1, after siOCT1 treatment. We also treated cells with vehicle or dihydrotestosterone (DHT) to analyzed the effects of OCT1 on AR function.

overall_design: Observation of androgen dependent gene expression changes in CRPC after treatmet with siRNAs targeting OCT1 using microarray.

first: Satoshi

last: Inoue


title: Expression profiling by RNA-Seq of breast cancer samples from patients in walnut-consuming and control groups

status: Public on Mar 10 2019

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: Consumption of walnuts has slowed breast cancer growth and/or reduced the risk of breast cancer in mice. The significantly reduced mean tumor size or numbers of tumors was associated with changing the expressions of many genes that are associated with cancer growth, survival and metastasis. Many women treated for breast cancer are interested in reducing the risk for recurrence. The study was a non-placebo, two-arm, clinical trial. Women with lumps large enough for research and pathology biopsies were recruited to the trial. One or two additional biopsies were taken for gene expression analyses using next generation RNA Sequencing methods. The subjects randomized to the walnut group immediately began to consume 2 ounces of walnuts per day until follow-up surgery, if surgery were needed. At follow up surgery, additional biopsies were taken from the surgically removed, cancerous tissue for additional gene expression analyses. Changes in gene expression compared to baseline were determined in tumors of each individual woman in walnut-consuming and control groups.

overall_design: Gene expression profiles of two samples from each of ten breast cancer patients were obtained via RNA-Seq in a 2x50bp paired-end design. The first sample was obtained from biopsy; the second sample was taken at the time of surgery 2-3 weeks later. Five patients consumed two one-ounce packets of walnuts daily between the biopsy and surgery, while the other five remained on their regular diet.

first: W

last: Hardman

last: Primerano

first: Mary

middle: T

last: Legenza

last: Morgan

first: Jun

last: Fan


title: Modeling and characterization of the dynamic gene regulatory networks underlying cancer drug resistance based on time-course RNA-seq data

status: Public on Mar 23 2019

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

summary: Drug resistance is a major cause for the failure of cancer chemotherapy or targeted therapy. However, the molecular regulatory mechanisms controlling the dynamic evolvement of drug resistance remain poorly understood. Thus, it is important to develop methods for unraveling gene regulatory mechanisms underlying the resistance to specific drugs. We used glioma differentiation therapy as a realistic case and time-course RNA-seq to investigate the temporal gene expression changes in sensitive and resistant cells. A computational method was developed to model and characterize the dynamic gene regulatory networks underlying cancer drug resistance based on time-course RNA-seq data.

overall_design: DBTRG-05MG/U87/LN18 tumor cells were treated with 1 mol/L dbcAMP for 3 days,respectively.And we used RNA-seq to detail the drug resistance network based on time-course RNA-seq data.

first: X

middle: Q

last: Sun

middle: C

last: Liu


title: Expression data of procambium/cambium in Arabidopsis root

status: Public on Mar 31 2019

city: Seoul

first: Ji-Young

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

institute: Seoul National University

summary: Vascular cambium is a secondary meristem which produces xylem (wood) inwards and phloem (bark) outwards. The activity of cambium leads to expansion in the diameters in plants, that is, secondary growth, and thus contributes to biomass increase. The regulation of cambium development is at multilevel including phytohormones and peptide-receptor kinase (CLE41/44-PXY) signalling pathways. However, only limited progress has been made on the transcriptional regulation level. To construct the transcriptional network that regulates cambium development, we performed a genome wide transcript profiling in sorted procambial and cambial cells in Arabidopsis roots. More than 500 genes were identified as cambium abundant genes via comparison against transcriptomes of other Arabidopsis root cell types. We then investigated the roles of almost all the cambial transcription factors (TFs) and some of their homologous genes during secondary growth. Many of the candidate TFs were highly expressed in cambium based on the promoter GUS fusion and in situ hybridization. An unbiased transcriptional regulatory network was constructed using transcript profiling data collected from inducible overexpression lines for selected candidate TFs and a few major nodes were identified in the network including WOX4 and KNAT1. Moreover, the severity of mutant phenotypes was predicted based on the network. Next, we used the predication as a guide and generated over 70 double mutants within the same or among different TF families to explore the genetic interactions of candidate genes. Phenotype characterization on the secondary growth of the mutants and the overexpression lines identified promoters and inhibitors of cambium activity. The phenotypic data also suggested the redundancy within and among TF families because the phenotypes could be enhanced when additional TFs were mutated. We also found that combinations of certain overexpression lines and mutants led to pronounced increase of cell proliferation or xylem differentiation and in the extreme case the formation of ectopic cambium. We herein propose that cambium development is orchestrated by a wide network at the transcriptional level, where each TF has a different contribution to cell proliferation and differentiation.

overall_design: About 200 roots of 8 day-old seedlings were dissected into three segments (about 1cm per segment) and the basal (zone 1, ARRI, cambium), middle (zone 2, ARRII, transition cambium), and apical (zone 3, ARRIII, procambium) regions were separately collected. Protoplasts from these root segments were isolated and sorted through FACS, and then RNA transcripts collected from GFP expressing protoplasts were profiled on the Affymetrix ATH1 arrays. Specifically, these genome-wide cell type specific data were generated by hybridizing amplified and labeled mRNA that was isolated from specific root cell types onto an Affymetrix ATH1 array.

first: Kaisa

last: Nieminen

first: Annakaisa

last: Elo

first: Ykä

last: Helariutta


title: Identification of elevated A-to-I editing sites due to expression of an active ADAR3 mutant in human glioblastoma cells

city: Davis

first: Peter

last: Beal

state: CA

address: 5469 chem annex, One Shields Ave

department: Chemistry

institute: University of California, Davis

type: Genome variation profiling by high throughput sequencing

summary: We have analyzed RNA-seq data to identify A-to-I editing sites in two groups of samples: one group isolated from human U87 cell line expressing an active ADAR3 mutant while the other isolated from U87 cell line expressing the inactive counterpart of the ADAR3 mutant. We compared these two groups of samples and identified sites whose editing levels are higher in the first group than in the second group.

overall_design: Examine A-to-I editing sites in two group of samples.

first: Yuru

last: Wang

first: Dong-hee

last: Chung

first: Leanna

last: Monteleone

first: Jie

last: Li

first: Yao

last: Chiang

first: Michael

middle: D

last: Toney


title: p38alpha and S1P-dependent SREBP2 activation by the SAM-competitive EZH2 inhibitor GSK343 limits its anticancer activity but creates a druggable vulnerability in hepatocellular carcinoma

first: Pei-Ming

last: Yang


title: PTENα/β paradoxically promote carcinogenesis through WDR5-H3K4me3 axis

status: Public on Feb 26 2019

city: shanghai

first: ge

last: mengkai

state: State...

address: shanghai

institute: Shanghai Jiao Tong University School of Medicine (SJTU-SM)


title: Exercise instructs hematopoietic progenitor cells and reduces chronic leukocytosis [ATAC-seq]

first: Vanessa

last: Frodermann

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

summary:
We show that regular physical activity decreases hematopoietic stem and progenitor cell (HSPC) proliferation in mice and results in reduced leukocyte production.
Effects in HSPC last due to exercise-induced changes in the HSPC epigenome, as assessed by ATAC-seq, which remained for weeks after running ceased.

overall_design: 7-8 weeks old C57BL/6 mice were individually housed and had access to exercise wheels for 6 weeks (Ex), or were housed with igloos (Sed). Another group had access to exercise wheels for 6 weeks followed by a 3 weeks wheel withdrawal (ExSed).

first: Matthias

last: Nahrendorf


title: Sprint exercise shares gene signatures with other exercise modes and hormone exposure and induces stronger upregulation of immediate early genes

status: Public on Feb 09 2019

city: Stockholm

first: Hakan

middle: Claes

last: Rundqvist

state: Huddinge

address: Alfred Nobels ale 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska institutet

summary:
Aim: To examine the global gene expression response to the profound metabolic and hormonal stress induced by acute sprint exercise.
Methods: Healthy women and men (n=14) performed 3 all-out cycle sprints interspersed by 20 min recovery. Muscle biopsies were obtained before the first and 2h and 20 min after the last sprint. Microarray analysis was performed to analyse the acute gene expression response. Repeated blood sample were also obtained.
Results: In skeletal muscle, a set of immediate early genes, FOS, NR4A3, MAFF, EGR1, JUNB were markedly upregulated after sprint exercise. These genes were also upregulated, but to a lesser extent, after other exercise modes and after insulin exposure. Gene ontology analysis from 879 differentially expressed genes revealed predicted activation of extracellular remodelling and fat metabolism, which was in common with the gene expression response to endurance and resistance exercise. Moreover, the gene expression pattern indicated an increased turnover of skeletal muscle mass after sprint exercise, which was in common with data on resistance exercise and GH exposure. Insulin and GH may be involved in sprint-induced changes in the transcriptome, based on the overlap noted between sprint- and hormone exposure-related signatures. Furthermore, there were correlations between sprint-induced changes in hormonal levels and changes in gene expression.
Conclusion: This is the first study reporting on global gene expression in skeletal muscle in response to acute sprint exercise. Several novel findings are presented related to novel sprint exercise - regulated genes as well as to shared gene signatures between sprint exercise, other exercise modes and exogenous hormone exposure.

overall_design: Skeletal muscle gene expression at rest and after acute sprint interval exercise (3x30-s all-out cycle sprints). The first biopsy sample was obtained randomly in either right or left leg before the first sprint. The second sample was obtained 2 h and 20 min after the third sprint from the opposite leg. Fourteen human subjects (Seven males and seven females) volunteered for the present study.


title: Oct4-driven epigenetic reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

institute: Masaryk University

summary: Oct4-driven cell fate conversion has recently become a novel tool for the generation of various cell types from differentiated somatic cells. Although, molecular mechanisms underlying this process are unknown, it is well documented that cells overexpressing Oct4 undergo transition from differentiated state into plastic state. This transition is associated with the acquisition of stem cells properties leading to epigenetically "open" state that is permissive to cell fate switch upon external stimuli. In order to contribute to our understanding of molecular mechanisms driving this process, we characterised human fibroblasts over-expressing Oct4 and performed comprehensive small-RNAseq analysis.

overall_design: MicroRNA profiles of human skin fibroblatsts overexpressing Oct4, controls: GFP expressing human fibroblasts, in biological triplicates, using Illumina

first: Jan

last: Oppelt

first: Lucie

last: Peskova


title: ZFP708 maintains DNA methylation during epigenetic reprogramming in embryos

first: Daniel

last: Messerschmidt


title: The transcription factor ERG regulates super-enhancers in endothelial cells [ERG ChIP-seq]

first: Graeme

last: Birdsey

overall_design: We used ChIP-seq to characterise the ERG binding profile in HUVEC.

first: Viktoria

last: Kalna


title: Branched chain amino acids impact health and lifespan indirectly via amino acid balance and appetite control

status: Public on Mar 11 2019

city: Sydney

first: Qiao-Ping

last: Wang

state: NSW

address: Johns Hopkins Dr

department: Charles Perkins Centre

country: Australia

institute: University of Sydney

summary: Elevated branched chain amino acids (BCAAs) are associated with obesity and insulin resistance. How long-term dietary BCAAs impact late-life health and lifespan is unknown. Here, we show that when dietary BCAAs are varied against a fixed, isocaloric macronutrient background, long-term exposure to high BCAA diets led to hyperphagia, obesity and reduced lifespan. These effects were not due to elevated BCAA per se or hepatic mTOR activation, but rather the shift in balance between dietary BCAAs and other AAs, notably tryptophan and threonine. Increasing the ratio of BCAAs to these AAs resulted in hyperphagia and was linked to central serotonin depletion. Preventing hyperphagia by calorie restriction or pair-feeding averted the health costs of a high BCAA diet. Our data highlight a role for amino acid quality in energy balance and show that health costs of chronic high BCAA intakes were not due to intrinsic toxicity; rather, to hyperphagia driven by AA imbalance.

overall_design: 3 animals per sex per diet were used. Mice were fed one of four diets (all 19% total protein, 63% carbohydrate, 18% fat, total energy density 14 kJ/g) varying in BCAA content (BCAA200: twice BCAA content of control diet AIN93G; BCAA100: standard content of BCAAs; and BCAA50 and BCAA20: containing one half and one fifth of standard content of BCAAs), and either euthanized at 15 months of age or maintained for determination of lifespan.

first: Samantha

last: Solon-Biet

first: Victoria

last: Cogger

first: Tamara

last: Pulpitel

first: Devin

last: Wahl

first: Ximonie

last: Clark

first: Alistair

last: Senior

first: Amanda

last: Brandon

first: Ruth

last: Perks

first: John

last: O’Sullivan

first: Yen

last: Koay

first: Kim

last: Bell-Anderson

first: Melkam

last: Kebede

first: Belinda

last: Yau

first: Clare

last: Atkinson

first: Gunbjorg

last: Svineng

first: Rosilene

last: Ribeiro

first: Jibran

last: Wali

first: Matthew

last: Piper

first: Robert

middle: G

last: Cumming

first: Vasant

last: Hirani

first: David

last: Handelsman

first: Paula

last: Juricic

first: Linda

last: Partridge

last: Raubenheimer

first: Gregory

last: Cooney

last: Le Couteur

first: Stephen

last: Simpson


title: Genome-wide binding of ZFP708/TRIM28 and linked H3K9me3 dynamics

first: Daniel

last: Messerschmidt

overall_design: HA-/Flag-tagged ZFP708 or Flag-tagged ZFP708 lacking KRAB domain were overexpressed in mouse embryonic stem cells to identify genome-wide binding sites by ChIP-sequencing. In ZFP708 overexpressing cells TRIM28/Kap1 recruitment and H3K9me3 dynamics were also assed by ChIP-sequencing.

first: Diana

last: Loh

first: Pierre-Alexis

last: Goy

first: Ernesto

last: Guccione


title: Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

status: Public on Mar 04 2019

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the viral gene expression cascade at the single-cell level, showing bifurcations and bottleneck states. Host gene expression changes are related to viral transcription. The role of cellular signaling pathways in infection is studied using trajectory analysis and the importance of the Nrf2 transcription factor studied in follow-up experiments.

overall_design: Human primary fibroblasts were infected with HSV-1 and single-cell RNA-sequencing was performed at different early time points after infection.

first: Vedran

last: Franke

first: Jennifer

last: Menegatti

first: Christine

last: Kocks

first: Barbara

last: Walch-Rückheim

first: Anastasiya

last: Boltengagen

first: Nikolaus

last: Rajewsky

first: Friedrich

last: Grässer

first: Altuna

last: Akalin

first: Markus

last: Landthaler


title: Generation of induced neural stem cells from urine derived cells by synthetic mRNA

status: Public on Feb 03 2019

first: Phil Jun

last: Kang

address: 1, 5-Ka, Anam-Dong, Sungbuk-ku

department: Department of Biotechnology

institute: Korea University

summary: Analysis of induced neural stem cells from urine derived cells by synthetic mRNA vs. H9 embryonic stem cell derived neural stem cells and urine derived cells. Results provide insight into molecular similarities between induced neural stem cells and H9 embryonic stem cells derived neural stem cells.

overall_design: Total RNA profiles of induced neural stem cells, H9 embryonic stem cells derived neural stem cells and urine derived cells were generated by RNA sequencing, in duplicate.

first: Seungkwon

last: You


title: Comparative transcriptome profiling of Chinese tongue sole in immune response against Vibrio harveyi infection

city: qingdao

first: Hao

last: Xu

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea fisheries Research Institution

summary: Vibrio harveyi is a major bacterial pathogen that can cause fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis). To comprehend the molecular mechanisms of C. semilaevis host response against V. harveyi infection, we performed transcriptome (RNA-seq) analysis of C. semilaevis from resistant family and susceptible family.

overall_design: RNA-seq analysis was perfomed from four groups, resistant and susceptible families unchallenged , and those challenged with V. harveyi for 24 hour. Three biological replicates each group were used for cDNA library construction and Illumina sequencing.

first: Songlin

last: Chen


title: Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [ChIP-Seq]

city: Tianjin

first: Xinyi

last: Cao

state: Tianjin

address: Tianjin Medical University No.22 Qixiangtai Road

institute: Collaborative Innovation Center of Tianjin for Medical Epigenetics

summary: Anaplastic thyroid carcinoma (ATC) is one of the most aggressive malignancy and accounts for the majority of thyroid cancer-related deaths. Despite intensive research, there remains no effective treatment for patients with ATC. Here, we identify THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), as a potent anti-ATC compound by high-throughput chemical screening. ATC cells, but not papillary thyroid cancer (PTC) cells, are exceptionally sensitive to CDK7 inhibition. Analyzing both gene expression profiles and super enhancer (SE) features reveals that the SE-mediated oncogenic transcriptional amplification renders the vulnerability of ATC cells to THZ1 treatment. Combining this integrative analysis with functional assays discovers a number of novel cancer genes of ATC, including PPP1R15A, SMG9 and KLF2. Inhibition of PPP1R15A with Guanabenz (GBZ) or Sephin1 greatly suppresses ATC growth. Significantly, the expression level of PPP1R15A is correlated with CDK7 expression in ATC tissue samples. Elevated expression of PPP1R15A and CDK7 are both associated with poor clinical prognosis in ATC patients. Importantly, GBZ or THZ1 treatment sensitizes ATC cells to conventional chemotherapy. Taken together, these findings demonstrate transcriptional addiction in ATC pathobiology and identify CDK7 and PPP1R15A as potential biomarkers and therapeutic targets for ATC.

overall_design: ChIP-sequencing using H3K27ac antibody in BCPAP and CAL-62 cell lines.

first: Yupeng


title: Hi-C of WT E14 mouse ES cells grown in serum and 2i media

status: Public on Jan 30 2019

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Dynamic reprogramming of global DNA methylation impacts on the genomic deposition of the Polycomb-mediated repressive histone mark H3K27me3. DNA hypomethylation in ground state embryonic stem cells (ESCs) results in a reversible redistribution of H3K27me3 from its normal target loci. Thus, a signalling induced shift of ESCs to ground state results in both DNA methylation and Polycomb patterns that are quite distinct from their primed counterparts. Here we investigated the impact of DNA methylation directed Polycomb redistribution on higher-order chromatin structure in the ground state. Using a targeted single-locus approach (FISH) we can demonstrate local decompaction at Hox loci in the ground state, which is consistent with genome-wide data (Hi-C) indicating that chromatin structure is globally altered in ground state relative to primed ESCs. Polycomb targets are similarly decompacted in hypomethylated E3.5 mouse blastocysts. ESC lines which maintain a high level of DNA methylation in ground state show no decompaction at Hox loci. Our results suggest that DNA-methylation mediated reprogramming of Polycomb binding drives higher order chromatin organisation in stem cells and early development.

overall_design: In situ Hi-C experiments on E14 mESCs in serum and 2i culture with two replicates per condition

first: Katy

last: McLaughlin

first: John

middle: P

last: Thomson

first: Heidi

middle: K

last: Mjoseng

first: Ruchi

last: Shukla

first: Iain

last: Williamson

first: Graeme

middle: R

last: Grimes

first: Robert

middle: S

last: Illingworth

first: Ian

last: Adams

first: Sari

last: Pennings

first: Wendy

last: Bickmore

first: Richard

last: Meehan


title: Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [RNA-Seq]

overall_design: mRNA profiles of BCPAP and CAL-62 cells treated with THZ1 or vehicle control


title: Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer

overall_design: Refer to individual Series


title: MCL cel lines upon OMP-52M51 treatment

status: Public on Jan 19 2019

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

country: Spain

institute: IDIBAPS-HOSPITAL CLINIC

summary: Treatment with the monoclonal Notch1-antibody OMP-52M51 prevented DLL4-dependent activation of Notch1 and suppressed induction of Notch target genes in NOTCH1 mutated cell lines

overall_design: Global RNA expression in MCL cell lines (jeKo and Mino) treated with OMP-52M51 for 48 h

first: E

last: Silkenstedt

first: M

last: lopez-Guerra

first: D

last: Colomer


title: All the regulated lncRNAs in breast cancer tissues compared to adjacent normal breast tissues

status: Public on Jan 26 2019

city: Nanjing

first: Liang

last: Jin

address: 24 Tongjiaxiang Avenue

institute: China Pharmaceutical University

summary: Circulating transcriptional landscapes between breast cancer tissues and adjacent normal tissues were compared using the Affymetrix Human OE LncRNA Microarray with probes for profiling of 63542 human lncRNAs. Goal was to investigate potential lncRNAs involved in breast cancer progression.

overall_design: The total RNAs of 3 paired breast cancer and adjacent normal tissues were extracted, and the global expression profile of lncRNAs was detected with Affymetrix Human OE LncRNA Microarray.


title: Circulating miRNA expression profiling in primary aldosteronism

status: Public on Feb 12 2019

city: Budapest

first: Abel

last: Decmann

address: Korányi str. 2a

department: Department of Internal Medicine and Oncology

country: Hungary

institute: Semmelweis University

summary: Introduction: Primary aldosteronism (PA) is a major cause of secondary hypertension. The two principal forms of PA are bilateral adrenal hyperplasia (BAH) and aldosterone-producing adenoma (APA) whose differentiation is clinically pivotal, due to their different treatments. Adrenal venous sampling (AVS) is considered to be the gold standard for the differentiation of the two clinical entities, but it is invasive, requires great expertise and is unavailable in many centers. There would be a major clinical need for a reliable and easily accessible diagnostic biomarker. Circulating microRNA were shown to be useful as minimally invasive diagnostic markers in many diseases, but their potential applicability in PA has not yet been investigated. Aims: To determine and compare the circulating microRNA expression profiles of AVS-confirmed APA and BAH plasma samples, and to evaluate their applicability as minimally invasive markers. Methods: 81 AVS-confirmed plasma samples were included. Next-generation sequencing (NGS) was performed on 30 EDTA-anticoagulated plasma samples. Significantly differently expressed miRNAs were validated by real-time RT-qPCR on all samples. Results: We have found relative overexpression of miR-30e-5p, miR-30d-5p, miR-223-3p and miR-7-5p in BAH compared to APA by NGS. Validation of 81 samples confirmed significant overexpression (p=0.03) of miR-7-5p. Regarding the microRNA expressional variations, APA is more heterogenous at the miRNA level compared to BAH. Conclusion: miR-7-5p was significantly overexpressed in BAH samples compared to APA samples, but its sensitivity and specificity values are not good enough for introduction to the clinical practice yet.

overall_design: Altogether 30 samples were investigated by high-throughput miRNA expression profiling (16 aldosterone-producing adenomas and 14 bilateral adrenal hyperplasias)

first: Peter

last: Igaz


title: Sexually Dimorphic Control of Parenting Behavior by the Medial Amygdala

status: Public on Feb 14 2019

city: Los Angeles

first: Ye

middle: Emily

last: Wu

address: 635 Charles E. Young Dr. South

country: USA

institute: UCLA

summary: Single-cell RNA sequencing of male and female mouse medial amygdala using Drop-Seq

overall_design: Drop-Seq was performed for medial amygdala cells dissociated from male and female C57BL/6J mice (8 - 10 weeks).

first: Weizhe

last: Hong

middle: E


title: Transcriptional profiles of sov mutant ovaries

status: Public on Jan 01 2019

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Stranded, single-end, polyA+, transcriptional profiles were created from ovaries of sterile and fertile sov heteroallelic mutants and Gal4 driven sov RNAi knockdowns.

overall_design: 15 ovaries from 4-5 day old post-eclosion females grown in uncrowded conditions were dissected and pooled for each biological replicate for a total of three replicates per genotype. Total RNA was extracted from tissues and polyA RNA was isolated and used to prepare stranded RNAseq libraries. 50 bp single-end sequencing was performed and mapped to Drosophila melanogaster release 6.21 genome.

first: Leif

last: Benner

first: Dorothy

middle: A

last: Lerit


title: Reversible LSD1 Inhibition with HCI-2509 induces the p53 gene expression signature in high-risk neuroblastoma cells

city: Salt Lake City

first: Sumati

last: Gupta

state: Utah

address: 2000 Circle of Hope

department: Medicine

institute: Huntsman Cancer Institute

summary: Lysine-Specific Demethylase 1 (LSD1) over-expression correlates with poorly differentiated neuroblastoma and predicts poor outcome despite multimodal therapy. We have studied the efficacy of reversible and specific LSD1 inhibition with HCI-2509 in neuroblastoma cell lines and particularly the effect of HCI-2509 on the transcriptomic profile in MYCN amplified NGP cells.  Cell survival assays show that HCI-2509 is cytotoxic to poorly differentiated neuroblastoma cell lines in low micromole or lower doses. Transcriptional profiling of NGP cells treated with HCI-2509 shows a significant effect on p53, cell cycle, MYCN and hypoxia pathway gene sets. HCI-2509 results in increased histone methyl marks and p53 levels along with cell cycle arrest in the G2/M phase and inhibition of colony formation of NGP cells. Our findings indicate that LSD1 inhibition with HCI-2509 has a multi-target effect in MYCN amplified high-risk neuroblastoma cells.

overall_design: One million NGP cells per well were plated in 6 well plates and treated with vehicle (DMSO) or 3 µM HCI-2509 for 4 and 24 hours in quadruplicate.

first: Timothy

last: Mosbruger

first: Alexis

last: Weston

first: Mohan

last: Kaadige

first: Sunil

last: Sharma

first: Kelly

last: Doyle

first: Andrew

last: Butterfield

first: Allison

last: Ast

first: Anupam

last: Verma


title: Transcriptomic profiling of mock-infected primary CD4+ T cells and a model of HIV latency treated with suberoylanilide hydroxamic acid (SAHA) and Romidepsin (RMD)

status: Public on Feb 08 2019

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary:
Purpose: The goal of this study is to identify host genes whose expression is perturbed in primary CD4+ T cells by histone deacetylase (HDAC) inhibitors (HDACi) SAHA and RMD, which have different potencies and specificities for various HDACs. The study aims to evaluate the effects of SAHA and RMD that may promote or inhibit reactivation of HIV provirus out of latency.
Methods: Peripheral blood mononuclear cells were collected from 4 HIV-seronegative donors. CD4+ T cells were isolated and utilized to generate an in vitro model of latent HIV infection (model developed in the Spina laboratory and previously described in Spina et al., 2013). Mock-infected cells were cultured in parallel to evaluate effects of SAHA and RMD that may be dependent on the exposure of cells to virus. Following generation of the model, cells were treated with SAHA, RMD or their solvent dimethyl sulfoxide (DMSO) for 24 hours. Mock-infected cells were treated in parallel. The experiment had 4 biological replicates, 6 conditions for each, for a total of 24 samples. ERCC spikes (Thermo Fisher Scientific, Inc.) were added to cell lysates based on cell number in each sample (10 ul of 1:800 dilution per million cells). Mix 1 was used for DMSO- and mix 2 for SAHA- and RMD-treated cells. After all samples were collected, RNA was extracted and subjected to deep sequencing by Expression Analysis, Inc. Sequence reads that passed quality filters were mapped using Tophat (human genome) or Bowtie (ERCC spikes and HIV) and counted using HTSeq. ERCC spikes with the same concentration in mixes 1 and 2 were utilized to remove unwanted technical variation. Any human gene which did not achieve at least 1 count per million reads in at least 4 samples or any ERCC that did not achieve at least 5 reads in at least 4 samples was discarded. Differential gene expression analysis was performed using library EdgeR in Bioconductor R. National Center for Biotechnology Information (NCBI) HIV-1 Human Interaction Database was then searched for genes that have been implicated in controlling HIV latency. EdgeR output was used to extract expression information of the genes of interest from the NCBI database to identify genes implicated in HIV latency that were modulated by SAHA and RMD. The resulting lists were manually curated to verify relevance to HIV latency, using the Description column of the NCBI database, as well as available PubMed references.
Results: Using a custom built data analysis pipeline, ~100 million reads per sample were mapped to the human genome (build hg38). After applying filtering criteria, 16058 human transcripts, 19 ERCC spikes transcripts, and HIV NL4-3 transcripts were identified with the Tophat/Bowtie and HTSeq workflow. Differential expression analysis was performed between SAHA or RMD-treated and DMSO-treated cells. In addition, differential modulation of gene expression by SAHA and RMD in the model of HIV latency and mock-infected cells was assessed using EdgeR. In mock-infected cells, SAHA upregulated 3,971 genes and downregulated 2,940 genes; RMD upregulated 5,068 genes and downregulated 4,050 genes. In the model of HIV latency, SAHA upregulated 3,498 genes and downregulated 2,904 genes; RMD upregulated 5,116 genes and downregulated 4,053 genes (FDR < 0.05). SAHA modulated 6, and RMD 11 genes differentially between mock-infected cells and the model of HIV latency. Following search of the NCBI HIV-1 Human Interaction Database, 27 genes upregulated and 29 downregulated in common between SAHA and RMD were found to be relevant to regulation of HIV latency; 31 were up- and 32 downregulated by RMD only; and 6 were up- and 2 were downregulated by SAHA only.
Conclusions: This study demonstrates that SAHA and RMD, which have different potencies and specificities for HDACs, modulate a set of overlapping genes implicated in regulation of HIV latency. Some of these genes may be explored as additional host targets for improving the outcomes of “shock and kill” strategies.

overall_design: Transcriptomic profiling of the in vitro model of HIV latency and mock-infected cells treated with SAHA, RMD or the solvent DMSO (N=4 donors) by deep sequencing at Expression Analysis, Inc.

first: Amey

last: Mukim

first: Cory

middle: H

last: White

first: Savitha

last: Deshmukh

first: Hosiana

last: Abewe

first: Douglas

last: Richman

first: Celsa

last: Spina


title: FOXO1 knockdown is toxic for Burkitt's lymphoma (BL) cell lines

status: Public on Dec 31 2018

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary: We found that FOXO1 knock-down  inhibits cell cycle progression in Burkitt's lymphoma (BL) cell lines BL41 and Namalwa.

overall_design: Burkitt's lymphoma (BL) cell lines BL41 and Namalwa were transduced with sh_hFOXO1.H-10381 in pRSI12-U6-sh-UbiC-TagRFP-2A-Puro lentiviral vector (DECIPHER shRNA Library, Human Module I (Cellecta, https://www.cellecta.com/) obtained from BioCat, Heidelberg, Germany).   On Day 4 after transduction total RNA was isolated with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng of total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.

first: Franziska

last: Gehringer

first: Thomas

last: Wirth


title: Genes altered in expression by knockdown of PTK2 in breast cancer cell lines

status: Public on Dec 28 2018

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

summary: PTK2 was knocked down by doxycycline-dependent expression of small hairpin RNA against PTK2 in Breast cancer cell lines.

overall_design: mRNA expression profiles of the breast cancer of Homo sapiens with or without expressing PTK2 were examined by Illumina Hi-seq 2500.

first: Kim

last: Yeon


title: Liver transcriptome study in lambs

status: Public on Feb 05 2019

city: Zaragoza

first: Jorge

last: Calvo

address: Avd. Montañana 930

department: Producción y Sanidad animal

institute: CITA

summary: Feeding animals with either concentrates  or alfalfa grazing has been proven to reduce the oxidative process that occurs in meat products. Indoor-kept lambs were fed a standard concentrate (n=7, C) before slaughtering all animals at 22–24 kg of live weight. Simultaneously, 7 unweaned lambs grazed in alfalfa paddocks (ALF) with their dams. Global transcriptomic data of liver with the Affymetrix® Ovine Gene 1.1 microarray was used. When ALF group was compared with C group, were identified 96 genes differentially expressed. Among these genes 92 were down- regulated and 4 were up- regulated.  The clusters corresponding to gene expression profiles from treatments  were clearly separated from each other. These differentially expressed genes were selected for a functional analysis by using DAVID. Three major gene clusters associated with “sterol biosynthesis (EBP, MVD, HMGCR, CYP51A1, HMGCS1, NR0B2, C14ORF1, FDFT1, SQLE, DHCR7, SC5DL, DHCR24, NSDHL) , “lipid biosynthetic process (ACACA, CYP51A1, FADS1, FADS2, SCD y SC5DL)”, “cholesterol metabolic process (EBP, MVD, HMGCR, CYP51A1, SQLE, DHCR7, HMGCS1, NR0B2, DHCR24, FDFT1, NSDHL)” were found.

overall_design: 14 male lambs were employed. 7 animals were fed basal concentrate,  and 7 animals grazed in alfalfa paddocks. Animals were slaughtered at 22-24 kg of live weight. Just after slaughter, a piece of liver were sampled from each animal.

first: Laura

last: González


title: TET2 regulates the neuroinflammatory response in microglia

city: London

first: Miguel

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

summary: Epigenetic mechanisms regulate distinct aspects of the inflammatory response in various immune cell types. Despite a central role for microglia in neuroinflammation and neurodegeneration little is known about their epigenetic regulation of the inflammatory response. We found that TET2 expression is increased in microglia upon stimulation with various inflammogens through a NF-kB-dependent pathway. RNA-seq analysis showed that TET2 modulates the transcriptional response of microglial cells to LPS.

overall_design: TET2-depleted or control microglial BV2 cells were treated with LPS for 3 hours.

first: Alejandro

last: Carrillo-Jimenez

first: Ozgen

last: Deniz

first: Maria

last: Niklison-Chirou

first: Karina

last: Bezerra-Salomao

first: Vassilis

last: Stratoulias

first: Rachel

last: Amouroux

first: Rocio

last: Ruiz

first: Ping

last: Yip

first: Anna

last: Vilalta

first: Mathilde

last: Cheray

first: Alexander

last: Scott-Egerton

first: Eloy

last: Rivas

first: Khadija

last: Tayara

first: Ana

middle: M

last: Espinosa-Oliva

first: Xianli

last: Shen

first: Guy

last: Brown

first: Petra

last: Hajkova

first: Bertrand

last: Joseph

first: Jose

last: Venero

last: Burguillos


title: Transcriptome and sRNA profiling of Maize dcl5 CRISPR null alleles

status: Public on Dec 17 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Small RNAs play important roles during plant development by regulating transcript levels of target mRNAs, maintaining genome integrity, and reinforcing DNA methylation. Dicer-like 5 (Dcl5) is proposed to be responsible for precise slicing to generate diverse 24-nt phased, secondary small interfering RNAs (phasiRNAs), which are exceptionally abundant in meiotic anthers of maize, rice, and other grasses 1. Importance and functions of these phasiRNAs remain unclear. Here we used the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas9 system to mutate Dcl5. We report that dcl5 mutants have few or no 24-nt phasiRNAs, develop short anthers and defective tapetal cells, and exhibit temperature-sensitive male fertility. We propose that DCL5 and 24-nt phasiRNAs are critical for fertility under growth regimes for optimal yield.

overall_design: RNA and sRNA-seq libraries were made from meiotic anthers of multiple Maize dcl5 null alleles along with the fertile siblings.

first: Chong

last: Teng

first: Han

last: Zhang

first: Reza

last: Hammond

first: Sandra

last: Mathioni

first: Virginia

last: Walbot