title: Dissecting the Role of H3K27 Acetylation and Methylation in PRC2 Mediated Control of Cellular Identity

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

institute: European Institute of Oncology

summary: The Polycomb repressive complexes PRC1 and PRC2 act non-redundantly at target genes to maintain transcriptional programs and ensure cellular identity. PRC2 methylates lysine 27 on histone H3 (H3K27me), while PRC1 mono-ubiquitinates histone H2A at lysine 119 (H2Aub1). Here we present engineered mouse embryonic stem cells (ESCs) targeting the PRC2 subunits EZH1 and EZH2 to discriminate between contributions of distinct H3K27 methylation states and the presence of PRC2/1 at chromatin. We generate catalytically inactive EZH2 mutant ESCs, demonstrating that H3K27 methylation, but not recruitment to the chromatin, is essential for proper ESC differentiation. We further show that EZH1 activity is sufficient to maintain repression of Polycomb targets by depositing H3K27me2/3 and preserving PRC1 recruitment. This occurs in the presence of altered H3K27me1 deposition at actively transcribed genes and by a diffused hyperacetylation of chromatin that compromises ESC developmental potential. Overall, this work provides insights for the contribution of diffuse chromatin invasion by acetyltransferases in PRC2-dependent loss of developmental control.

overall_design: Evaluation of SUZ12 and RING1B chromatin binding and of H3K27me1, H3K27me2, H3K27me3, H3k27ac and H2AK119ub deposition in different CRISPR/Cas9-edited mouse embryonic stem cells.

first: Elisa

last: Lavarone

first: Caterina

last: Barbieri


title: Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties [methylation]

status: Public on Feb 28 2019

city: Baltimore

first: Wenbing

last: Xie

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Department of Oncology

country: USA

institute: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine

summary: UHRF1 is essential for targeting DNA methyltransferases (DNMT’s) to replicating DNA to establish de novo DNA methylation and maintain it. While, UHRF1 domains are defined, including requirement for an E3 ligase region, for de novo methylation, those essential for maintenance have been difficult to outline. Herein, via a new assay, chromatin histone-binding and a hemimethylated DNA reader domains, but not the ligase domain are found essential for cancer-specific DNA methylation maintenance in human colorectal cancer (CRC) cells.  Disrupting each essential domain phenocopies UHRF1 depletion for global DNA demethylation, reactivation of tumor suppressor genes (TSGs), and reduction in CRC invasion and metastatic properties. Moreover, there is strong negative correlation between high UHRF1 expression, low TSG expression, and abnormal methylation with CRC progression and overall survival. Our battery of findings suggest the value of targeting specific domains of  UHRF1 for cancer therapy and adding a precision medicine approach through use of the biomarker associations we define.

overall_design: Bisulphite converted DNA from the 30 samples to test DNA methylation alterations in endogenous UHRF1 depleted HCT116 and RKO cells complemented with various domain mutants.

first: Xiangqian

last: Kong

first: Yong

last: Tao

first: Stephen

last: Brown

first: Yi

last: Cai

first: Michael

last: Topper

first: Ray-Whay

middle: C

last: Yen

first: Cynthia

middle: A

last: Zahnow

first: Limin

last: Xia

middle: B

last: Baylin


title: Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties [expression]

overall_design: Examination of the gene expression alterations in endogenous UHRF1 depleted HCT116 and RKO cells complemented with various UHRF1 domain mutants..


title: Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming.

status: Public on Mar 12 2019

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

type: Expression profiling by high throughput sequencing

summary: Some somatic cells are plastic, having the capacity to convert into other specialized cells (transdifferentiation) or into induced pluripotent stem cells (iPSCs, reprogramming) in response to transcription factor over-expression. To explore what makes a cell plastic and whether susceptibility to different cell conversion processes is coupled, we exposed bone marrow derived pre-B cells to two different transcription factor protocols that efficiently convert them either into macrophages (iMac) or iPS cells, and monitored the two processes over time using single cell gene expression analysis.

overall_design: We isolated CD19+ B cell precursors from the bone marrow of reprogrammable mice and infected them with a retrovirus encoding a hormone inducible form of C/EBPα (C/EBPα-ER-hCD4). After expansion in culture, we induced them to either trans-differentiate to macrophages or to reprogram into iPSCs. To induce the macrophage fate, we treated the cells with beta-estradiol to activate C/EBPα for up to 114h. To induce an iPSC fate, we treated them with beta-estradiol for 18 hours and, after washing out the hormone, added doxycycline to induce OSKM. We collected samples before induction (0h), at 6h, 18h, 42h, 66h and 114h after C/EBPα induction during transdifferentiation, and at days 2, 4, 6 and 8 after OSKM induction in 18h-pulsed cells. We collected two pools of 192 cells at each time point and sequenced their mRNA using MARS-Seq.

first: Holger

last: Heyn

last: Rodríguez-Esteban


title: CpGs induce differentiation of Atlantic salmon mononuclear phagocytes into cells with dendritic morphology and a proinflammatory transcriptional profile but an exhausted allostimulatory activity

status: Public on Feb 26 2019

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Due to their ability to present foreign antigens and prime naïve T cells, macrophages and dendritic cells (DCs) are referred to as professional antigen-presenting cells (APCs). Although activated macrophages may function as APCs, these cells are particularly effective at directly engaging pathogens through phagocytosis, and production of antimicrobial compounds. On the other hand, DCs possess superb antigen-presenting and costimulatory capacity and they are essential for commencement and regulation of adaptive immune responses. In in vitro models, development of mature mammalian DCs from monocytes requires sequential exposure to growth factors (including GM-CSF and IL-4) and proinflammatory stimuli such as toll-like receptor (TLR) ligands. Currently, except for IL-4/13, neither orthologues nor functional analogues of the growth factors which are essential for the differentiation of mammalian DCs (including GM-CSF and FLT3) have been identified in teleosts and data about differentiation of piscine APCs is scant. In the present study, primary salmon mononuclear phagocytes (MPs) stimulated in vitro for 5-7 days with a B-class CpG oligodeoxynucleotides (ODN 2006PS) underwent morphological differentiation and developed “dendritic” morphology, characterized by long, branching pseudopodia. Transcriptional profiling showed that these cells expressed high levels of proinflammatory mediators characteristic for M1 polarized MPs. However, the cells treated with CpGs for 7 days downregulated their surface MHCII molecules as well as their capacity to endocytose ovalbumin and exhibited attenuated allostimulatory activity. This concurred with transcriptional downregulation of costimulatory CD80/86 and upregulation of inhibitory CD274 (B7-H1) genes. Despite their exhausted allostimulatory activity, these cells were still responsive to re-stimulation with gardiquimod (a TLR7/8 ligand) and further upregulated a wide array of immune genes including proinflammatory mediators such as intereukin-1 beta and tumor necrosis factor. Overall, the presented data highlight the disparate effects TLR ligands may have on the proinflammatory status of APCs, on one side, and their antigen-presenting/costimulatory functions, on the other. These findings also indicate that despite the poor phylogenetic conservation of the growth factors involved in the differentiation of DCs, some of the processes that orchestrate the development and the differentiation of professional APCs are conserved between teleosts in mammals.

overall_design: Primary salmon mononuclear phagocytes (MPs) were isolated from head kidney and cultured in vitro for up to 7 days. RNA samples were harvested from control (non-stimulated) cells after 24 hours and 7 days of in vitro culture. Stimulated samples included: MPs stimulated for 24 h with 20 μg/ml of poly IC; MPs stimulated with 20μg/ml of polyIC or 2 uM CpG (2006PS) for 7 days and control cells as well as MPs stimulated with polyIC and CpGs for 6 days and restimulated for another 24 h with Gardiquimod. The Gardiquimod-stimulated samples were hybridized to a common reference – the day 7 non-stimulated samples. The other sampels were compared with the control sample harvested after 24 hours of culture.

first: Krasnov

last: Aleksei

first: Dimitar

last: Iliev


title: Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency and patterns

status: Public on Mar 08 2019

city: Delft

first: Joana

middle: P

last: Goncalves

address: Van Mourik Broekmanweg 6

department: Intelligent Systems

country: Netherlands

institute: Delft University of Technology

summary: Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR/Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. We leverage our TRIP technology to integrate ~1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5′ overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.

overall_design: Mutation profiling upon RNA-guided Cas9 targeting of (i) mouse embryonic stem (mES) cell line, EStTA-PB-B18, containing the same 36 mPGK-driven TRIP barcoded reporter integrations per cell (EStTA-PB-B18); (ii) TRIP cell pool containing ~1k barcoded reporters integrated heterogeneously throughout the genomes of the cells in the pool (GEMP-O). Cell line was targeted in independent experiments using three single-guide RNAs (sgRNA1-3). Pool was targeted in independent experiments using sgRNA2 with or without a custom-designed ssODN, and with sgRNA3. We also did expression profiling of the TRIP cell line and pool before Cas9 targeting (see GEO accession GSE48606 for cell line expression, and this submission for the pool expression).  Files related to re-analyzed samples from GSE48606 are linked below as supplementary files.

first: Santiago

last: Gisler

first: Waseem

last: Akhtar

first: Johann

last: de Jong

first: Alexey

middle: V

last: Pindyurin

first: Lodewyk

middle: F

last: Wessels

first: Maarten

last: van Lohuizen


title: ChIP-seq from GM12878 (ENCSR439WAF)

status: Public on Mar 03 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
E4F1 ChIP-seq on human GM12878

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


title: ChIP-seq from GM23338 (ENCSR871KYB)

summary:
Chip-Seq on PGP1 iPSC

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


title: ChIP-seq from GM12878 (ENCSR974OFJ)

summary:
KLF5 ChIP-seq on human GM12878

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


title: MicroRNA-mediated suppression of the TGF-β pathway confers transmissible and reversible CDK4/6 inhibitor resistance (array II)

status: Public on Mar 04 2019

city: boston

first: Liam

last: Cornell

state: MASSACHUSETTS

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

summary: CDK4/6 inhibition is now part of the standard armamentarium for patients with estrogen receptor (ER)-positive breast cancer, so that defining mechanisms of resistance is a pressing issue. Here, we identify increased CDK6 expression as a key determinant of acquired resistance after exposure to palbociclib in ER-positive breast cancer cells. Increased CDK6 in resistant cells was dependent on TGF-β pathway suppression via miR-432-5p expression. Exosomal miR-432-5p expression mediated transfer of the resistance phenotype between neighboring cell populations. We confirmed these data in pre-treatment and post-progression biopsies from a parotid cancer patient who had responded to ribociclib, demonstrating clinical relevance of this mechanism. Additionally, the CDK4/6 inhibitor resistance phenotype can be reversed in vitro and in vivo by a prolonged drug holiday.

overall_design: T47D cells were cultured to palbociclib resistance. In this experiment we extracted RNA from parental, resistant and Ex-resistant (resistant cells after prolonged drug removal) cells. We used the affymetrix Human Genome U133+ 2.0 array to analyse gene expression

first: Geoffrey

middle: I

last: Shapiro


title: RNA-seq of microglia isolated from the hippocampi of young and aged mice

status: Public on Mar 01 2019

city: palo alto

first: John

last: Pluvinage

state: California

address: 3801 Miranda Ave Rm D3-131

institute: Stanford

summary: Sequencing data related to the manuscript entitled, "CD22 blockade restores homeostatic microglial phagocytosis in the aging brain."

overall_design: Hippocampi from young (3 month old) and aged (20 month old) mice were microdissected following perfusion. Primary microglia were isolated by gentle dounce homogenization of the brain, magentic myelin removal, and FACS-purification of ~20,000 live CD11b+CD45lo cells. Microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples were used for library preparation. cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). After normalization and pooling, libraries were sequenced on a Novaseq 6000 (Illumina) using paired-end 150bp reads. Raw sequencing files were demultiplexed with bcl2fastq, trimmed with fastx_trimmer, reads were aligned using STAR, the count matrix was generated using samtools, and differential expression analysis was performed using DESeq2 with standard settings.

first: Liana

last: Bonanno


title: ChIP-seq from GM23338 (ENCSR061DGF)


title: Transcriptomic analysis of the Xrn1 depletion by Auxin-degron shutoff

status: Public on Feb 22 2019

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: The goal of the project was to study the effects on transcription and mRNA stability of the Xrn1 sudden depletion. We analyzed the effect of Xrn1 depletion caused by protein degradation of an Auxin-degron fusion on the transcription rates, mRNA stabilities and mRNA levels by doing Genomic Run-On (GRO) experiments at 30 min after Auxin addition with a control at 0 min.

overall_design: Cells were grown in YPD at 30ºC to 0.5 OD600. At 0 min and 30 min after Auxin addition cells were spun-down and collected. Please note that each sample record represents three replicates (more details in the sample description field).

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez


title: Malaria Host Pathogen Interaction Center Experiment 30: Pilot experiment for Macaca mulatta infected with Plasmodium knowlesi Malayan strain sporozoites to produce and integrate measures of acute primary infection.

status: Public on Feb 25 2019

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC has continued with support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC.

sample_organism:
Plasmodium knowlesi
Macaca mulatta

platform_organism:
Plasmodium knowlesi
Macaca mulatta

overall_design: Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in two malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age.  After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected.  Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone. The P. knowlesi sporozoites were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention.  After inoculation, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, metabolomic, telemetric and histopathological measurements. The experiment was designed for pathology studies, with terminal necropsies on days 11 (RKy15) or 19 (Red16).  The anti-malarial drug artemether was subcuratively administered selectively to one subject (REd16) during the primary parasitemia to suppress clinical complications. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, proteomic, lipidomic, and immunological analyses. Physiological data were continuously captured via telemetry.  Within the MaHPIC, this project is known as â??Experiment 30â??.  This dataset was produced by Steven E Bosinger, Nirav Patel, and Gregory K Tharp at Emory University. To access other publicly available results from E30 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).The MaHPIC Consortium

middle: W

last: Barnwell

first: Steven

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Regina

middle: J

last: Cordy

first: Jeremy

middle: D

last: DeBarry

middle: R

first: Allison

last: Hankus

first: Jay

last: Humphrey

first: Nicolas

last: Lackman

first: Stacey

last: Lapp

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Chester

last: Joyner

first: Mariko

middle: S

last: Peterson

first: Gregory

middle: K

last: Tharp

first: Juan

last: Gutierrez

first: Rabindra

middle: M

last: Tirouvanziam


title: ChIP-seq from GM23338 (ENCSR917MAH)

first: ENCODE

last: DCC


title: H3K9 promotes under-replication of pericentromeric heterochromatin in Drosophila salivary gland polytene chromosomes

status: Public on Feb 21 2019

city: Chapel Hill

first: Robert

last: Duronio

state: NC

address: CB #3280, Coker Hall

institute: University of North Carolina at Chapel Hill

summary: We replaced the endogenous histones of Drosophila melanogaster with either histones containing an H3K9R mutation or histones containing an H4K16R mutation to interrogate direct functions for histone residues in salivary gland endoreplication. We performed genomic DNA sequencing in HWT (Histone Wild Type) control, H3K9R, and H4K16R females. We found that H3K9 promotes under-replication of pericentromeric heterochromatin but not along chromosome arms and H4K16 is dispensable for under-replication.

overall_design: Experiments were performed on endogenous histone mutants rescued with a wild type (HWT), H4K16R mutant, or H3K9R mutant transgenic arrays. Genomic DNA sequencing experiments were carried out in duplicate.

first: Robin

middle: L

last: Armstrong


title: ChIP-seq from GM12878 (ENCSR900XDB)

summary:
ZFP36 ChIP-seq on human GM12878

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


title: Music performance regulates microRNAs in professional musicians

city: Helsinki

first: Irma

last: Järvelä

address: Department of Medical Genetics, University of Helsinki, P.O. Box 720

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

type: Non-coding RNA profiling by high throughput sequencing

summary: The dataset was used to study the effect of 2 hours of western classical music concert performance on the peripheral blood microRNA transcriptome in professional musicians.

overall_design: MicroRNAs were extracted from the peripheral blood of the professional musicians (N=10) immediately before and after 2 hours of western classical music concert performance and sequenced using Illumina HiSeq. Differential expression analysis was then performed to compare the microRNA expressions to assess the effect of 2 hours of western classical music-performance on the peripheral blood microRNA transcriptome in professional musicians.

first: Preethy Sasidharan

last: Nair

first: Tuire

last: Kuusi

first: Minna

last: Ahvenainen


title: WGBS from GM23248 (ENCSR625HZA)

type: Methylation profiling by high throughput sequencing

summary:
The libraries contained in this Experiment come from whole genome bisulfite sequencing of primary cell skin fibroblasts from the PGP1 donor.

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


title: Genome-wide BRD4, PolII and p65 occupancy as well as  chromatin modifications in bone marrow derived macrophages from BRD4 conditional KO mice

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

summary: We are reporting here genome wide distribution of BRD4 in bone marrow derived macrophages at steady state level and in reponse to LPS stimulation. In both condition, BRD4 distribution was found to be widespread in intragenic as well as intergenic regions with enrichment specifically near TSS. Characteristically BRD4 signal were highly enriched on enhancers of some active genes and hence were classified as BRD4 rich super-enhancers (>12kb long stretches). Super-enhancers are formed, in some instances  by redistribution of BRD4 on LPS stimulated genes. BRD4 binding well correlated PolII binding at the chromatin acetylated at H3K27,  H3K9 and H4tetraK.  Interestingly many LPS induced BRD4 independent genes, despite BRD4 loss in the KO,  maintained PolII binding at the chromatin enriched with acetylated lysines at H3K27, H3K9 and H4tetraK. Additionally among some BRD4 independent LPS inducible genes we detected stronger p65 enrichment in the KO. In contrast, P65 binding was not detected in BRD4 dependent genes. These observations provided  evidence of plasticity of epigenetic changes in retaining inflammatory reponses in macrophages.

overall_design: Bone marrow derived macrophages were obtained from Brd4Fl/Fl;Ert2-cre and Brd4Fl/Fl mice (WT), Brd4 was deleted from the former by treating bone marrow cells with 4-hydroxytamixfen (KO). For inflammatory stimulus differentiated macrophages were treated with LPS (100ng/ml) for 4 hours.

first: Wenjing

last: Yang

first: Keiko

last: Ozato


title: Exome sequencing data analysis to characterize rare germline copy number variants involved in colorectal cancer predisposition

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Colorectal cancer (CRC) represents the third most common cancer worldwide. Next generation sequencing (NGS) appearance has allowed us to produce huge amount of data and, in order to fully exploit its usage, copy number variants (CVN) detection software have been developed. In this study, we analyze germline DNA whole-exome sequencing (WES) data from 38 families with strong CRC aggregation without alterations in known hereditary genes to detect rare candidate CNVs to CRC predisposition using ExomeDepth and CoNIFER tools. Variants shared between family members were compared to Database of Genomic Variants (DGV) catalogue and our Spanish database. CNVs finally selected were validated and segregation analysis were performed using Comparative Genome Hybridization (CGH). Gene expression arrays and qRT-PCR were conducted in both germline and tumor cDNA to check possible effects at transcription level. Immunohistochemistry (IHC) studies were also carried out. Whith this,  21 candidate CNV corresponding to 16 duplications and 5 deletions were detected by calling tools. After multiple filtering steps, only the duplication in chromosome 1 in family 7 stood out as interesting. Validation by CGH confirmed the duplication and correct family segregation. TTF2, TRIM45, VTCN1 and miR942 are embedded in chromosome 1 duplication. Expression studies pointed to TTF2 and miR942 overexpression in carriers, and tumor IHC showed TTF2 protein overexpression and underexpression of the TMEM158 protein. Also known as RIS1, TMEM158 is a predicted target of miR942 and has been claimed to be a candidate tumor-supressor. All in all, chromosome 1 duplication may correspond to the mutational event involved in CRC predisposition in the carrier family by overexpressing TTF2 and miR942, leading to TMEM158 underexpression.  Keywords: colorectal cancer, next generation sequencing, copy number variant,  duplication, predisposition.

overall_design: Expression profiling in a group of CCR  (n=4) samples respect other CONTROL (n=4). A sample with the gene duplication is included.

first: J

first: S

last: Castellvi-Bel

last: Franch


title: ChIP-seq from GM23338 (ENCSR071NFQ)


title: Next Generation Sequencing (NGS) of expression profile from unstimulated  and LPS stimulated bone marrow derived macrophages from control and BRD4 conditional KO mice

summary:
Method:  mRNA profiles were generated from pair-end sequencing of duplicate samples using Illumina  Hiseq 2000.
Results: Genes with an expression change of more than 2 fold were  considered to be differentially expresed

overall_design: Macrophages are cells belongs to innate immune system, which  response to pathogen by the production of inflammatory proteins those that are effective in both combating pathogen and wound healing. Using microarray approach with BET inhibitors  it was shown that many of the inflammatory response genes were under control of BET proteins.  Purpose of this study was  to assess the effect of BRD4 KO in NGS derived transcriptome profiles of both stimulated and unstimulated macrophages.


title: ChIP-seq from GM12878 (ENCSR212YKD)

summary:
SKIL ChIP-seq on human GM12878

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


title: ChIP-seq from GM12878 (ENCSR041XML)

summary:
SRF ChIP-seq on human GM12878

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


title: ChIP-seq and RNA-seq for RhpR in KB and MM medium

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas syringae, the leading cause of crop diseases world-wide, uses type III secretion system (T3SS) to invade host plants. Our previous studies demonstrate that two-component system RhpRS enable P. syringae to coordinate T3SS gene expression, which is dependent on the phosphorylation state of RhpR in different environmental conditions. Homologs of RhpRS are distributed in a wide range of bacterial species, indicating a general regulatory mechanism. However, it remains elusive that how RhpRS relies on external signals and phosphorylation state to exercise its regulatory functions. To this end, we performed ChIP-seq assays to identify specific binding sites of RhpR and RhpRD70A in either King’s B (KB, T3SS-inhibiting medium) or minimal medium (MM, T3SS-inducing medium). Through data analysis, we identified 125 KB-dependent binding sites and 188 phosphorylation-dependent binding sites of RhpR. In KB, RhpR directly positively regulated cytochrome c550 production (via ccmA) and alcohol dehydrogenase activity (via adhB), but negatively regulated anthranilate synthase activity (via trpG) and protease activity (via hemB). Besides, phosphorylated RhpR (RhpR-P) directly negatively regulated T3SS (via hrpR and hopR1), swimming motility (via flhA), c-di-GMP level (via PSPPH_2590) and biofilm formation (via algD), while positively regulated twitching motility (via fimA) and lipopolysaccharide production (via PSPPH_2653). Our RNA-seq analyses newly identified 474 and 840 genes that regulated by RhpR in KB and MM respectively. Collectively, the present study revealed that rich nutrient condition allows RhpR to directly regulate the multiple metabolic pathways of P. syringae, while phosphorylation enables RhpR to specifically control virulence and cell envelope. RhpRS governs both virulence and multiple metabolic pathways by tuning its phosphorylation and sensing environmental signals in KB, respectively.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design: ChIP-seq for RhpR and RhpR-D70A in KB and MM medium; RNA-seq for RhpS and RhpRS in KB and MM medium

last: Deng


title: Evidence for HOXC6 as a potential molecular marker for non-small cell lung cancer

status: Public on Feb 20 2019

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

country: China

institute: The Affiliated Hospital of Southwest Medical University

summary: HOXC6 is a transcription factor that regulates cell differentiation during embryonic development which is highly expressed in NSCLC, and it may enhance lung cancer progression by regulating the expression of pro-tumorigenic genes involved in proliferation, migration, and invasion. Our study highlighted the oncogenic potential of HOXC6, and suggests that it may be a novel biomarker for the diagnosis and treatment of NSCLC.

overall_design: The expression and protein levels of HOXC6 were assessed in 30 pairs of NSCLC tissue samples by qRT-PCR and immunohistochemistry, respectively. HOXC6 was transfected into the NSCLC cell lines A549 and PC9, and used to investigate its effect on proliferation, migration, and invasion using CFSE, wound healing, and Matrigel invasion assays. Next-generation sequencing with 3 independent replicates was also used to identify downstream targets of HOXC6 and to gain insights into the molecular mechanisms underlying its biological function.

first: Yingcheng

first: Xiaoping

last: Tang

first: Xueqin

last: Song

first: Yong

last: Cao

first: Li

first: Xu

last: Liu

first: Yan

last: Li

first: Feng

last: Chen

first: Haisu

last: Wan


title: Transcriptional analysis between Streptomyces clavuligerus::pIB139 and S. clavuligerus::pimM

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

institute: University of León

summary:
The objective was to analyze the differential expression between the control strain and S. clavuligerus::pimM.
Experiment type  Expression profiling by array

overall_design: Six experimental conditions were assayed, two strains (Streptomyces clavuligerus::pIB139, S. clavuligerus::pimM) in three culture times (84 h, 90 h and 96 h). Two biological replicates for each condition.

first: Y

last: Martínez-Burgo

first: A

last: Rodríguez-Gracía

first: P

last: Liras


title: Integrated analysis of lncRNA and mRNA repertoires in Marek's disease infected spleens identifies genes relevant to resistance

status: Public on Feb 18 2019

city: Cincinnati

first: Lei

middle: Frank

last: Huang

state: Ohio

address: 2600 Clifton Ave

institute: Uiversity of Cincinnati

summary:
Purpose: Marek's disease virus (MDV) is an oncogenic herpesvirus that can induce T-cell lymphoma. Long noncoding RNA (lncRNA) strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without any lesion after MDV infection, and five noninfected spleens (NS) from chickens, to explore the underlying mechanism of host resistance to Marek's disease (MD).
Results: By using precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed mRNAs, putative lncRNAs and known lncRNAs were profiled. Some previously reported MD resistance candidate genes, such as CTLA4, HDAC9 and CD72, were also found in our differentially expressed genes list. Moreover, we found that several intergroup specifically deregulated genes were involved in important biological processes and pathways, including B cell activation and Wnt signaling pathway. We conducted co-expression network using WGCNA and identified several hub genes that may play pivotal roles in MD resistance and tumorigenesis, e.g. CTLA4, SWAP70, CXCL12 and JCHAIN. According to the expression relationship between lncRNAs and MD resistance candidate mRNAs, five deregulated lncRNAs may implicate the chicken immunity by directly or indirectly regulating those hub genes.
Conclusions: We profiled both lncRNA and mRNA expression patterns in MDV-infected chicken spleens. Expression variations of intergroup specifically deregulated genes engaged in important immune process likely contributed to robust immune system in the survivors. Some oncogenesis or MD resistance related genes deregulated between groups, like CTLA4, HDAC9 and CD72 were found. Co-expression network analysis manifested that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their impact on expression of CTLA4, SWAP70 and some other genes that are critical in many important biological processes, such as B lymphocyte proliferation and activation.

overall_design: Examination of splenic lncRNAs and mRNAs repertoires of 17 chickens with different Marek's disease resistance and identification of Marek's disease resistance candidate lncRNAs.

first: Ling

last: Lian

first: Zhen

last: You


title: Anti-cancer drugs curaxins target the 3D genome organization

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

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

overall_design: Refer to individual Series


title: Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: Cohesin subunits, the Nipped-B cohesin loader, the MED1 and MED30 subunits of the Mediator complex, and the Fs(1)h BET domain protein were mapped by ChIP-seq in ML-DmBG3-c2 cells and their effects on each other's association with promoters, enhancers, Polycomb Response Elements, and DNA replication origins were measured. DNA replication in early S phase was measured by ChIP-seq and correlated with functional element occupancy by cohesin.

overall_design: Occupancy of functional features by different cohesin subunits and Nipped-B were compared, the effects on cohesin subunit and Nipped-B occupancy when different cohesin subunits and  MED30 were depleted by RNAi relative to mock-treated controls were measured. The effects on cohesin subunit and Nipped-B occupancy when Fs(1)h chromosome binding was inhibited by the JQ1 inhibitor were measured relative to mock-treated controls.


title: Anti-cancer drugs curaxins target the 3D genome organization [ChIP-seq]

summary: We have recently discovered a class of anti-cancer agents, curaxins, which suppress transcription of oncogenes. Here we demonstrate that curaxins preferentially downregulate expression of genes controlled by enhancers and super-enhancers via interrupting enhancer/promoter spatial communication. Our observations made both on a model of enhancer-regulated transcription of chromatinized template and on cultured cancer cells allow classifying curaxins as a novel type of epigenetic drugs that target the 3D genome organization.

overall_design:
Processed and raw ChIP-seq data for control and CBL0137-treated HT1080 cells.
Please note that [1] each bigwig processed data file was generated from both ChIP and input sample data, and is linked to the corresponding ChIP sample records [2] the bed files were generated from all 8 sample data.

first: Sergey

last: Razin


title: Transcriptomic profile of Sbash and Crossroads actinobacteriophages during various stages of growth.

city: Pittsburgh

first: Rebekah

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: The goal of this sequencing project was to measure transcription levels of Sbash and Crossroads actinobacteriophages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes), in order to study which genes contribute to superinfection exclusion.

sample_organism:
Mycobacterium phage Crossroads
Mycobacterium phage Sbash

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit during lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes) of phages Sbash and Crossroads.

first: Graham

last: Hatfull

first: Gabrielle

last: Gentile

first: Daniel

middle: A

last: Russell

first: Rebecca

last: Garlena


title: Anti-cancer drugs curaxins target the 3D genome organization [HiC]

overall_design: Processed and raw HiC data for control and CBL0137-treated HT1080 cells.


title: RNA-seq, ChIP-seq and ATAC-seq analysis of MKL1 blocked cells during reprogramming

city: New Haven

first: Xiao

last: Hu

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

summary: Actins and regulators of actin dynamics generate contractile forces providing major mechanical and structural support for the cell. Whether and how they actively participate in cell fate control is not clear. Here, we report the actin responsive transcription factor complex MKL1/SRF, the major transcriptional regulator of large numbers of actin cytoskeletal genes, as an important regulator of genomic accessibility and cell fate outcome. Somatic cells with weaker MKL1/SRF activity progress toward pluripotency efficiently while sustained MKL1/SRF activity at a level seen in typical fibroblasts is sufficient to stall cells on their trajectory toward pluripotency. This altered cell fate outcome is associated with an overactive actin cytoskeleton, which connects to chromatin via the LINC complex, preventing its conversion into a relaxed, open conformation that allows sufficient accessibility to pluripotency-inducing transcription factors. Interfering with actin polymerization at appropriate times promotes pluripotency induction. Thus, we reveal a previously unappreciated aspect of cell fate control exerted by the actin based cytoskeletal system.

overall_design: Transcriptome of reprogramming cells at day 6 or day 25 with or without constitutively active MKL1 (caMKL1) were compared. Cells of both conditions at day 25 were also analyzed for Oct4 and SRF binding by ChIP-seq. Cells of both conditions at day 25, as well as starting MEFs were analyzed for histone modifications H3K4me3, H3K27ac and H3K27me3. WT ES cells with or without caMKL1 expression, and SRFf/f and SRFdelta/delta iPS cells were compared for chromatin accessibility by ATAC-seq analysis.


title: Transcriptome of human keratinocytes with or without HPV16 oncogene expression

city: Heidelberg

first: Martina

last: Niebler

address: Im Neuenheimer Feld 242

country: Germany

institute: German Cancer Research Center

summary: We used freshly established immortalized human keratinocytes with a well-defined HPV16 E6 E7 expression cassette to get a more complete and less biased overview about global changes induced by HPV16 using RNA-seq. We identified novel factors regulated by HPV oncogenes that could serve an essential role in cancer development.

overall_design: mRNA profiles of human Keratinocytes transduced with HPV16-E6/E7 constructs and empty vectors in triplicates, sequenced with Illumina Hiseq 2000.


title: cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

summary: We present cisTopic, a probabilistic framework to simultaneously discover co-accessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). On a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain, and transcription-factor perturbation dynamics, we demonstrate that topic modelling can be exploited for a robust identification of cell types, enhancers, and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity within cell populations.

overall_design:
Time series scATAC-seq (Fluidigm C1) and bulk OmniATAC-seq of SOX10 knockdown-induced phenotype switching in two melanoma cell lines.
ChIP-seq of H3K27Ac on four melanoma cell lines.

first: C

last: Bravo Gonzalez Blas

first: L

last: Minnoye

first: S


title: Developmental regulation of heterochromatin establishment at the maternal to zygotic transition

city: Athens

first: Mary

last: Goll

state: Select State

address: 120 E. Green Street

department: Genetics

institute: University of Georgia

summary: Heterochromatin has important functions in the organization of nuclear structure, the maintenance of genome integrity, and the regulation of gene expression programs1-3. Here, we demonstrate that the genome of the early zebrafish embryo is packaged in an atypical chromatin state that lacks features characteristic of heterochromatin. The heterochromatic histone modification, histone H3 lysine 9 trimethyl (H3K9me3), is undetectable in embryonic chromatin and embryonic nuclei are devoid of condensed chromatin prior to activation of the zygotic genome. The BAF complex catalytic subunit Smarca2 is a guardian of this unique chromatin state, and miR-430 mediated degradation of maternal smarca2 RNA is required for heterochromatin establishment at the maternal to zygotic transition. Our results reveal a period of profound chromatin reorganization in the early zebrafish embryo and identify Smarca2 as an essential regulator of heterochromatin establishment during early development.

overall_design: Zebrafish embryo samples collected at 2.5, 4.5, and 6 hours post fertilization. Cells lysed and subjected to chromatin immunoprecipitation. 20 total samples, two replicates, Scramble Morpholino control

first: Kathrin

last: Laue

first: Srivarsha

last: Rajshekar

first: Abigail

last: Courtney

first: Zachary

last: Lewis


title: Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

institute: Guizhou Normal University

summary: Rosa roxburghii Tratt belongs to the Rosaceae family, and the fruit is flavorful, economic, and high nutritious, providing health benefits. MYB proteins play key roles in R. roxburghii’ development and fruit quality. However, the available genomic and transcriptomic information are extremely deficient. Here, a normalized cDNA library was constructed using five tissues, stem, leaf, flower, young fruit, and mature fruit, with three repetitions, and sequenced using the Illumina HiSeq 3000 platform. De novo assembly was performed, and 470.66 million clean reads were obtained. In total, 63,727 unigenes, with an average GC content of 42.08%, were determined and 59,358 were annotated. In addition, 9,354 unigenes were assigned the Gene Ontology category, and 20,202 unigenes were assigned to 25 Eukaryotic Ortholog Groups. Additionally, 19,507 unigenes were classified into 140 pathways of the Kyoto Encyclopedia of Genes and Genomes database. Using the transcriptome, 163 unigenes associated with MYB were detected. Among these genes, there were total 75 genes which strikingly expressed in various tissues, including 10 R1 MYB, 42 R2R3 MYB, 1 R1R2R3 MYB, 3 MYB and 19 atypical MYB-like proteins. The expression levels of 12 MYB genes randomly selected for qRT-PCR analysis were consistent with the RNA-seq results. A total of 37,545 microsatellites were detected, with an average EST-SSR frequency of 0.59 (37,545/63,727). This transcriptome data will be valuable for identifying genes of interest and studying their expression and evolution.

overall_design: Five tissues, including stem, leaf, flower, young fruit (50 days after flowering) and mature fruit (120 days after flowering) from wild Rosa roxburghii Tratt were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with three replicates were sequenced via Illumina HiSeqTM 3000.

first: Xiaolong

last: Huang

first: Lisheng

last: Zhai

first: Zhengting

last: Yang

first: Yin

last: Yi


title: Transcriptomic analyses of a cnidarian colonized by native or non-native Symbiodinium species

status: Public on Feb 27 2019

city: Townsville

first: David

middle: John

last: Miller

state: Queensland

address: 1 James Cook Drive, Douglas

department: Molecular and Cell Biology

country: Australia

institute: James Cook University

summary: We report the transcriptomic analyses of a tropical coralliomrpharian, Ricordea yuma, following the establishment of symbiosis with either native symbiont or non-native symbiont. We examined the expression profiles, and results showed distinct metabolic consequences for the cnidarian host when they host different symbionts.

overall_design:
Examination of gene expression profiles in a cnidarian host colonized with a native or non-native Symbiodinium speices

Group C was colonized with native Symbiodinium species (Symbiodinium goreaui)
Group D was with the non-native Symbiodinium (Symbiodinium trenchii)

first: Mei-Fang

last: Lin


title: Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties

city: Baltimore

first: Wenbing

last: Xie

address: 1650 Orleans Street, CRB1, Room 530

department: Department of Oncology

institute: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine

type:
Expression profiling by array
Methylation profiling by array


title: Differential expression in wild-type and mutant neurofibroma and MPNST cell lines

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Using RNA-seq we characterized gene expression changes occuring upon knockout of EZH2, EZH1, EZH1+EZH2 or SUZ12 in a neurofibroma cell line. We also investigated the transcriptional consequences of EZH1+EZH2 double knockout in a SUZ12-mutant MPNST cell line.

overall_design: Examination of transcript abundance in wild-type and mutant ipNF05.5 or 88.14 cells. Two biological replicates were performed for wild-type and mutant ipNF05.5 cell lines. Three biological replicates were performed for wild-type and mutant 88.14 cell lines.

first: Michel

last: Wassef

first: Armelle

last: Luscan

first: Dina

last: Zielinski

first: Setareh

last: Aflaki

first: Pascal

last: Jansen

first: Aude

last: Battistella

first: Carole

last: Kersouani

first: Margaret

last: Wallace

last: Vermeulen

last: Vidaud

first: Eric

last: Pasmant

first: Raphaël

last: Margueron


title: Molecular features of PDGFRa+ mesenchymal progenitors and progeny in the mammary gland

city: Toronto

first: Julie

last: Livingstone

state: Ontario

address: 661 University Avenue

country: Canada

institute: Ontario Institute for Cancer Research

summary: We performed RNA-seq on FACS-purified GFP+ and tdTomato+ stromal and luminal mammary populations from untreated and hormone stimulated adult PdgfraCreR26mTmG lineage tracing mice. Unsupervised hierarchical clustering of the top 20% most variable genes resulted in clustering of GFP+ and tdTomato+ stromal subsets into distinct groups. Distance-analysis of DEGs between GFP+ and tdTomato+ fractions in stromal and luminal lineages showed GFP+ stromal cells to have more similar transcriptomes to luminal cells than to tdTomato+ stroma. DEGs between GFP+ and tdTomato+ stromal subsets were enriched in pathways regulating Lysosomes, Focal adhesion, ECM-receptor interaction, Actin cytoskeleton and PI3K-Akt signaling. Hormone stimulation perturbed multiple cancer-associated pathways, as well as Endocytosis, Focal Adhesion and the Phosphatidylinositol System – all important in cell migration.

overall_design: RNA-seq analysis of distinct mammary stromal subsets

first: Purna

last: Joshi

first: Katayoon

last: Kasaian

first: Rama

last: Khokha

first: Paul

middle: C

last: Boutros


title: RNA-seq analysis of gene regulations by the combination treatment of crizotinib plus cisplatin in established MCA205 tumors

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Immunogenic cell death (ICD) converts dying cancer cells into a therapeutic vaccine and stimulates antitumor immune responses. Here we unravel the results of an unbiased screen identifying high-dose (10 µM) crizotinib as an ICD-inducing tyrosine kinase inhibitor that has exceptional antineoplastic activity when combined with non-ICD inducing chemotherapeutics like cisplatin. The combination of cisplatin and high-dose crizotinib induces ICD in non-small cell lung carcinoma (NSCLC) cells and effectively controls the growth of distinct (transplantable, carcinogen- or oncogene induced) orthotopic NSCLC models. These anticancer effects are linked to increased T lymphocyte infiltration and are abolished by T cell depletion or interferon-g neutralization. Crizotinib plus cisplatin leads to an increase in the expression of PD-1 and PD-L1 in tumors, coupled to a strong sensitization of NSCLC to immunotherapy with PD-1 antibodies. Hence, a sequential combination treatment consisting in conventional chemotherapy together with crizotinib, followed by immune checkpoint blockade may be active against NSCLC.

overall_design: Two groups: 4 replicats of control samples; 4 replicats of cisplatin plus crizotinib treated samples

first: Peng

last: Liu

first: Liwei

last: Zhao

first: Oliver

last: Kepp

first: Guido

last: Kroemer


title: A serum miRNA classifier diagnoses bone and soft tissue sarcomas across various histological subtypes

status: Public on Feb 14 2019

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

summary: A serum miRNA combination could be a powerful classifier for the detection of patients with bone and soft tissue sarcomas.

overall_design: Total 892 patients with bone and soft tissue tumors, including malignant, intermediate, and benign tumors, were included. Furthermore, serum samples of 275 healthy controls and 240 patients with other cancers were used as references for the analyses.

first: Naofumi

last: Asano

first: Juntaro

last: Matsuzaki

first: Makiko

last: Ichikawa

first: Junpei

last: Kawauchi

first: Satoko

last: Takizawa

first: Hiromi

last: Sakamoto

first: Hideo

last: Morioka

first: Morio

last: Matsumoto

first: Masaya

last: Nakamura

first: Akihiko

last: Yoshida

first: Eisuke

last: Kobayashi

first: Yoshikazu

last: Tanzawa

first: Tadashi

last: Kondo

first: Naoto

last: Tsuchiya

first: Akira

last: Kawai

first: Takahiro

last: Ochiya


title: Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (ATAC-seq)

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Silencing of the somatic cell-type specific gene expression programs is a critical yet poorly understood step in nuclear reprogramming. To uncover chromatin-related pathways important for maintaining cell identity, we carried out a reprogramming screen using inhibitors of chromatin factors. Here we identify two independent acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators EP300 and CBP as potent enhancers of reprogramming. EP300/CBP bromodomain inhibition is critical during early stages of reprogramming, significantly accelerates the emergence of iPSCs and, when combined with Dot1L inhibition, enables efficient derivation of human iPSCs with Oct4 and Sox2 alone. In contrast, complete inhibition of catalytic acetyl-transferase activity of EP300/CBP prevents reprogramming. Genome-wide expression analyses indicate that EP300/CBP bromodomain inhibition diminishes the expression of somatic-specific genes without affecting the induction of pluripotency regulators. Through expression analyses, we identify the master mesenchymal transcription factor PRRX1 as a functionally important target in reprogramming that is downregulated upon EP300/CBP bromodomain inhibition. Collectively, our data uncover a role for bromodomain-mediated interactions of EP300/CBP in sustaining cell type specific gene expression programs and maintaining somatic cell identity

overall_design: Examination of open chromatin in iPSC cells. Cells were grown in culture media and then incubated with DMSO or CBP30 compounds for 24 hours.

middle: P

first: Tamer

middle: T

last: Onder


title: Inhibition of YAP in human HCC cells

status: Public on Feb 13 2019

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In vertebrates, the evolutionary conserved Hippo pathway fine-tunes organ size under physiological conditions such as tissue regeneration through the transcriptional regulation of pro-proliferative and anti-apoptotic genes. Here we want to identify downstream effectors of YAP, which is the most important transcriptional activator of this pathway.

overall_design: Nonsense/Scrambled siRNA-transfected and gene-specific siRNAs (YAP1, YAP2) were transently transfected in HepG2 cells (20 nM each). Total mRNA was extracted 24 hours after transfection.

first: Kai

last: Breuhahn


title: YPR2 is a light dependent regulator of carbon and secondary metabolism in Trichoderma reesei

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: We show that YPR2, a transcription factor associated with the SOR cluster, has functions beyond regulation of this cluster in carbon and secondary metabolism and exerts its major function in darkness. It impacts production of secondary metabolites, particularly of Alamethicin and Orsellinic acid.

overall_design: Strains of this study were grown on Mandels Andreotti Minimal Medium with 1 % w/v microcrystalline cellulose as  carbon source in constant light or constant darkness

first: Eva

last: Hitzenhammer


title: Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming

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

overall_design: Refer to individual Series


title: FoxK1/2 – New Components in Insulin Regulation of Cellular and Mitochondrial Metabolism

city: Boston

first: Alfred

last: Ramirez

state: MA

address: One Joslin Place

institute: Joslin Diabetes Center

summary: A major target of insulin signaling is the FoxO family of Forkhead transcription factors, which translocate from the nucleus to the cytoplasm following insulin-stimulated phosphorylation. Here we show that the Forkhead transcription factors FoxK1 and FoxK2 are also downstream targets of insulin action, but that following insulin stimulation, they translocate from the cytoplasm to nucleus, reciprocal to the translocation of FoxO1. FoxK1/FoxK2 translocation to the nucleus is dependent on the Akt-mTOR pathway, while its localization to the cytoplasm in the basal state is dependent on GSK3. Knockdown of FoxK1 and FoxK2 in liver cells results in upregulation of genes related to apoptosis and down-regulation of genes involved in cell cycle and lipid metabolism. This is associated with decreased cell proliferation and altered mitochondrial fatty acid metabolism. Thus, FoxK1/K2 are reciprocally regulated to FoxO1 following insulin stimulation and play a novel role in the control of apoptosis, metabolism and mitochondrial function.

overall_design: RNA-seq of Control, FOXK1 KD, FOXK2 KD, and Double FoxK1/2 knockdown AML12 cell lines with and without insulin stimulation.

first: Masaji

last: Sakaguchi

first: C

last: Kahn


title: ChIP-seq analysis of transcription factor AtrR binding across the Aspergillus fumigatus genome

status: Public on Feb 11 2019

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

summary: To determine the genomic binding sites for the Aspergillus fumigatus transcription factor AtrR, we utilized three different strains.  One was the wild-type AfS35 which contains a wild-type copy of atrR but lacks any HA tag.  The other two are both derived from AfS35 but contain a 3X HA tag replacing the stop codon of atrR.  These strains are SPF89 and SPF112, respectively.  SPF89 uses the wild-type atrR promoter to drive expression of the epitope-tagged allele while SPF112 uses the much strong hspA promoter to drive production of the same protein.

overall_design: ChIP-seq using AtrR-3X HA expressed from either the wild-type or strong hspA promoter

first: Sanjoy

last: Paul

first: Mark

last: Stamnes


title: RNA-seq analysis of alleles of the atrR transcription factor-encoding gene in Aspergillus fumigatus

summary: Determine the transcriptomic response of Aspergillus fumigatus strains to different alleles of atrR

overall_design: RNA-seq in strains containing a wild-type version of atrR, a null allele or two different hyperactive mutants (atrR-3X HA or hspA-atrR)


title: Reprogramming of meiotic chromatin architecture during primate spermatogenesis

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

summary: Chromatin organization undergoes drastic reprogramming during gametogenesis . However, the three-dimensional chromatin structure and its reprogramming remain largely unknown, with even less known for primates. Here, by using a low-input Hi-C method we developed recently, we examined re-organization of 3D chromatin architecture during spermatogenesis in rhesus monkey (Macaca mulatta). Interestingly, we found that topologically associating domains (TADs) are partially dissolved in spermatogonia and are further depleted at the pachytene stage, before they gradually become consolidated in round spermatids and mature sperm. Strikingly, in local regions, pachytene chromatin is uniquely characterized by highly refined compartments that alternate between transcribing regions (Refined-A) and non-transcribed regions (Refined-B). Refined A/B occurs genomewide except for the X chromosome, which is inactivated at this stage. Interestingly, such chromatin organization remains intact upon transcription inhibition but is disrupted in spermatocytes deficient in SYCP2, a core component of synaptonemal complex. Strikingly, this is accompanied by the restoration of TADs in these mutant cells, suggesting that synaptonemal complex may restrict TADs and permit the emergence of strong local compartments. Taken together, these data reveal extensive reprogramming of higher-order meiotic chromatin architecture during mammalian gametogenesis.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: Rhesus monkey spermatogonia (SPA), pachytene spermatocytes (PAC), round spermatids (RS) and sperm were obtained, together with fibroblast as control. Mouse PAC were treated with amantin to test the effect of trancription inhibition. Sycp2 KO or Top6bl KO mouse PAC-like cells were used to explore the contribution of synaptonemal complex towards higher order chromatin organization. HiC, STEM-seq and RNA-seq were performed in these cells at various stages during spermatogenesis.

first: Yao

last: Wang

first: Yu

last: Zhang

first: Zhenhai

last: Du

first: Hanben

first: Xin

last: Wu


title: ChIP-Seq analysis for GFI1B, Beta-Catenin, LSD1 and histone marks in response to Wnt treatment

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

summary: Gfi1b is a DNA binding transcriptional repressor highly expressed in hematopoietic stem cells (HSCs) and megakaryocytes (MKs). Gfi1b deficiency leads to the expansion of both cell types and abrogates the ability of MKs to respond to integrin substrates with spreading and movement. Here we show that Gfi1b is present in complexes with ²-catenin and its co-factors Pontin52, CHD8, TLE3 and CtBP1 and can regulate Wnt/²-catenin dependent gene expression. In reporter assays, Gfi1b can activate TCF-dependent transcription and this activation is enhanced upon treatment with Wnt3a. This requires the interaction between Gfi1b and lysine demethylase 1 (LSD1), but is independent of the ability of Gfi1b to bind DNA. This suggests that a tripartite ²-catenin/Gfi1b/LSD1 complex exists that regulates Wnt/²-catenin target genes. Consistently, expression of many canonical Wnt/²-catenin target genes is deregulated in Gfi1b-deficient cells and many of these target genes are co-occupied by Gfi1b, ²-catenin and LSD1 at promoter sites. When Gfi1b deficient cells were treated with Wnt3a, their normal cellularity was restored and Gfi1b-deficient MKs regained their ability to spread on integrin substrates. This suggests that Gfi1b controls both the cellularity and functional integrity of HSCs and MKs by regulating Wnt/²-catenin signaling pathway.

overall_design: Chromatin immunoprecipitation was carried out in K562 cells for GFI1B, Beta-Catenin, LSD1, H3, H3K4me1, H3K9me2. ChIP was carried in both the presence and absence of Wnt3a treatment

first: Peiman

last: Shooshtarizadeh

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: Role of cohesin in cancer development

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

summary: The aim of this project is to understand the role of cohesin in both genome instability and colorectal cancer development

overall_design: 11 samples, 3 control, 4 wild type, 4 mutated samples (biological replicates). SRP142391 and PRJNA451395

first: Antonio

last: Musio


title: Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins

status: Public on Feb 08 2019

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

institute: Universitat Pompeu Fabra

summary: To study the role of the exonuclease Xrn1 in translational control, we performed ribosome profiling and RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in translational control. Therefore, we could overcome experimental limitations associated to stable deletion mutants.

overall_design: mRNA and ribosome footprints were obtained as described in (Ingolia, 2009) from BY25598 cells (Nishimura and Kanemaki, 2014) modified to express an Xrn1 protein tagged with an auxin inducible degron (AID). Libraries were obtained from cells treated with auxin for 30 minutes (t30) and compared from libraries from untreated controls (t0). After 30 minutes of treatment, Xrn1 protein was reduced to less than 10%. For the Xrn1-D208A mutant, a BY4741 background was used. Wild-type and mutant strains were grown to logarithmic phase and collected at approximately 0.5 OD.

last: Diez

first: Bernat

last: Blasco-Moreno

first: Leire

last: de Campos-Mata

first: René

last: Böttcher

first: José

last: García-Martínez

first: Danny

last: Nedialkova

first: Jennifer

last: Jungfleisch

first: Baldomero

last: Oliva

first: Mordechai

last: Choder

first: Sebastian

last: Leidel

last: Pérez-Ortín

first: Shiladitya

last: Chattopadhyay

first: Maria-Eugenia

last: Gas


title: Interplay between mitochondria and diet mediates pathogen and stress resistance in C. elegans.

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

country: USA

institute: Rice University

summary: To understand the impact of a diet on host health, we performed a number of assays with C. elegans reared on OP50 or HT115 E. coli. We observed that HT115 provided a substantial increase in resistance to Liquid Killing and abiotic stresses (e.g., heat shock, oxidative stress). This phenomenon was independent of the worms’ innate immune system.  In the absence of any other obvious candidates, we turned to microarray transcriptional profiling to gain an unbiased picture of the differences that result from feeding C. elegans with HT115 instead of OP50. To our surprise, there was a relatively small number of genes differentially expressed between worms fed OP50 and HT115. Amongst them were several mitochondrially-associated genes, suggesting that the relevant difference may involve this organelle. Using a variety of approaches, we determined that worms fed HT115 exhibit increased mitochondrial health than their OP50 counterparts. Furthermore, supplementation of growing OP50 with cobalamin recapitulated virtually all of the HT115 phenotypes.

overall_design: There are 6 samples total that comprise three biological replicates of glp-4 young adult animals grown on OP50 or HT115 E. coli


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [TransplantRNA-SEQ]

status: Public on Feb 07 2019

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

summary: Investigation of the transcriptional consequences of Bcor loss in bone marrow transplant

overall_design: Whole bone marrow from BcorΔE9-10 mice were transplanted to PTPRCA recipients. After 20 weeks myeloid progenitor cells were sorted and 3' RNA sequencing performed.

first: Stephin

last: Vervoort


title: Identification of small noncoding RNAs as sperm quality biomarkers for in vitro fertilization

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: We investigated differentially expressed sncRNAs in human sperm as candidate markers for evaluating sperm quality during IVF. We demonstrated that differentially expressed tsRNAs, rsRNAs and miRNAs are linked to sperm quality according to embryo quality, even though these sperm samples were all considered normal by the traditional semen-parameter assessment. Therefore, the sncRNAs, especially tsRNAs and rsRNAs, may be potential clinical biomarkers for the assessment of sperm quality in IVF.

overall_design: We performed small noncoding RNA profiling for 87 human sperm samples by deep sequencing

first: Minmin

last: Hua

first: Ying

last: Chen

first: Fengjuan

last: Zhang

first: Beiying

last: Xu

first: Suying

first: Guowu

first: Huijuan

last: Shi

first: Ligang

last: Wu


title: Transcriptomic profile of CarolAnn, Blueberry, Utz and Kita actinobacteriophages during various stages of growth.

city: Pittsburgh

first: Rebekah

last: Dedrick

address: 4249 Fifth Ave

institute: University of Pittsburgh

summary: The goal of this sequencing project was to measure transcription levels of CarolAnn, Blueberry, Utz and Kita actinobacteriophages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours), in order to study which genes contribute to superinfection exclusion.

sample_organism:
Gordonia phage Kita
Gordonia phage Blueberry
Gordonia phage Utz
Gordonia phage CarolAnn

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit during lysogeny, early infection (30 minutes), and late infection (2 hours ) of phages Kita and CarolAnn.

first: Graham

middle: F

last: Hatfull

first: Matthew

last: Montgomery


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis


title: Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (ChIP-seq II)

first: Adam

last: Cribbs

overall_design:
Examination of H3K27ac, H3K18ac, H3K4me1 and H3K4me3 histone modifications in iPSC cells.
Antibodies used:

H3K27ac: Active Motif 39133
H3K18ac: Abcam ab1191
H3K4me1: Diagenode C15410194
H3K4me3: Merck Millipore 07-473

For both ChIP and RNA-Seq experiments, cells were treated with compounds for 5 days. Followings are the final concentrations used:

SGC-CBP30: 0.5 µM
I-CBP112: 1 µM
A485: 1 µM

first: Tamer

last: Onder


title: Reversible Histone Glycation Drives Disease-Associated Changes in Chromatin Architecture

first: Yael

last: David

address: 1275 York Ave

department: Chemical Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Glycation is a covalent protein modification that accumulates in the cellular environment. Histone proteins are particularly susceptible to glycation due to their extremely long half-lives and nucleophilic disordered tails. Here, we performed ATAC-seq on 293T cells cultured in the presence or absence of 0.5mM methylglioxal, a reactive glycolytic intermediate, for 12 hours. We demonstrate that methylglioxal treatment is associated with changes in histone occupancy and chromatin architecture globally.

overall_design: 293T cells were cultured in the presence or absence of 0.5 mM MGO for 12 hours. ATAC-seq libraries were generated from 50,000 cells from each condition.

first: Nathaniel

last: Omans


title: Tanycyte-independent control of hypothalamic leptin signaling

status: Public on Feb 19 2019

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

summary:
Purpose: 1. Bulk-RNA-Seq was performed to identify tancytye-enriched genes. 2. scRNA-Seq was performed to profile hypothalamic cells following leptin treatment
Conclusions: Leptin receptor expression in tanycytes is either absent or undetectably low, that tanycytes do not directly regulate hypothalamic leptin signaling, and that leptin regulates gene expression in diverse hypothalamic cell types through both direct and indirect mechanisms.

overall_design:
Methods 1 (Bulk-RNA-Seq). Flow-sorted RNA samples from Rax-EGFP BAC transgenic mice were sent to the Deep Sequencing and Microarray Core (Johns Hopkins University) for library preparation and sequencing. Briefly, polyadenylated RNA was purified from the total RNA samples using Oligo dT conjugated magnetic beads and prepared for single-end sequencing according to the Illumina TruSeq RNA Sample Preparation Kit v2 (# RS-122-2001, Illumina). The libraries were sequenced for paired-end 75 cycles using the TruSeq SBS kit on NextSeq 500 system. Filtered sequencing reads were mapped to the mouse reference genome (mm10) using TopHat. FPKM value for each gene was estimated using Cufflink.
Methods 2 (scRNA-Seq). Mice brain coronal slices (aCSF- or leptin-infused) were dissociated using Act-Seq protocol and re-suspended cells were loaded into V2 10x Genomics Chromium Single Cell system, and libraries were sequenced on Illumina NextSeq with ~150 million reads per library. Sequencing results were processed 10x Genomics pipeline. Seurat V2 was used to perform downstream analysis following the standard pipeline using cells with more than 500 genes and 1000 UMI counts.

first: Sooyeon

last: Yoo

first: David

last: Cha

first: Dong

middle: W

first: Thanh

last: Hoang

first: Seth

last: Blackshaw


title: RNA-seq of iPSC-ECs treated under normoglycemic and hyperglycemic conditions with and without MDL-28170 treatment

status: Public on Feb 15 2019

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

summary: Two healthy iPSC lines were differentiated into ECs. iPSC-ECs were then treated under normoglycemic (5.5mM glucose) or hyperglycemic (33mM glucose) conditions with and without MDL-28170 (2.5 uM) for 72 hours.

overall_design: RNA-seq of iPSC-ECs under normoglycemia or hyperglycemia; with and without calpain inhibition (MDL-28170) over a period of 72 hours.

first: Sang-Ging

last: Ong


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [20wChiP-seq]

first: Madison

last: Kelly

summary: Investigation of the epigenetic profile induced by Bcor loss

overall_design: BcorΔE9-10 or relevant WT control mice were aged for 20 weeks, then myeloid progenitor cells were isolated and ChiP-sequencing was performed.

middle: J

first: Stephin

last: Vervoort


title: The pluripotency factor NANOG controls primitive hematopoiesis and directly regulates Tal1.

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

summary: Progenitors of the first hematopoietic cells in the mouse arise in the early embryo from Brachyury-positive multipotent cells in the posterior-proximal region of the epiblast, but the mechanisms that specify primitive blood cells are still largely unknown. Pluripotency factors maintain uncommitted cells of the blastocyst and embryonic stem cells in the pluripotent state. However, little is known about the role played by these factors during later development, despite their being expressed in the postimplantation epiblast. Using a dual transgene system for controlled expression at postimplantation stages, we found that Nanog blocks primitive hematopoiesis in the gastrulating embryo, resulting in a loss of red blood cells and downregulation of erythropoietic genes. Accordingly, Nanog deficient embryonic stem cells are prone to erythropoietic differentiation. Moreover, Nanog expression in adults prevents the maturation of erythroid cells. By analysis of previous data for NANOG binding during stem cell differentiation and CRISPR/Cas9 genome editing, we found that Tal1 is a direct NANOG target. Our results show that Nanog regulates primitive hematopoiesis by directly repressing critical erythroid lineage specifiers.

overall_design: MEPs mRNA profiles of adult mice Nanog-tg treated and untreated with doxycycline were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Julio

last: Sainz de Aja


title: Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (RNA-seq fibroblasts)

address: Windmill Road

institute: University of Oxford

summary: Silencing of the somatic cell-type specific gene expression programs is a critical yet poorly understood step in nuclear reprogramming. To uncover chromatin-related pathways important for maintaining cell identity, we carried out a reprogramming screen using inhibitors of chromatin factors. Here we identify two independent acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators EP300 and CBP as potent enhancers of reprogramming. EP300/CBP bromodomain inhibition is critical during early stages of reprogramming, significantly accelerates the emergence of iPSCs and, when combined with Dot1L inhibition, enables efficient derivation of human iPSCs with Oct4 and Sox2 alone. In contrast, complete inhibition of catalytic acetyl-transferase activity of EP300/CBP prevents reprogramming. Genome-wide expression analyses indicate that EP300/CBP bromodomain inhibition diminishes the expression of somatic-specific genes without affecting the induction of pluripotency regulators. Through expression analyses, we identify the master mesenchymal transcription factor PRRX1 as a functionally important target in reprogramming that is downregulated upon EP300/CBP bromodomain inhibition. Collectively, our data uncover a role for bromodomain-mediated interactions of EP300/CBP in sustaining cell type specific gene expression programs and maintaining somatic cell identity

overall_design: RNA-seq of OSKM-infected or uninfected fibroblasts treated with DMSO, CBP-30, ICBP112, or A485.


title: Transcriptome of XP-B/CS cells

status: Public on Feb 01 2019

city: Illkirch

first: Frederic

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

institute: IGBMC

summary: We compared the transcriptome of an XP-B/CS cell to that of the recovered cell line

overall_design: Patient XP-B/CS cells were restored through the stable expression of wild-type XPB tagged with GFP and the transcriptome of patient cell and recovered cell was determined and compared

last: COIN

first: Jeremy

last: Sandoz


title: Transcriptome of a long-lived mutant nematode with severe mitochondrial deficiency

status: Public on Feb 12 2019

city: Bonn

first: Daniele

last: Bano

address: Sigmund-Freud-Strasse 27

institute: DZNE

summary: Inhibition of insulin/IGF-1 signaling (IIS) represents a promising avenue for the treatment of mitochondrial diseases, although many of the molecular mechanisms underlying this beneficial effect remain elusive. Here, we analyze the transcriptome of a well established model for mitochondrial deficiency, gas-1(fc21) mutant nematodes, which when placed in a genetic context of IIS inhibition, undergo metabolic rewiring leading to a massive lifespan extension

overall_design: 5 biological replicates each of wild-type, gas-1(fc21) and age-1(hx546);gas-1(fc21) mutant nematodes (L4 stage) were analyzed by RNA Next Generation Sequencing

first: Anna

last: Gioran

first: Antonia

last: Piazzesi

first: Fabio

last: Bertan

first: Lena

last: Wischhof

first: Jonas

last: Schroer

first: Pierluigi

last: Nicotera


title: Long noncoding RNA MALAT1 activates HIV-1 infection by detaching polycomb repressive complex 2 from binding to the promoter of long terminal repeat for mediating epigenetic silencing

city: Wuhan

first: LI

last: LI

state: Hubei

address: 185 Donghu Road

institute: wuhan university school of basic medical sciences

summary: Accumulating data have emphasized the critical role of long noncoding RNAs (lncRNAs) in regulating HIV-1 replication. LncRNAs may repress or active HIV-1 replication and latency through regulating different cellular machineries. Our RNA-Sequencing (RNA-Seq) revealed the up-regulation of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), a lncRNA being mainly described in cancer cells that associates with cancer pathogenesis, in HIV-1 infected CD4+ T cells

overall_design: HIV-1NL4-3-infected and uninfected CD4+ T cells, sequenced on Hiseq X10 sequencer (Illumina)

first: Wei

last: Hou

first: Di

last: Qu


title: Gene expression in mature and immature human ES-derived beta cells, and sorted beta-cells from adult islets

city: San Francisco

first: Gopika

last: Nair

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: UCSF

summary: This submission comprises RNA-Seq profiling of in vivo differentiated pancreatic beta cells types and primary islet-derived pancreatic beta cell sources. The study reports that re-aggregation of immature beta-like cells (d20Beta) and removal of progenitor cells leads to further maturation in vitro resulting in beta-cells (eBCBeta) that are closer to human primary islet-derived beta-cells(IsletBeta). As a control stem cell derived spheres were dissocated, reassociated and taken through till the end of the protocol (NECBeta).

overall_design: 2 samples each of eBCBeta, NECBeta, d20Beta and IsletBeta were for RNA-seq by using SMARTer Stranded Total RNA Sample Prep Kit – Low Input Mammalian Kit (Clontech) kits for library preparation after RNA integrity was confirmed. Sequencing was carried out on the Illumina platform


title: Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

first: Jin-Wen

last: Song

state: Beijing

address: No. 100, West Fourth Ring Road, Fengtai District

institute: Beijing 302 Hospital

summary: Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.

first: Xue

last: Liu


title: Gender-specific transcriptomic changes with high fat diet

status: Public on Jan 31 2019

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: we investigated the effect of HFD on the transcriptome in the heads and bodies of male and female flies kept on either HFD or regular diet (RD). Using comprehensive genomic analyses which include high-throughput transcriptome sequencing, pathway enrichment and gene network analyses, we found that HFD induces a number of responses that are  sexually dimorphic in nature. There was a robust transcriptional response consisting of a downregulation of stress-related genes in the heads and glycoside hydrolase activity genes in the bodies of males. In the females, the HFD led to an increased transcriptional change in lipid metabolism.

overall_design: Examination of head and body of male and female Drosophila kept on High fat and regular diet.

first: Gabriel

middle: G

last: Haddad

first: Tsering

last: Stobdan


title: iPS derived melanocyte precursor cells

city: kobe

first: Chieko

last: Hosaka

institute: kobe dermatology

summary: We found distinct and self-renewal cell linages that could differentiate into melanocytes, named melanocyte precursor cells (MPCs) in which MPCs revealed drastically differntiation to authentic melanocytes by a small amount of GSK3β inhibitor in about seven days.  Comparing MPCs ,iPSCs and melanocytes, we showed wnt sigal systems in differentiation to melanocytes.

overall_design: We extracted total RNA from iPSCs, MPCs,induced melanocytes from iPSCs and human epidermal melanocytes and hybridized them to Agilent gene expression microarrays.

first: Chikako

last: Nishigori


title: WRN knockout effects upon gene expression in SW48 and OVK18

city: Boston

first: Edmond

last: Chan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: To determine gene expression changes upon CRISPR/Cas9-mediated WRN knockout in SW48 and OVK18. 72 hours after transduction of sgRNA into Cas9 expressing cells, RNA was harvested and submitted for sequencing.

overall_design: Cas9 expressing SW48 and OVK18 cells were transduced with either a negative control sgRNA targeting an intergenic region of chromosome 2 (sgCh2-2), or one of two sgRNAs targeting WRN (sgWRN2, sgWRN3)

first: Tsukasa

last: Shibue


title: Natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis.

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Cancer predisposing allelic variants have shown to be notoriously difficult to identify by conventional GWA studies. Searching for preferential co-occurrence with defined somatically acquired oncogenic lesions can significantly contribute to the identification of such alleles1. We here show that a natural Wnt-7b allelic variant in the mouse, which is not associated with increased tumour susceptibility, strongly synergizes with loss of the Cdkn2ab tumour suppressor locus in cancer development. Previously, we reported that Cdkn2ab-/- mice, generated from 129P2 ES cells develop skin carcinomas 2. The incidence of these carcinomas dropped gradually in the course of backcrossing to the FVB/N background suggesting that one or more 129P2 alleles cooperate with Cdkn2ab deficiency in skin carcinogenesis. Here we show that this skin cancer phenotype is linked to a 20Mb region of 129P2 chromosome 15 harboring the Wnt7b and Pdgfb genes. Both Wnt7b and Pdgfb are preferentially expressed from the 129P2 allele in skin carcinomas and derived cell lines. ChIPseq analysis showed enrichment of H3K27-Ac, a mark for active enhancers, in the 5’ region of the Wnt7b 129P2 gene. Moreover, the Wnt7b 129P2 allele appeared sufficient to cause in vitro transformation and anchorage-independent growth of Cdkn2ab deficient cell lines. Further we show that Wnt7b contributes to transformation through Cdk6 activation. Our observations imply that normally occurring variations in Wnt expression can elicit transformation of cells upon Cdkn2ab locus loss and point to a critical role of the Cdkn2ab locus in keeping the oncogenic potential of physiological levels of Wnt signaling in check. Consequently, it will be worthwhile to explore whether human tumours that show loss of CDKN2ab are associated with distinct allelic variants causing enhanced WNT signaling.

overall_design: ChIPseq for H3K27ac was performed in Cdkn2ab mutant FVB/129P2 backcross cells.

first: Robin

middle: H

first: Elzo

last: de Wit


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [spleen Treg and Tconv RbpjKO expression]

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

summary: The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses was observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch as well as T-cell polarization into TH2 effector cells. The observed phenotype was environment-dependent and could be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopted open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing footprint of transcription factor Gata-3. The over-expression of Ilt3 rendered Rbpj-deficient Treg cells incompatible to specifically restrain TH2 responses, finally leading to severe and fatal lymphoproliferative disease.

overall_design: We isolated spleen cells from Treg Rbpj-deficient animals and wildtype counterparts. Cells were stained with antibodies and cell populations sorted by FACS. Total RNA was isolated and measured with gene expression microarry.

first: Markus

last: Feuerer


title: AtrR is an essential determinant of azole resistance in Aspergillus fumigatus

city: Iowa City

first: Scott

last: Moye-Rowley

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

institute: University of Iowa

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

overall_design: Refer to individual Series


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [ATAC-seq]

first: Madison

last: Kelly

address: 413 E69th Street

institute: Weill Cornell Medicine

summary: Investigation of the chromatin accessibility in myeloid progenitor cells

overall_design: Relevant WT control mice were aged for 20 weeks, myeloid progenitor cells were sorted and ATAC-seq was performed

first: Stephin

last: Vervoort


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [BcorKrasRNA-seq]

summary: Investigation of the transcriptional profile of BcorΔE9-10KrasG12D myeloid progenitors

overall_design: Splenocytes from BcorΔE9-10KrasG12D mice were transplanted into PTPRCA recipients, after 4 weeks donor-derived KL cells were isolated and RNA sequencing performed


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [spleen RbpjKO sick expression]

overall_design: We isolated spleen cells from affected Treg Rbpj-deficient animals and wildtype counterparts. Cells were stained with antibodies and cell populations sorted by FACS. Total RNA was isolated and measured with gene expression microarry.


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [spleen Rbpj WT and Rbpj KO ATAC-seq]

overall_design: We isolated spleens from affected and control animals; target cells were FACS-sorted and the ATAC procedure was performed and samples were indexed and sequenced


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [TargetedCRISPRscreen]

summary: Investigating Bcor target genes in BcorΔE9-10KrasG12D leukaemia with a custom CRISPR dropout screen

overall_design: BcorΔE9-10KrasG12D cell line was transduced with a custom CRISPR library and a dropout screen was performed.


title: Widespread transposable element-driven oncogene expression in cancers

status: Public on Feb 05 2019

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: Transposable elements act as promiscuous cryptic promoters that upregulate oncogenes (“onco-exaptation”) in many cancers.

overall_design: OmniATAC-seq were generated for H1299 lung cancer cell line. RNA-seq, WGBS-seq and omniATAC-seq were generated for H838 lung cancer cell line. nanoCAGE-seq was generated for H727 lung cancer cell line.

first: Hyo

middle: S

last: Jang

first: Ting

last: Wang


title: Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

city: Santa Cruz

first: Christopher

last: Villarreal

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

summary: Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. First, we systematically evaluated the fidelity of organoid models to primary human and macaque cortex, finding organoid models preserve gene regulatory networks related to cell types and developmental processes but exhibit increased metabolic stress. Second, we identified 261 genes differentially expressed in human compared to chimpanzee organoids and macaque cortex. Many of these genes overlap with human-specific segmental duplications and a subset suggest increased PI3K/AKT/mTOR activation in human outer radial glia. Together, our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design:
Single cell mRNA sequencing of iPS-derived neural and glial progenitor cells using the Fluidigm C1 system

This series includes re-analysis of publicly available data in accessions: phs000989.v3, GSE99951, GSE86207, GSE75140. Sample metadata and accession IDs for the re-analyzed samples are included in the file "GSE124299_metadata_on_processed_samples.xlsx" available on the foot of this record.

The following samples have no raw data due to data loss: GSM3569728, GSM3569738, GSM3571601, GSM3571606, GSM3571615, GSM3571621, GSM3571625, and GSM3571631

first: Alex

last: Pollen


title: RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-embryos, named as 'ETX-embryos'.

city: Shanghai

first: Ran

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: We analyze the difference between ETX-side1 cells and ETX-side2 cells. Side1 cells are associated with the anterior domain of the natural embryo, side2 cells are associated with the posterior domain of natural embryo.

overall_design: Examination of gene expression patterns of cells selected from different domains of 3 individual ETX-embryo (individuals labelled as A, B, C).

first: Berna

last: Sozen

first: Gianluca

last: Amadei

first: Andy

last: Cox


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [BcorKrasChIP-seq]

city: New York

summary: Investigation of the transcriptional changes in BcorΔE9-10KrasG12D myeloid progenitors

overall_design: BcorΔE9-10KrasG12D tumours were transplanted into PTPRCA recipients, after 4 weeks donor-derived KL cells were isolated and RNA sequencing performed


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [affected and unaffected spleen Treg and Tconv RbpjKO and RbpjWT expression]

overall_design: We isolated spleen cells from affected Treg Rbpj-deficient animals, unaffected Treg Rbpj-deficient animals and wildtype counterparts. Cells were stained with antibodies and cell populations sorted by FACS. Total RNA was isolated and measured with gene expression microarry.