title: Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer (RNA-Seq)

summary: Metastasis is the cause of death for 90% of cancer patients, but little is known about how cancer cells adapt to and colonize new tissue environments. Using clinical samples and primary/metastatic cell lines, we found metastatic colorectal cancer (CRC) cells lose their colon-specific gene transcription program and gain a liver-specific gene transcription program as they metastasize in the liver. We revealed this transcription reprogramming is driven by a reshaped epigenetic landscape of both typical and super-enhancers. Further, we identified FOXA2, a liver-specific transcription factor, plays a key role in this transcription reprogramming and the colonization of metastatic CRC cells in the liver. Notably, this transcription reprogramming is also observed in multiple cancer types. Our data demonstrate that epigenetically reprogrammed tissue-specific transcription promotes metastasis and should be targeted therapeutically.

overall_design: Examination of 4 different histone modifications and transcriptome in 2 cell lines.

first: Shuaishuai

last: Teng


title: transcriptomic comparison of CpG and MPL treatment in bone marrow derived dendritic cells (BMDC)

status: Public on Jun 29 2020

city: Saranac Lake

first: Deborah

last: Brown

state: New York

address: 154 Algonquin Ave

country: USA

institute: Trudeau Institute

type: Expression profiling by high throughput sequencing

summary: We report the comparison of TLR9 agonist CpG and TLR4 agonist MPL alone and in combination on the gene expression patterns in murine BMDC

overall_design: We analyze BMDC preparations treated with media (control), CpG at 0.2 µg/ml, MPL at 0.01 µg/ml or a combination of CpG+MPL at 0.2 µg/ml and 0.01 µg/ml (CpG+MPL hi) and CpG+MPL at 0.1 µg/ml + 0.005 µg/ml (CpG+MPL low). Each replicate is a BMDC preparation from a different mouse.

middle: M

first: Anna

middle: T

last: Lampe


title: Gene expression profiles of atrial and ventriclular compartments in mouse embryonic hearts and induced heart organoids

status: Public on Jun 30 2020

city: Tokyo

first: Akito

last: Sutani

address: 1-5-45, Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

summary: We generated mouse heart organoids from mouse embryonic stem cells. The heart organoids showed both atrium-like and ventricle-like morphology similar to those of embryonic hearts. Therefore we performed RNA-seq analysis to compare atrial and ventricular gene expression profiles between mouse embryonic hearts and induced heart organoids.

overall_design: RNA-seq in atrial and ventriclular compartments of mouse ebryonic hearts and induced heart organoids, three samples respectively

first: Jiyoung

last: Lee

first: Fumitoshi

last: Ishino


title: The DREAM complexes prevent genomic hypermethylation by repressing the expression of genes required for maintenance of DNA methylation

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state of IRF5+/+ and IRF5-/- CD4+ mouse T cells

city: New Haven

first: Clara

last: Abraham

state: CT

address: 333 Cedar Street, 1080 LMP

institute: Yale University

summary: Genetic variants in IRF5 are associated with multiple immune-mediated diseases.  IRF5 has been predominantly focused on for its regulation of myeloid-derived cells.  We found that IRF5 contributes to CD4+ T cell outcomes and that it regulates early T cell receptor-initiated signaling and subsequently translocates to the nucleus where it binds to promoters of various genes regulated with T cell activation.   We report the chromatin state of freshly isolated and activated IRF5+/+ and IRF5-/- CD4+ T cells in vitro.  While there are minimal differential peaks between freshly isolated IRF5+/+ and IRF5-/- CD4+ T cells, once activated multiple differential peaks are observed between IRF5+/+ and IRF5-/- CD4+ T cells.

overall_design: ATAC-seq in untreated and 72 hour activated IRF5+/+ and IRF5-/- mouse CD4+ T cells in vitro

first: Jie

last: Yan

first: Dejian

last: Zhao


title: Inducible transgene expression in PDX models in vivo identifies KLF4 as a therapeutic target for B-ALL

status: Public on Jun 27 2020

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: Clinically relevant methods are not available that prioritize and validate potential therapeutic targets for individual tumors from the vast amount of tumor descriptive expression data.   We established inducible transgene expression in clinically relevant patient-derived xenograft (PDX) models in vivo to fill this gap.   With this technique at hand, we analyzed the role of the transcription factor Krüppel-like factor 4 (KLF4) in B-cell acute lymphoblastic leukemia (B-ALL) PDX models at different disease stages. In competitive preclinical in vivo trials, we found that re-expression of wild type KLF4 reduced the leukemia load in PDX models of B-ALL, with the strongest effects being observed after conventional chemotherapy in minimal residual disease (MRD). A nonfunctional KLF4 mutant had no effect on this model. The re-expression of KLF4 sensitized tumor cells in the PDX model towards systemic chemotherapy in vivo. It is of major translational relevance that azacitidine upregulated KLF4 levels in the PDX model and a KLF4 knockout reduced azacitidine-induced cell death, suggesting that azacitidine can regulate KLF4 re-expression. These results support the application of azacitidine in patients with B-ALL as a therapeutic option to regulate KLF4. Genetic engineering of PDX models allows the examination of the function of dysregulated genes like KLF4 in a highly clinically relevant translational context, and it also enables the selection of therapeutic targets in individual tumors and links their functions to clinically available drugs, which will facilitate personalized treatment in the future.

overall_design:
mock-expressing control and wtKLF4-expressing ALL-265 PDX cell subpopulations were isolated from mice and sorted. In summary, 12 wtKLF4 and 6 mock samples were analyzed.
--------------------------------------------------
Authors state "German law that prohibits us to make raw sequencing data publicly available".

first: Wen-Hsin

last: Liu

first: Tobias

last: Herold


title: RPA and RAD51 ChIP-seq from B6 and B6xCAST F1 PRDM9-Humanized/CAST mouse testes

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

country: United Kingdom

institute: Oxford University

summary: Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) and proceeds via binding of RPA, RAD51 and DMC1 to single-stranded DNA (ssDNA) substrates created after the formation of DSBs. Here, we report high-resolution in vivo maps of RPA and RAD51 binding in meiosis, mapping their binding locations and lifespans in a B6 and a genetically modified B6xCAST F1 mouse. We ascribe signals separately to the individual homologous chromosomes in the hybrid mouse, thereby separating the signal of binding to the chromosome where DSBs occurred and the chromosome that was used as template for repair. Together with super-resolution microscopy and DMC1 binding maps, we show that DMC1 and RAD51 have distinct spatial localization on ssDNA: whereas DMC1 binds near the break-site, RAD51 binds away from it. We characterize the D-loop, a critical intermediate bound by RPA, in vivo. These data show that DMC1, not RAD51, performs strand exchange in mammalian meiosis. We find that the localisation of D-loop intermediates is similar in crossover and non-crossover pathways, with a longer lifespan for crossover-destined intermediates. These findings answer long-standing questions about the molecular intermediates of recombination.

overall_design: Examination of RPA and RAD51 binding in the testes of C57BL/6J wild-type and (C57BL/6J x CAST/Eij)F1 PRDM9-Humanized/CAST mice

first: Peter

last: Donnelly


title: Metformin on human macrophages

city: London

first: Joseph

middle: J

last: Boyle

address: Du Cane Rd

department: NHLI

institute: Imperial College London

summary:
Metformin on human macrophages
Human blood derived macrophages were treated with 10micromolar Metformin (Sigma-Aldrich) for 4h

overall_design: Paired treated and untreated samples from 4 donors


title: Ikk2-mediated inflammatory activation of arterial endothelial cells promotes the development and progression of atherosclerosis

status: Public on Jun 28 2020

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

summary: Inflammatory activation of endothelial cells is considered to be the first step in the development of atherosclerosis. Here, we determined the consequences of chronic endothelial NF-κB activation on the development and progression of atherosclerosis as well as plaque regression.

overall_design: We established a conditional transgenic mouse model, expressing a tamoxifen-inducible, constitutively active form of IKK2 exclusively in arterial endothelial cells (caIKK2EC mice). Mice were fed a Western-style diet and endothelial IKK2 was activated either at early or late stages of atherosclerosis. MRNA profile of whole aortas was generated by deep sequencing, using Illumina HiSeq3000/4000 instrument.

first: Marion

last: Mussbacher

first: Manuel

last: Salzmann

first: José

last: Basílio

first: Barbara

last: Haigl

first: Viola

last: Gleitsmann

first: Bianca

middle: E

last: Suur

first: Florian

last: Puhm

first: Bernhard

last: Moser

first: Bastian

last: Hoesel

first: Caroline

last: Ungerböck

first: Mario

last: Kuttke

last: Hochreiter

first: Maria

last: Forteza

first: Christoph

last: Binder

first: Daniel

middle: F

last: Ketelhuth

first: Alice

last: Assinger

middle: A


title: Transcriptome analysis reveals conditions for culturing human primitive undifferentiated spermatogonia

city: La Jolla

first: Kun

last: Tan

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

summary: Spermatogonial stem cells (SSCs) are essential for the generation of sperm and have potential therapeutic value for male infertility, which afflicts >100 million men world-wide.  To devise SSC therapy approaches, it is critical to first develop methods to culture human SSCs in vitro. Here, we report on a transcriptome approach to address this question. Using single-cell RNA-seq (scRNAseq), immunofluorescence, and germ-cell xenograft transplantation analyses, we identified a cell-surface protein, PLPPR3, that purifies human primitive undifferentiated spermatogonia (uSPG) enriched for SSCs. Comparative RNAseq analysis of PLPPR3+ cells (primitive uSPG) with KIT+ cells (enriched for differentiating [d] SPG) revealed that these two stages differentially express a remarkably large number of genes, including genes encoding key components in the TGF, GDNF, AKT, and JAK-STAT signaling pathways. Using scRNAseq analysis and conventional approaches, we tested the effect of manipulating these signaling pathways on cultured human SPG. This revealed that GDNF and BMP8B broadly support the culture of SPG, Activin A supports more advanced SPG, and one condition—AKT pathway inhibition—had the unique ability to selectively support primitive uSPG. These findings have implications for methods to culture and expand human SSCs for therapeutic uses in the future.

overall_design: Bulk RNAseq was performed on PLPPR3+ and KIT+ cells FACS purified from 4 independent human testicular biopsy samples (aged from 30 to 41). For single cell RNA-Seq, testicular cells from biopsies obtained from two fertile men aged 32- and 37-years, respectively, were cultured under different conditions (FGF2 alone vs AKT-I+FGF2) for two weeks and then collected for sequencing.

first: Miles

last: Wilkinson


title: P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy

status: Public on Jun 26 2020

city: Cambridge

first: Alejandro

last: Rojas

state: MA

address: 26 Landsdowne Street

institute: Fulcrum Therapeutics

summary: Here, we describe the identification and characterization of p38α as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent and specific inhibitors of p38α/β, we show a robust reduction of DUX4 expression, activity and cell death across FSHD1 and FSHD2 patient-derived lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38α/β inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38α in the aberrant activation of DUX4 in FSHD and support the potential of p38α/β inhibitors as effective therapeutics to treat FSHD at its root cause.

overall_design: RNA-seq profiles of wt myoblasts and FSHD myotubes  treated with pamapimod and losmapimod


title: Transcriptome analysis after disruption of nuclear F-actin in mouse embryos

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

institute: Kyushu University

summary: We find that filamentous actin (F-actin) is formed in pronuclei of mouse zygotes, disruption of which resulted in abnormal development of mouse embryos. To further explain the molecular mechanism, transcriptome analysis was performed following the artificial disruption of nuclear F-actin by overexpression of mutant actin R62D or G15S in nuclei.

overall_design: Nuclear F-actin in zygotes was disrupted by overexpressing actin mutant R62D in pronuclei (R62D-1 and R62D-2). As controls, wild type actin was overexpressed in nuclei (WT-1 or WT-2) or non-injected embryos were used (Actin-control-1 and Actin-control-2). In a different set of experiments, Nuclear F-actin in zygotes was disrupted by overexpressing Exportin 6 together with actin mutant R62D in pronuclei (Exp6+R62D-1-3) or abnormal nuclear F-actin formation was induced by expressing actin mutant G15S in pronuclei (G15S-1-3). As a control, non-injected embryos were used (Non-1-3). RNA-seq was performed using the mouse 2-cell stage embryos, collected at 32 hours post insemination.


title: Next generation sequencing for temporal analysis at high altitude in Indian and  Kyrgyz healthy males

city: North Delhi

first: PRIYA

last: GAUR

state: Delhi

address: DIPAS, DRDO, Lucknow Road, Timarpur, (Near vishwavidyalaya metro station),Delhi

country: India

institute: Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The aim of the study is to analyse the time series analysis at high altitude to dynamically capture the complete drift impringes in humans and specific selection of decisive time point for therapeutic interventions.

overall_design: High Altitude time point analysis to find out the physiological and molecular mechanism of acclimatization in healthy males

first: Priya

last: Gaur

first: Akpay

middle: S

last: Sarybaev

first: Praveen

last: Vats


title: RNAseq on tumors isolated from CT26 tumor bearing mice

city: Brussels

first: Grégoire

last: de Streel

state: Woluwe-Saint-Lambert

address: 75 Avenue Hippocrate

department: de Duve Institute

country: Belgium

institute: UCLOUVAIN

summary: The aim of this work was to evaluate modifications of transriptomal landscape of tumors after treatment with anti-GARP:TGFb mAb combined or not with anti-PD1 mAb.

overall_design: Five mice per treatment group, for a total of 40 mice, were sub-cutaneoulsy injected with 1e+6 CT26 tumor cells and subsequantly treated with mAbs or combinaitions of mAbs at days 6, 9 and 12 after tumor implentation. On day 13, tumors were collected and pieces were isolated for RNA extration and RT. Sequencing was performed on Illumina Hiseq200 plateform with the following requirement : read length : 100pb / number of reads per sample : 30M / paired-ends

first: Sophie

last: Lucas


title: The Evolving Immune Microenvironment of Human B-cell Acute Lymphoblastic Leukemia [CITE-Seq]

city: New York

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Single-cell RNA-seq analysis of primary human bone marrow immune populations isolated from B-ALL patient samples (matched diagnosis, remission and relapse), and healthy bone marrow donor samples.

overall_design: Single-cell RNA-sequencing libraries of primary human bone marrow immune populations. B-ALL patient bone marrow samples were separated into CD19+ B cell and CD19-CD45+ non-B cell fractions by flow-based sorting and then mixed at a ratio of 1:5 CD19+:CD19-CD45+ followed by scRNA-Seq.

first: Matthew

last: Witkowski

first: Aristotelis

last: Tsirigos

first: Iannis

last: Aifantis


title: lincNORS: A Noncoding Regulator of the Cellular Sterol Homeostasis II

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W Walnut Street

institute: Indiana University School of Medicine

summary: We hereby provide the initial portrait of lincNORS, a spliced lincRNA generated by the MIR193BHG locus, entirely distinct from the previously described miR-193b-365a tandem. While inducible by low O2 in a variety of cells and associated with hypoxia in vivo, our studies show that lincNORS is subject to multiple regulatory inputs, including estrogen signals. Biochemically, this lincRNA fine-tunes cellular sterol/steroid biosynthesis by repressing the expression of multiple pathway components. Mechanistically, the function of lincNORS requires the presence of RALY, an RNA-binding protein recently implicated in cholesterol homeostasis. We also noticed the proximity between this locus and naturally-occurring genetic variations highly significant for sterol/steroid -related phenotypes, in particular the age of sexual maturation. An integrative analysis of these variants provided a more formal link between these phenotypes and lincNORS, further strengthening the case for its biological relevance.

overall_design: RNAseq was used to investigate the transcriptional changes when lincNORS level is knockdown by siRNA or overexpressed in MCF-7 cells.

first: Xue

last: Wu

first: Brad

last: Hancock

first: Milan

last: Radovich


title: Comparative transcriptomic analysis of WT, FOXK1/2 KO, DKO cells and FOXK1 KO cells with reconstitution of several FOXK1 mutants

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

summary: The goal of this study was to apply Next Generation Sequencing analyses to identify genes and pathways regulated by the FOXK1 and FOXK2 transcription factor in HeLa cells and to see whether reconstitution of FOXK1 WT and mutants can rescue the altered gene regulation in FOXK1 KO cells. Gene Ontology (GO) analysis did not uncover any dysregulated DNA damage–related pathways upon FOXKs KO. We found that cells reconstituted with any of the three FOXK1 mutants could largely rescue dysregulated gene expression in FOXK1 KO cells, similar to cells reconstituted with WT FOXK1. These suggesting that FOXK1's role in DNA damage response is not by direct transcriptional regulation of DNA damage related pathways and all the three FOXK1 mutants could not affect transcription.

overall_design: mRNA profiles of WT, FOXK1 KO, FOXK2 KO, FOKK1&FOXK2 DKO and FOXK1 KO+FOXK1 WT, FOXK1 KO+FOXK1 F201A, FOXK1 KO+FOXK1 H355A, FOXK1 KO+FOXK1 F201A&H355A in HeLa cells.


title: lincNORS: A Noncoding Regulator of the Cellular Sterol Homeostasis


title: Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer (ChIP-Seq)

first: Yang

middle: Eric

last: Li

state: Beijing

address: Room 2-110, Biotechnology Building, School of Life Sciences, Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

summary: Metastasis is the cause of death for 90% of cancer patients, but little is known about how cancer cells adapt to and colonize new tissue environments. Using clinical samples and primary/metastatic cell lines, we found metastatic colorectal cancer (CRC) cells lose their colon-specific gene transcription program and gain a liver-specific gene transcription program as they metastasize in the liver. We revealed this transcription reprogramming is driven by a reshaped epigenetic landscape of both typical and super-enhancers. Further, we identified FOXA2, a liver-specific transcription factor, plays a key role in this transcription reprogramming and the colonization of metastatic CRC cells in the liver. Notably, this transcription reprogramming is also observed in multiple cancer types. Our data demonstrate that epigenetically reprogrammed tissue-specific transcription promotes metastasis and should be targeted therapeutically.

overall_design: Examination of 4 different histone modifications and transcriptome in 2 cell lines.

first: Shuaishuai

last: Teng


title: Transcriptome analysis of mesothelial cells induced by intraperitoneal injections of crocidolite in rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: Malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. The granuloma capturing crocidolite contribute to mutagenesis, cell death and regenerative activity. To clarify the biological responses of mesothelial cells after crocidolite exposure, we compared the microarray gene expression profiles of no treatment and crocidolite exposure (1 wks) mesothelial cells induced by intraperitoneal injections.

overall_design: Crocidolite exposure protocol was performed using specific pathogen-free male Fischer344 rats. A total of 6 microarrays were used for the expression analysis: The first 3 microarrays were used for no treatment peritoneal mesothelial cells, the next 3 microarrays for crocidolite exposure (1 wks) mesothelial cells.

first: Ito

last: Fumiya

last: Akatsuka


title: lincNORS: A Noncoding Regulator of the Cellular Sterol Homeostasis I

overall_design: Hypoxia regulated genes (coding and long noncoding) was identified by transcriptomic profiling of MCF-7 cells under hypoxia (1% O2, 24 hrs) versus normoxia (21% O2, 24 hrs).

first: Aaron

last: Buechlein

first: Kenneth

middle: P

last: Nephew


title: Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational  Assembly of Initiation Factor Complexes [Human]

city: Canberra

first: Susan

last: Wagner

state: ACT

address: 131 Garran Road

department: The John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Translational control targeting mainly the initiation phase is central to the regulation of  gene expression. Understanding all of its aspects requires substantial technological  advancements. Here we modified yeast Translational Complex Profile sequencing  (TCP-seq), related to ribosome profiling, and adopted it for mammalian cells. Human  TCP-seq, capable of capturing footprints of 40S subunits (40Ses) in addition to 80S  ribosomes (80Ses), revealed that mammalian and yeast 40Ses distribute similarly  across 5’UTRs indicating considerable evolutionary conservation. We further  developed a variation called Selective TCP-seq (Sel-TCP-seq) enabling selection for  40Ses and 80Ses associated with an immuno-targeted factor in yeast and human. Sel-  TCP-seq demonstrated that eIF2 and eIF3 travel along 5’UTRs with scanning 40Ses to  successively dissociate upon start codon recognition. Manifesting the Sel-TCP-seq  versatility for gene expression studies, we also identified four initiating 48S  conformational intermediates, provided novel insights into ATF4 and GCN4 mRNA  translational control, and demonstrated co-translational assembly of initiation factor  complexes.

overall_design: 2 replicates for 40S and 80S TCP-seq, 1 replicate for eIF3b bound 40S Sel-TCP-seq and mRNA

first: Anna

last: Herrmannova

first: Vladislava

last: Hronova

first: Neelam

last: Sen

first: Ross

middle: D

last: Hannan

first: Alan

middle: G

last: Hinnebusch

first: Nikolay

last: Shirokikh

first: Thomas

last: Preiss

first: Leos

last: Valasek


title: MARS-seq data from primary cortical neurons

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: We analyze gene expression data of Lis1 and MeCP2 mutant mice

overall_design: Four genotypes were examined

first: Liraz

last: Keidar

first: Aditya

last: Kshirsagar


title: circRNAs in human brains of Parkinson's disease

city: Jerusalem

first: Hermona

last: Soreq

address: The Edmond J. Safra Campus, Givat Ram

department: Department of Biological Chemistry

institute: The Hebrew University of Jerusalem

summary: total RNA sequencing of Parkinson's disease 3 regions of human brain

overall_design: ribo-depleted RNA libraries of Parkinson's disease and control samples of 3 brain regions: Amygdala (AMG), Substantia nigra (SN) and medil temporal gyrus (MTG)

first: Soreq

last: Hermona

first: Kadener

last: Sebastian

first: Hanan

last: Mor


title: Genome binding/occupancy profiling of Smad4 in Th17 cells cultured at 37°C and 39.5°C after 24 hours.

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

summary: Smad4 was required for febrile temperature enhanced Th17 differentiation. In order to further understand the mechanisms whereby Smad4 enhance Th17 differentiation, we conducted ChIP-seq analysis of Smad4 in Th17 cells cutured 37°C and 39.5°C after 24 hours.

overall_design: Naïve CD4+ T cells were sorted from wild type mice and differentiated under IL-6 plus TGF-β1 condition at 37°C and 39.5°C for 24 hours. The collected cells were then subjected to ChIP and construction of library for ChIP-seq.

first: Lu

last: Ni

first: Xiaohong

last: Zhao


title: The RNA exosome shapes the expression of key protein-coding genes

city: Copenhagen

first: Mengjun

last: Wu

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs, while the majority of mRNAs are protected through their 3’ polyadenylation and nuclear export. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or key components of nucleoplasmic exosome adaptor complexes, we identify a number of transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts and two classes of pc-genes, which both employ a single, annotated TSS across cells and tissues, but the former class primarily produces full-length, exosome-sensitive transcripts, whereas the latter primarily produces prematurely terminated transcripts.  Genes within the former class often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to strong upstream TSSs on the opposite strand. We also show that when genes have multiple active TSSs, alternative TSSs that produce exosome sensitive transcripts typically do not contribute substantially to overall gene expression, and most such exosome sensitive transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-gene regions and imply a direct role for nuclear RNA turnover in the expression regulation of a subset of pc- genes.

overall_design: HeLa cells transfected with siRNAs

first: Evdoxia

last: Karadoulama

first: Marta

last: Lloret-Llinares

first: Jerome

middle: O

last: Rouviere

first: Christian

last: Vaagensø

first: Martin

last: Moravec

first: Bingnan

last: Li

first: Jingwen

last: Wang

first: Guifen

first: Maria

last: Gockert

first: Vicent

last: Pelechano

first: Torben

middle: H

last: Jensen

first: Albin

last: Sandelin


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing [Hs Fiber-seq]

status: Public on Jun 25 2020

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases.  Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).

overall_design: Fiber-seq, AdMTase-seq and m6A-IP-seq on Drosophila S2-DRSC cells. Fiber-seq and AdMTase-seq on human K562 cells. AdMTase-seq on human Hela cells.

first: Andrew

last: Stergachis


title: Lacrimal gland myoepithelial cells are altered in a mouse model of dry eye disease

city: Valladolid

first: Laura

last: García-Posadas

address: Paseo de Belén 17

country: Spain

institute: IOBA-University of Valladolid

summary:
The purpose of this study was to determine the pathogenic changes that occur  in myoepithelial cells (MECs) from lacrimal glands of a mouse model of Sjogren’s syndrome. MECs were cultured from lacrimal glands of C57BL/6J (wild type, WT), and thrombospondin 1 knockout null (TSP1 -/- ) mice.
We used microarray to analyzed the differential expression of genes in cultured MECs of TSP1-/- and wild type (WT) mice.

overall_design: Lacrimal gland myoepithelial cells were isolated and cultured from TSP1-/- and WT mice. Then, total RNA was isolated from cultured cells and gene expression was analyzed with Affymetrix GeneChip Mouse Gene 2.0 ST Array (41,345 transcripts) to detect differences in expression between health and dry eye disease.

first: Robin

middle: R

last: Hodges

first: Tor

last: Utheim

first: Ole

middle: K

last: Olstad

first: Vanessa

last: Delcroix

first: Helen

last: Makarenkova

first: Darlene

last: Dartt


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing [Dm Fiber-seq]


title: Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational  Assembly of Initiation Factor Complexes [Yeast]

first: Susan

last: Wagner

overall_design: 3 sets; set1: 3 replicates for 40S and 80S TCP-seq, 1 replicate for each eIF3a, eIF3c and eIF2beta bound 40S Sel-TCP-seq and 1 replicate each for eIF3a and eIF3c bound 80S Sel-TCP-seq (1-1, 1-2, 1-3); set2+3: 2 more replicates (in addition to set1) of 80S TCP-seq and eIF3a bound 80S Sel-TCP-seq (2-1, 3-1)

first: Anna

last: Herrmannova

first: Vladislava

last: Hronova

first: Neelam

last: Sen

first: Ross

last: Hannan

first: Alan

last: Hinnebusch

first: Nikolay

last: Shirokikh

first: Thomas

last: Preiss

first: Leos

last: Valasek


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing [DNAseI-seq]

first: John

last: Stamatoyannopoulos

first: Andrew

last: Stergachis


title: Wnt activation as a therapeutic strategy in medulloblastoma

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: Medulloblastoma (MB), the most common malignant pediatric brain tumor, is defined by four molecular subgroups (Wnt, Shh, Group 3, Group 4) based on transcriptional and epigenetic profiles. Wnt MB accounts for 10% of cases with the majority harboring somatic CTNNB1 mutations and chromosomal alterations for monosomy 6. Clinically, Wnt MBs have the most favorable prognosis with a >95% 5-year survivorship. By contrast, non-Wnt MBs are characterized by metastatic disease, increased rates of recurrence, and intermediate-poor overall survivorship. Given that Wnt MBs represent the only subgroup in which metastasis is not indicative of a poor prognosis, it has been suggested that Wnt signaling may contribute to their remarkable response to therapy. Using primary patient-derived MB brain tumor-initiating cell  (BTIC) lines, we have characterized intrinsic differences in the tumor-initiating capacity of Wnt and non-Wnt MBs. In this work, we aimed to discover if Wnt activation in non-Wnt MBs could serve as a rationale for therapy employing a novel substrate-competitive peptide Wnt agonist. Our preclinical work establishes activated Wnt signaling as an innovative treatment paradigm with high clinical utility in childhood MB and provides evidence for the context-specific tumor suppressive function of the Wnt/β-catenin pathway.

overall_design: We compared the transcriptome of MB BTIC lines generated from Wnt (BT853), Group 3 (SU_MB002), and Group 4 (ICB1299). Each sample had triplicates (A, B, C). Further, we compared the transcriptome of control (PBS) and Wnt-activating drug-treated (L807mts) samples for SU_MB002 and ICB1299. These were also prepared in triplicates (A, B, C). Lastly, we compared the transcriptome of SU_MB002 cells that were flow cytometrically sorted for expression of endogenous Wnt activity based on TCF reporter expression for GFP (TGP_POS) compared to those cells that were negative based on TCF reporter expression for GFP (TGP_NEG). These samples were also prepared and analyzed as triplicates (A, B, C).

first: Branavan

last: Manoranjan

first: Chitra

last: Venugopal

last: Dvorkin-Gheva


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing [Hs AdMTase-seq]


title: Genome-wide maps of 5hmC levels in mouse Inguinal white adipose tissue

status: Public on Jun 24 2020

city: Albany

first: Sneha

last: Damal Villivalam

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

summary: Using high throughput sequencing we report 5hmC levels, and gene expression changes in mouse Inguinal white adipose tissue upon exposure to room temperature and 7 days to cold in Tet1 floxed wild-type control and adipose selectiveTet1 KO mice.

overall_design: Examination of 5hmC levels in mouse Inguinal white adipose tissue between Tet1 floxed wild-type control and adipose specific Tet1 KO mice. Genomic DNA isolated from the iWAT of mice kept at RT or exposed to cold for 7 days.  2 mice were used per condition.

first: Sona

last: Kang


title: Genome-wide maps of gene expression and 5hmC levels in mouse Inguinal white adipose tissue

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

overall_design: Refer to individual Series


title: Reversible 5-formyluracil DNA-histone crosslinks: formation and biological effects

city: Wuhan

first: Weiwu

last: Zeng

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

institute: Wuhan University

summary: 5-Formyluracil (5fU) is a vital DNA modification that widely presents in cells and organisms. A unique feature of 5fU is the presence of a potentially reactive aldehyde group in its structure, which can realize addition and condensation reactions. However, the biological function details of 5fU are still largely elusive; especially the relationship with protein is still unclear. Herein, we have first showed that 5fU bases have strong affinity with proteins and can yield reversible DNA-protein conjugates with nuclear proteins even under certain spatial space. Besides, 5fU can influence physical properties of nucleosome even chromatin by increasing nucleosome occupancy and stability. What’s more, we firstly confirmed the existence of 5fU-histone crosslinking in thyroid carcinoma tissue by the CHIP of histone H4 combined with LC-MS. These results suggesting the DNA−protein crosslinks (DPC) formation between 5fU and nucleosome core particles may play a potential role in vivo, such as influencing DNA transactions, altering chromatin structure, and stabilizing the nucleosome. In addition, the Schiff base resulted by 5fU may provide us a new direction for capture even quantification of this modification nucleobase based on this condensation reaction with proteins for further epigenetic studies.

overall_design: PAGE, LC-MS, next-generation sequencing were applied to detect the interaction between 5fU and histones.

first: G

last: Zou

first: C

last: Liu

first: W

first: X

last: Zhou


title: Genome-wide maps of gene expression in mouse  Inguinal white adipose tissue

summary: Using high throughput sequencing we report gene expression changes in mouse inguinal adipocytes from WT and Tet1 adipose-selective KO mice  housed room temperature and exposed to 4 degree of cold for 4 hours

overall_design: Examination of  gene expression changes in fractionated mouse Inguinal adiocytes from WT and Tet1 KO mice.   Total RNA was isolated from mouse iWAT kept at RT or exposed to cold for 4 hours. 3 mice were used in each group per condition.


title: Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

summary: Systems biology approaches address the challenge of translating sequence information into function. In this study, we described the Pseudomonas aeruginosa PA14 proteomic landscape and quantified environment-driven changes in protein levels by the use of LC-MS techniques. Previously recorded mRNA data allowed a comparison of RNA to protein ratios for each individual gene and, thus, to explore the relationship between an mRNA being differentially expressed between environmental conditions and the mRNA-protein correlation for that gene. We developed a Random Forest-based predictor for protein levels and found that the mRNA to protein correlation was higher for genes/proteins that undergo dynamic changes. One example of a discrepancy between protein and predicted protein levels was observed for a phage-related gene cluster, which was translated into low protein levels under standard growth conditions. However, under SOS-inducing conditions more protein was produced and the prediction of protein levels based on mRNA abundancy became more accurate. In conclusion, our systems biology approach sheds light on complex mRNA to protein level relationships and uncovered condition-dependent post-transcriptional regulatory events.

overall_design: P. aeruginosa PA14 was pre-cultured in in 4 mL lysogeny broth (LB) in glass tubes at 37 °C shaking at 180 rpm. For main experiments a 10 mL culture was prepared from one pre-culture in LB starting at optical density (OD)600 = 0.02. For ciprofloxacin treatment main cultures were grown until OD600 = 0.5 and then treated for 3 h with sub-inhibitory (sub-MIC) concentrations of ciprofloxacin.

first: Jelena

last: Erdmann

first: Ariane

last: Khaledi

first: Andreas

last: Pich

first: Susanne

last: Häussler


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing

first: John

last: Stamatoyannopoulos

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Articular cartilage regeneration by activated skeletal stem cells

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Osteoarthritis (OA) is a degenerative disease resulting in irreversible, progressive destruction of articular cartilage1. The etiology of OA is complex and involves a variety of factors, including genetic predisposition, acute injury and chronic inflammation2-4. Here we investigate the ability of resident skeletal stem-cell (SSC) populations to regenerate cartilage in relation to age, a possible contributor to the development of osteoarthritis. We demonstrate that aging is associated with progressive loss of SSCs and diminished chondrogenesis in the joints of both mice and humans. However, a local expansion of SSCs could still be triggered in the chondral surface of adult limb joints in mice by stimulating a regenerative response using microfracture (MF) surgery. Although MF-activated SSCs tended to form fibrous tissues, localized co-delivery of BMP2 and soluble VEGFR1 (sVEGFR1), a VEGF receptor antagonist, in a hydrogel skewed differentiation of MF-activated SSCs toward articular cartilage. These data indicate that following MF, a resident stem-cell population can be induced to generate cartilage for treatment of localized chondral disease in OA.

overall_design: Microarray gene expression profiling of mSSCs and bulk tissues from healthy newborn (post-natal day 3, P3), healthy adult (9-to-25-week-old, Ad), and microfractured adult joints (Ad/MF) and mSSCs from Ad/MF joints treated with control (PBS), BMP2, and VEGFR1

first: Matthew

last: Murphy

first: Lauren

last: Koepke

first: Michael

last: Lopez

first: Xinming

last: Tong

first: Thomas

last: Ambrosi

first: Owen

last: Marecic

first: Yuting

last: Wang

first: Ryan

middle: C

last: Ransom

first: Malachia

middle: Y

last: Hoover

first: Holly

last: Steininger

first: Liming

last: Zhao

first: Marcin

last: Walkiewicz

first: Natalina

last: Quarto

first: Derrick

last: Wan

first: Irving

middle: L

last: Weissman

first: Stuart

middle: B

last: Goodman

first: Fan

last: Yang

last: Longaker

first: Charles

last: Chan


title: Permissive epigenomic states endow reprogramming competence to a broad range of transcriptional regulators

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: Identifying molecular targets that regulate reprogramming competence of transcription factors in donor cells broadens our understanding of reprogramming process. Here, by a chemical screen targeting major epigenetic pathways in human reprogramming, we discovered that inhibiting specific epigenetic roadblocks allows iPSC generation with almost all OCT factors. Amongst these epigenetic pathways was not only DOT1L-mediated H3K79 methylation but also other modifications catalyzed by LSD1, DNMTs and HDACs, and we found that simultaneous inhibition of these pathways not only dramatically enhances reprogramming competence of most OCT factors but in fact enables to dismantle species-dependent reprograming competence of OCT6, NR5A1, NR5A2, TET1 and GATA3. Harnessing these permissive epigenetic states, we performed an additional screen with 98 transcriptional regulators. Thereby, we identified 25 novel genes that can functionally replace OCT4 in inducing pluripotency. Our findings provide a conceptional framework for understanding how transcription factors elicit reprogramming in dependency of the donor cell epigenome that differs across species.

overall_design: Examination of OCT4 and OCT7 binding events in cells undergoing reprogramming.

first: Kee-Pyo

last: Kim

first: Hans

last: Schoeler


title: Single-cell RNA-seq and ATAC-seq of zebrafish retina

city: Shanghai

first: Lei

last: Du

address: No. 320, Yueyang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

summary: To study the transcriptomic and chromatin accessibility heterogeneity of zebrafish retinal progenitor cells

overall_design: 2 retinal samples from embryonic zebrafish

first: Mei

first: Jie

last: He


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [H3K9me3 ChIP-seq]

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

summary: Within mammalian nuclear space, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs), associated with transcriptional repression. However, the molecular mechanisms underlying these 3D chromatin architectures remain undeciphered. Here, we demonstrate the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. Topors knockdown in mouse hepatocytes results in cell proliferation and migration promotion, as well as arrest in the S phase of the cell cycle. RNA-seq analysis shows that 373 genes are up-regulated, some of which are associated with nuclear structure, and 316 genes exhibit down-regulated, many related to metabolic process. Chromatin accessibility is inclined to alter in the intergenic regions, including enhancers. Chromatin-lamina interactions decrease globally, and the coverage of LADs reduces from 53.31% to 46.52%. Furthermore, Topors knockdown leads to significantly increasing interactions between A and B compartments in cis and in trans. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. Collectively, our data reveal that TOPORS functions as a regulator in chromosome folding, providing novel insights into the architectural role of tumor suppressors in higher-order genome organization.

overall_design: H3K9me3 ChIP-seq data in Control and Topors knockdown cells.


title: A positive, growth-based PAM screen reveals non-canonical motifs recognized by the S. pyogenes Cas9

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: We report non-canonical PAM sequences for SpyCas9 that were revealed from a novel growth-based PAM screen in E. coli.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Next-generation sequencing was used to identify enriched PAM sequences from a 5N PAM library in E. coli. The library with and without IPTG induction was sent for sequencing to determine enrichment. NGS was also used to evaluate indel formation in U2OS cells after targeting by SpyCas9.

first: Daphne

last: Collias

first: Ryan

middle: T

last: Leenay

first: Rebecca

last: Slotkowski

first: Zhicheng

last: Zuo

first: Scott

last: Collins

first: Brooke

last: McGirr

first: Jin

last: Liu


title: Metastasis-specific gene expression in autochthonous and allograft mouse mammary tumor models: stratification and identification of targetable signatures

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Transcriptomic study of metastases generated by many of the most widely used mouse models of breast cancer metastasis

overall_design: Paired primary tumor and metastatic tissues were collected from several mouse models of metastatic breast cancer. RNA sequencing was then performed in order to characterize the differences between metastasis-specific gene expression in different models, and also to identify shared metastasis-specific transcriptomic characteristics.

first: Christina

last: Ross

first: Karol

last: Szczepanek

last: lee

first: Howard

last: Yang

first: Cody

middle: J

last: Peer

first: Jessica

last: Kindrick

first: Priya

last: Shankarappa

first: Zhi-Wei

last: Lin

first: Jack

last: Sanford

first: William

last: Figg

first: Kent

last: Hunter


title: Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

summary: Transcription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5′ enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.

overall_design: Samples were analysed in total from a strain carrying HTP tagged RNAPI and untagged strain as a negative control. Duplicate experiments were carried out.

middle: W

first: Elisabeth

last: Petfalski

first: Benjamin

last: Goddard

first: Sarah

last: French

first: Aleksandra

last: Helwak

first: David

last: Tollervey


title: Striatal cultured neurons single-nucleus RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains single-nucleus RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of transcriptional response to dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM). The goal of this experiment was to define the transcriptional response to each of these stimulations across distinct cell types in cultured neurons. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples. Samples were embryonic day 18 rat primary striatal neurons cultured for 11 days in vitro prior to treatment with vehicle (neurobasal media), dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM) for 1hr. Neurons were cultured on 12w plates (~250,000 neurons/well), treated with described stimuli for 1hr, washed, and harvested in lysis buffer prior to isolation of nuclei via centrifugation and FACS sorting. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

middle: A

last: Phillps

first: Corey

last: Duke

first: Jennifer

last: Tuscher

first: Morgan

middle: E

last: Zipperly

first: Lara

last: Ianov


title: Dopaplex RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

summary: This dataset contains whole-genome RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of multiplexed CRISPR/dCas9 gene activation of 16 genes induced by dopamine receptor activation. The goal of this experiment was to define the transcriptional response to multiplexed CRISPR-based upregulation of 16 dopamine-induced genes (Tent5b, Junb, Prox1, Nr4a2, Nptx1, Gsx1, Gadd45g, Btg2, Fosb, Nr4a1, Egr4, Fos, Sstr2, Gadd45b, Egr3, & Egr2), together termed "Dopaplex", as compared to a LacZ control sgRNA.

overall_design: This experiment contains 11 biological samples, each of which underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Samples were treated with Lacz sgRNA or Dopaplex sgRNAs (targeting the 16 genes outlined above), in addition to a dCas9-VPR fusion for CRISPR-based transcriptional activation. Datasets were obtained using RNA-seq from PolyA+ fractions fractions of RNA. Each sample has multiple files, corresponding to different sequencing lanes (e.g., L001, L002, etc) or different reads (e.g., R1, R2).

first: Katherine

last: Savell


summary: The goal of this experiment was to determine how dopamine receptor activation in medium spiny neurons alters rapid transcriptional programs. To identify genes altered by dopamine, we used a rat primary striatal neuronal culture system in which striatal neurons were removed from the rat brain at embryonic day 18, cultured for 11 days in vitro using standard neuronal conditions, and treated neurons with either vehicle (neurobasal media) or dopamine (at a concentration of 1µM) for 1hr. This dataset contains PolyA+ RNA-seq results from this experiment, in which we identified 100 upregulated genes and 3 downregulated genes after dopamine stimulation using DESeq2 pipelines.

overall_design:
RNA-seq 1hr dopamine dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response".
This experiment contains 6 biological samples, each of which underwent directional, paired-end PolyA+ RNA-seq on an Illumina HiSeq v4 instrument. Samples were treated with neurobasal media (vehicle; samples S37-1, S37-3, and S37-5), or 1µM dopamine (samples S37-2, S37-4, and S37-6) . Datasets were obtained using RNA-seq from PolyA+ fractions fractions of RNA.

first: Faraz

last: Sultan


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [RNA-seq]

first: Luzhang

last: Ji

overall_design: RNA-seq data in Ctrl and Topors KD AML12 cells.


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [PML ChIP-seq]

overall_design: PML ChIP-seq data in Ctrl and Topors KD AML12 cells.


title: Single-molecule regulatory architectures captured by chromatin fiber sequencing [Dm AdMTase-seq]

first: John

last: Stamatoyannopoulos

summary: We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases.  Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).

overall_design: Fiber-seq, AdMTase-seq and m6A-IP-seq on Drosophila S2-DRSC cells. Fiber-seq and AdMTase-seq on human K562 cells. AdMTase-seq on human Hela cells.

first: Andrew

last: Stergachis


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [ATAC-seq]

overall_design: ATAC-seq data in Ctrl and Topors KD AML12 cells.


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [H3K27ac ChIP]

overall_design: H3K27ac ChIP-seq data in Control and Topors knockdown cells.


title: Zuo1 supports G4 structure formation and directs repair towards nucleotide excision repair

status: Public on Jun 23 2020

city: Bonn

first: Stefan

middle: Andreas

last: Juranek

state: NRW

address: Venusber-Campus 1

department: Medizinische Klinik III

institute: UK Bonn

summary: Nucleic acids can fold into G-quadruplex (G4) structures that can fine tune biological processes. Proteins are required to recognize G4 structures and coordinate their function. We identify Zuo1 as a novel G4-binding protein in a yeast one-hybrid screen. Biochemical and molecular experiments in yeast confirm that Zuo1 specifically binds to G4 structures in vitro and in vivo. In vivo in the absence of Zuo1 less G4 structures form, cell growth slows and cells become UV sensitive. Subsequent experiments reveal that these cellular changes are due to reduced levels of G4 structures. Interestingly, Zuo1 function and binding to G4 structures results in the recruitment of nucleotide excision repair (NER) factors, which has a positive effect on genome stability. Cells lacking functional NER as well as Zuo1 accumulate G4s structures, which become accessible for translesion synthesis. Our results suggest a model in which Zuo1 supports NER function and regulates the choice of the DNA repair pathway near G4 structures.

overall_design: Examination of the Zuo1 binding sites in the yeast chromatin

first: Alessio

last: De Magis

first: Silvia

last: Götz

first: Mona

last: Hajikazemi

first: Enikő

last: Fekete-Szücs

first: Marco

last: Caterino

first: Katrin

last: Paeschke


title: Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction [ChIP-Seq]

city: Guangzhou

first: LI

last: LINPENG

address: KAIYUAN ROAD 190

institute: GIBH

summary: Metabolic activity possess a crucial role during cell fate determination. Here, we show that maternal transcriptional factor Glis1 could not only promote normal MEF reprogramming but also enable aging MEF reprogramming. By association ChIP-seq and RNA-seq, we found that Glis1 could bind and activate glycolytic genes, and bind and suppress somatic state genes simultaneously during reprogramming. While knockdown phosphoglyceric kinase (Pgk1) impeded reprogramming efficiency which indicates that Glis1-glycolytic process axes is required for Glis1 function. Metabolic analysis indicated that the level of acetyl-CoA has a significant fluctuation upon Glis1 induction or silence. Acetate, a precursor of acetyl-CoA rescued the effects on reprogramming in a time-dependent manner when knockdown endogenous Glis1. The fluctuation of Ac-CoA changed the level of H3K27Ac, especially in pluripotent genes and “second wave” genes promoter, and activated the expression of endogenous pluripotency genes in advance subsequently. In conclusion, we demonstrate the exactly novel mechanism of Glis1 in pluripotency acquisition.

overall_design: Examination of Glis1 binding during reprogramming process and  histone modifications H3K27Ac in SKO+Flag,SKO+Glis1 on day 5 and day8

first: Linpeng

last: Li

first: Keshi

last: Chen

first: Yi

last: Wu


title: TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [DamID]

type: Genome variation profiling by genome tiling array

overall_design: LAMINB1 DamID data in shCtrl and shTopors treated AML12 cells.


title: A single cell transcriptional atlas of early synovial joint development

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 7,329 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and in vitro characterization of prospectively isolated populations, we have identified the transcriptional profiles of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.

overall_design: We sampled Gdf5-lineage cells of the murine knee at embryonic time points e12.5, e13.5, e14.5, and e15.5 and subjected them to single cell RNAseq analysis via 10x.

first: Qin

last: Bian


title: Blockade of the G-CSFR or C5 in a murine model of unilateral warm renal ischemia-reperfusion injury (IRI).

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

institute: WEHI

summary: Purpose: Understand gene transcriptional changes in kidney cell populations after ischemia-reperfusion injury and after treatment with either a neutralizing mAb to the G-CSFR or a neutralizing mAb to C5.

overall_design: Renal RNA profiles comparing sham operated mice (n=3) to mice with ischemia-reperfusion injury treated with either isotype control mAb (n=3), anti-G-CSFR mAb (n=3) or anti-C5 mAb (n=3).

first: Ingela

last: Vikstrom

first: Monther

last: Alhamdoosh

first: Milica

last: Ng

first: Adriana

last: Baz Morelli

first: Jennifer

last: McRae

first: Martin

last: Pearse

first: Peter

last: Cowan

first: Anjan K.

last: Bongoni

first: Evelyn J.

last: Salvaris

first: Nella

last: Fisicaro


title: Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction [RNA-Seq]

first: LI

last: LINPENG

overall_design: reprogramming cell mRNA profiles of day8 SKO+Flag and SKO+Glis1 were generated by deep sequencin, using Illumina Hiseq 4000.


title: Enhancer RNAs mediate estrogen-induced decommissioning of selective enhancers by recruiting ER and its cofactor

city: San Antonio

first: Kexin

last: Xu

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

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

overall_design: Refer to individual Series


title: Enhancer RNA mediate estrogen-induced transcriptional repression by recruiting ERa and its cofactor to selective enhancers [RNA-Seq]

summary: Estrogen receptor alpha (ERα) signaling mainly occupies on distal enhancers within genome and plays an essential role in ERα-positive breast cancer. ERα usually requires co-factors to regulate the enhancer activity. By analysis of genome-wide nascent transcript profiling in breast cancer cells, we identified a special group of eRNAs that are functionally important for estrogen-induced transcriptional repression. In addition to stabilizing promoter-enhancer looping structure, these eRNAs recruit ERα to particular enhancers of target genes, facilitate the hierarchical formation of a functional transcriptional complex, and cause gene silencing. Interestingly, we found that ERα directly binds to eRNAs and its DNA-binding domain mediates the interaction with RNA molecules. Our ChIP-seq data in MCF-7 cells indicating that ERαwas not able to bind to E2-activated enhancers, which is consistent with the DNA-binding function reported before; moreover the DBD-truncated ERα was not able to bind to E2-repressed enhancers as well, which further supports our hypothesis that eRNA from E2-repressed enhancers help to recruit ERα to specific enhancers through the interaction with DBD domain. Substitution of ERα-DDBD showed a global effect on both induction and repression of ERα target genes as examined by RNA-seq. Further, these eRNAs help with the formation of a specific ERα-centered transcriptional complex and promote the association of the histone demethylase KDM2A, which dismisses RNA polymerase II from designated enhancers and suppresses transcription of target genes. Our work demonstrated that eRNAs, as a distinctive class of cis-acting molecules besides chromatin regulatory elements, play an important role in modulating and refining locus-specific transcriptional program.

overall_design:
MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shControl(for vector group) or shER(for WT and dDBD group) targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for six hours.
total RNA etraction followed by high throughput sequencing (RNA-seq)

first: Zhang

last: Zhao

first: Yang

last: Mei

first: Xu

last: Kexin


title: Epigenetic priming by Dppa2/4 in pluripotency facilitates multi-lineage commitment

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Epigenetic priming factors establish a permissive epigenetic landscape which is not required until a later developmental or physiological time point, temporally uncoupling the presence of these factors with their phenotypic effects. One classic example of epigenetic priming is in the context of bivalent chromatin, found in pluripotent stem cells and early embryos at key developmental gene promoters marked by both activating-associated H3K4me3 and repressive-associated H3K27me3 histone modifications. It is currently unknown how these bivalent domains are targeted, or precisely how they impact on lineage commitment. Here we show that the small heterodimerising non-enzymatic DNA binding proteins Developmental Pluripotency Associated 2 (Dppa2) and 4 (Dppa4) act as epigenetic priming factors to establish bivalency at a subset of developmental genes. Dppa2/4 localise to the +1 nucleosome position of bivalent genes and while they are not required for pluripotency in embryonic stem cells (ESCs), double knockout cells fail to exit pluripotency and to differentiate efficiently, with delays in upregulating bivalently marked lineage genes. Proteomics reveal that Dppa2/4 interact on chromatin with members of the COMPASS and Polycomb complexes important for H3K4me3 and H3K27me3 deposition, respectively. Epigenetic profiling reveals a striking loss of H3K4me3, H3K27me3, and their associated enzymatic machinery at a significant subset of bivalent promoters in Dppa2/4 mutants, in addition to loss of H2A.Z and chromatin accessibility. In wild-type ESCs, these “Dppa2/4-dependent” bivalent promoters are characterised by low H3K4me3 enrichment and breadth, near-absent expression levels and initiating but not elongating RNA polymerase. Notably, Dppa2/4-dependent promoters are less evolutionarily conserved suggesting that they lack additional safeguard measures to maintain bivalency at these genes in the absence of Dppa2/4. Concomitantly with the loss of bivalency, Dppa2/4-dependent bivalent promoters gain DNA methylation and consequently are no longer able to be effectively activated upon ESC differentiation, leading to defects in cell fate acquisition. Our findings reveal a targeting principle for bivalency to developmental gene promoters poising them for future lineage specific gene activation.

overall_design: Effects of Dppa2/4 loss on the transcriptome (RNAseq) and epigenome (ChIP-seq, NOME-seq) in mouse embryonic stem cells and differentiating cells

first: M

last: Eckersley-Maslin

first: W

last: Reik


title: Enhancer RNA mediate estrogen-induced transcriptional repression by recruiting ERa and its cofactor to selective enhancers [ChIP-Seq]

overall_design:
For MCF7 cells with different ER truncations, MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shER targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for 30 min.ER_pbox/WT ChIP was done in full medium condition.
Chromatin Immunoprecipitation (ChIP) assay followed by high throughput sequencing (ChIP-seq)


title: Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction


title: Comparison of P18 mouse epidermis from K5-FGFR1/FGFR2 knockout and wild-type mice

city: Zurich

first: LUIGI

last: MADDALUNO

address: Otto Stern Weg 7

country: Switzerland

institute: ETH

summary: Fibroblast growth factors (FGFs) are master regulators of organogenesis and tissue homeostasis. We generated FGF receptor (FGFR)-deficient mice to unravel their functions in the skin. These mice revealed interesting phenotypic abnormalities, including loss of skin appendages, cutaneous inflammation, keratinocyte hyperproliferation, and acanthosis. To gain insight into the underlying molecular mechanisms, we wanted to identify genes, which are differentially expressed in the skin of wild-type and mutant mice before the onset of phenotypic alterations.

overall_design: RNA from epidermis of K5-FGFR1/FGFR2 knockout mice and wild-type littermates at postnatal day 18 was isolated. The epidermis was separated from underlying dermis by dispase treatment, according to the isolation protocol of Chomczynski P (1987), and immediately frozen in liquid nitrogen. Samples from three mice per genotype were pooled and subjected to Affymetrix microarray hybridization (N=3 pools per genotype).

first: S

last: Werner

first: J

last: Yang

last: Meyer

first: L

last: Maddaluno


title: The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage [ChIP-Seq]

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

institute: Henry Ford Health System

summary: Tissue-resident macrophages (TRMs) play central roles in local tissue development and immunity. However, how to control TRM ontogeny and maintenance remains unclear. We performed transcriptional and histone modification analyses of alveolar macrophages in mice with myeloid-specific (Csf1rCre) deletion of HDAC3 using bulk RNA-seq, single-cell RNA-seq and ChIP-seq. We report that HDAC3 deficiency results in metabolic disorders and increased cell death of the fetal lung TRMs, which is partially regulated through directly targeting PPAR-γ. Although the loss of AMs in the absence of HDAC3 is not AM subset specific, the transcriptome changes in HDAC3 deficient AM subsets are different. We propose that HDAC3 serves a key epigenetic regulator that controls embryonic TRM ontogeny and maintenance.

overall_design: HDAC3 ChIP-sequencing and deep sequencing of two different histone modifications in lung alveolar macrophages from Csf1rCre+HDAC3fl/fl KO and Csf1rCre-HDAC3fl/fl WT adult mice.

first: Yi

last: Yao

first: Queping

last: Liu

first: Indra

last: Adrianto

first: James

last: Glassbrook

first: Xiaojun

last: Wu

first: Congcong

last: Yin

first: Yu

last: Wang

first: Jun

last: Zhang

first: Hongmei

last: Peng

first: Zheng

last: Dong

first: Frederic

last: Geissmann

first: Li

last: Zhou


title: Differential expression of endogenous retroelements (long terminal repeats) in ADA2 depleted primary endothelial cells (HUVECs)

status: Public on Jun 20 2020

city: San Diego

first: Rekha

last: Dhanwani

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

type: Non-coding RNA profiling by high throughput sequencing

summary: Adenosine deaminase 2 deficiency (DADA2) is an inherited disorder which can cause vasculitis of medium-sized blood vessels. The disease is caused by mutations in the CECR1 gene, which encodes a key metabolic enzyme (ADA2) in the purine pathway. It is not clear how DADA2 leads to vasculitis, and there are currently limited treatment options. We, therefore, to discern the role of endogenous retroviral elements (ERV) in ADA2 associated vasculitis, studied the altered expression profile of endogenous retroelements in primary endothelial cells in ADA2 depleted setting.  The LTR specific transcriptional analysis revealed a robust increase in LTR signature in unstimulated siADA2-treated cells.

overall_design: Three technical replicates of  each condition were taken 1. HUVEC transfected with non-targeting si RNA refrefred as Control and 2. HUVECs transfected with siRNA targeing ADA2 molecule refrered as ADA2.

first: Sonia

last: Sharma


title: IGF2BP1 is a drugable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [HepG2 small RNA]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary:
The IGF2 mRNA-binding protein 1 (IGF2BP1) is a post-transcriptional enhancer of tumor growth. However, conserved effector pathway(s) and the feasibility of targeting IGF2BP1 in cancer cells remained elusive.
We demonstrate that IGF2BP1 is a conserved regulator of E2F-driven gene expression and cancer cell cycle progression. IGF2BP1 promotes positive regulators of G1/S transition by stabilizing the respective mRNAs. This regulation is 3’UTR-, miRNA- and m6A-dependent, suggesting a conserved role of m6A-enhanced cell cycle progression across cancers. IGF2BP1 stabilizes E2F-encoding mRNAs and some of their target transcripts revealing a post-transcriptional super-enhancer role of the protein in E2F-driven gene expression. The small molecule BTYNB disrupts this super-enhancer function by impairing IGF2BP1-RNA association and consequently interferes with tumor cell proliferation and tumor growth.

overall_design: small RNA-Seq of HepG2 cells

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Marcell

last: Lederer

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alice

last: Wedler

first: Jacob

last: Haase

first: Jean

last: Bertoldo

first: Patrick

last: Michl

first: Stefan

last: Hüttelmaier


title: RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

city: Pittsburgh

first: Kevin

last: Levine

state: Pennsylvania

address: 204 Craft Ave

institute: University of Pittsburgh

summary: Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive ductal carcinoma (IDC). ILC cells exhibit anchorage-independent growth in ultra-low attachment (ULA) suspension cultures, which is largely attributed to the loss of E-cadherin. In addition to anoikis resistance, herein we show that human ILC cell lines exhibit enhanced cell proliferation in ULA cultures as compared to IDC cells. Proteomic comparison of ILC and IDC cell lines identified induction of PI3K/Akt and p90-RSK pathways specifically in ULA culture in ILC cells. Further transcriptional profiling uncovered unique upregulation of the inhibitors of differentiation family transcription factors ID1 and ID3 in ILC ULA culture, the knockdown of which diminished the anchorage-independent growth of ILC cell lines through cell cycle arrest. We find that ID1 and ID3 expression is higher in human ILC tumors as compared to IDC, correlated with worse prognosis uniquely in patients with ILC and associated with upregulation of  angiogenesis and matrisome-related genes. Altogether, our comprehensive study of anchorage independence in human ILC cell lines provides mechanistic insights and clinical implications for metastatic dissemination of ILC and implicates ID1 and ID3 as novel drivers and therapeutic targets for lobular breast cancer.

overall_design: MDA-MB-134-VI (MM134) and SUM44PE (SUM44) ILC cell lines and MCF7 and T47D IDC cell lines were grown in attached (2D) and suspension (ultra-low attachment, ULA) plates for 24 hours, in triplicate. RNA-Seq was carried out using an Illumina NextSeq 500. Raw sequence data were mapped to hg38 genome (ensembl release version 82) and transcript counts were quantified with Salmon (version 0.8.2). Transcript counts were converted to gene counts using tximport and biomaRt (sep2015.archive.ensembl.org).

first: Nilgun

last: Tasdemir

first: Kai

last: Ding

first: Laura

last: Savariau

middle: M

first: Tian

last: Du

first: Ashuvinee

last: Elangovan

first: Emily

last: Bossart

first: Adrian

middle: V

last: Lee

first: Nancy

last: Davidson

first: Steffi

last: Oesterreich


title: Comparison of transcript profiles of acclimated and de-acclimated Arabidopsis plants to high light, cold and heat.

status: Public on Jun 21 2020

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

institute: Centre for Research in Agrigenomics

summary:
Purpose: Acclimation referes to reversible responses that plants trigger under frequently and moderate changes in natural environments, mostly light intensity and temperature. To better understand acclimation in Arabidopsis thaliana, modulators and integrators for this process should be identified. To achieve this goal, a dynamic set-up was designed to systematically cultivate Arabidopsis plants under moderate high light, heat and cold and a multiple high-throughput strategy was conducted to monitor changes in transcriptome, proteome and metabolome. As part of this comprehensive characterisation, lncRNA-Seq has been carried out to investigate transcriptome changes and further integrated in conditional correlation networks.
Methods: lncRNA-Seq libraries were prepared from 14-d-old plants cultivated under standard control conditions or acclimated to high light, cold or heat for 4 d and then de-acclimated under normal conditions for 4 additional days.  Standard Illumina protocols were used for lncRNA-Seq sequencing. Unless some quality issue in libraries was detected, triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. FPKM reads were quantified with Cufflinks to provide processed data files and differential expression analysis were conducted with featureCounts/DEseq2 pipeline.
Results: lncRNA-Seq libraries contained 10 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the corresponding control and FDR ≤ 0.05 was applied. Transcripts significantly different in at least one time-point were considered for subsequent analysis. Accordingly, high light treatments caused changes in 2683 transcripts, followed by 3470 under heat and 6882 under cold. Further data analysis revealed that more than 12% of all altered transcripts were commonly miss-regulated among the three treatments. From a dynamic point of view, transcriptional changes occurred from 3h to 4d of treatment in all treatments and tend to recover to the initial state after 2 and 4d of de-acclimation.
Conclusions: the reversibility of the transcriptional changes during the recovery phase validated the conditions of our set-up to investigate acclimation. Moreover, the existance of a common fraction of transcripts that responded to the three conditions unveiled a central response to acclimation.

overall_design: Transcriptome profiling of pools from shoots of 14-d-old Arabidopsis plants treated with standard controls or acclimated and de-acclimated to high light, heat and cold for 4d. Illumina Sequencing protocols were applied to biologically independent triplicates, unless indicated otherwise.

first: Antoni

last: Garcia-Molina


title: Gene expression comparison, WT and PDAP1-deficient primary B lymphocytes

status: Public on Jun 19 2020

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

institute: Max-Delbrück-centrum

summary: Class switch recombination (CSR) and somatic hypermutation (SHM) are antibody gene diversification reactions occurring in mature B cells that are essential for protective humoral immunity. CSR and SHM are initiated following activation by the antigen, and are dependent on efficient induction of activation-induced cytidine deaminase (AID). Therefore, mature B cell viability and fitness are crucial to mount effective immune responses. Here, we identified PDGFA-associated protein 1 (Pdap1) as an essential regulator of cellular homeostasis in mature B cells. Pdap1 deficiency leads to sustained expression of the integrated stress response (ISR) effector activating transcription factor 4 (Atf4) and induction of the ISR transcriptional program, increased cell death, and defective AID expression. As a consequence, loss of Pdap1 reduces germinal center B cell formation and impairs CSR and SHM. Thus, Pdap1 protects mature B cells against chronic ISR activation, and ensures efficient antibody diversification by promoting their survival and optimal function.

overall_design: Two conditions were tested: stimulation with LPS and IL-4 (to induce CSR to IgG1) or LPS, BAFF and TGFbeta (to induce CSR to IgG2b). Samples were harvested from control and Pdap1F/FCd19Cre/+ splenocyte cultures 48 h after stimulation. Three biological replicates (= mice) per sample were employed for the analysis (control mice: C1 to C3; Pdap1F/FCd19Cre/+ mice: P1 to P3).

first: Michela

last: Di Virgilio

first: Verónica

last: Delgado-Benito

first: Maria

last: Berruezo-Llacuna

first: Wiebke

last: Winkler

first: Sandhya

last: Balasubramanian

first: Devakumar

last: Sundaravinayagam

first: Robin

last: Graf

first: Ali

last: Rahjouei

first: Madlen

last: Driesner

first: Lisa

last: Keller

first: Martin

last: Janz

first: Altuna

last: Akalin


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [A549, ES2, MV3, PANC1 small RNA]

first: Markus

last: Glaß

summary: The IGF2 mRNA-binding protein 1 (IGF2BP1) is a post-transcriptional enhancer of tumor growth. However, conserved effector pathway(s) and the feasibility of targeting IGF2BP1 in cancer cells remained elusive.   We demonstrate that IGF2BP1 is a conserved regulator of E2F-driven gene expression and cancer cell cycle progression. IGF2BP1 promotes positive regulators of G1/S transition by stabilizing the respective mRNAs. This regulation is 3’UTR-, miRNA- and m6A-dependent, suggesting a conserved role of m6A-enhanced cell cycle progression across cancers. IGF2BP1 stabilizes E2F-encoding mRNAs and some of their target transcripts revealing a post-transcriptional super-enhancer role of the protein in E2F-driven gene expression. The small molecule BTYNB disrupts this super-enhancer function by impairing IGF2BP1-RNA association and consequently interferes with tumor cell proliferation and tumor growth.

overall_design: small RNA-Seq of four cancer derived cell lines

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Marcell

last: Lederer

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alice

last: Wedler

first: Jacob

last: Haase

first: Jean

last: Bertoldo

first: Patrick

last: Michl

first: Stefan

last: Hüttelmaier


title: RNA-seq analysis in human REH pre-B lymphoblastic cells in response to XIST-KD

first: Yanfeng

last: Zhang

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

summary: We performed RNA-seq experiments to modulate levels of XIST RNA.  We inhibited XIST activity in REH lymphocytic cells via knockdown of XIST expression by short hairpin (sh) RNA. We confirmed that the RNA level of XIST was greatly reduced in shRNA-XIST cells by both RNA-seq and qPCR analyses, relative to cells transfected with a scrambled shRNA.

overall_design: RNA-seq of control and shXIST REH cells

first: Devin

last: Absher


title: RNA seq to compare gene expression profiles between Npm1 WT and Npm1 knockdown cells

status: Public on Jun 22 2020

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Mouse KrasG12D/P53-/-(KP) lung tumor cells were transfected with pLKO.1-Tet on-shNpm1-3(N3), pLKO.1-Tet on-shNpm1-4(N4) or pLKO.1-Tet on-shNpm1-5 (N5) and then selected by using 2ug/ml puromycin, to establish the 3 stable cell lines. These 3 stable cell lines (N3, N4 or N5) were treated with 100ng/ml Doxycline and then the total RNA of the treated and untreated cells were harvested for RNA seq.

overall_design: Examination of differential gene expression profils in KP-shNpm1-3 (N3), KP-shNpm1-4 (N4) and KP-shNpm1-5 (N5) cells with or without Doxycycline treatment

first: Fei

last: Li

first: Kwok-Kin

last: Wong


title: In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age [dataset I]

city: Seattle

first: Nicole

middle: A P

last: Lieberman

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

summary: We examined host gene expression across infection status, viral load, age, and sex among RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong interferon-driven antiviral response and reduced transcription of ribosomal proteins. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load. B cells and neutrophils were higher in patients with lower viral load. Older individuals had reduced expression of chemokines CXCL9/10/11, their cognate receptor CXCR3, and CD8A and granzyme B. Males had reduced B and NK cell-specific transcripts and increased NFkB inhibitors. Our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.

overall_design:
Examination of differential expression of host genes in response to SARS-CoV-2 infection
NOTE: submitter declares that the raw data have not been submitted due to patient privacy concerns.

first: Alex

last: Greninger


title: Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [PD_hMeDIP_Seq]

city: Grand Rapids

first: Lee

last: Marshall

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: Epigenetic control of enhancers is centrally involved in modifying neuronal functions and may contribute to Parkinson's disease (PD) pathogenesis. Here, we comprehensively profile DNA methylation at enhancers genome-wide in neurons of 57 PD patients and 48 healthy individuals. There is a widespread increase in cytosine modifications at enhancers in PD neurons, which is partly due to elevated hydroxymethylation levels. Epigenetic dysregulation of enhancers in PD converge on transcriptional abnormalities affecting neuronal signaling and immune activation pathways. In particular, PD patients exhibit an epigenetic and transcriptional upregulation of TET2, a master-regulator of cytosine modification status. TET2 inactivation in a neuronal cell line enriches for cytosine modification changes that are reciprocal to those observed in PD neurons. Furthermore, Tet2 inactivation in mice fully prevents dopaminergic neuronal loss in the substantia nigra induced by prior inflammation. Tet2 loss in mice also attenuates transcriptional immune responses to an inflammatory trigger. Thus, widespread epigenetic dysregulation of enhancers in PD neurons may, in part, be mediated by increased TET2 expression. Decreased Tet2 activity is neuroprotective, in vivo, and may be a novel therapeutic target for PD.

overall_design: In order to determine the extent to which 5-hydroxymethylcytosine contributes to the epigenetically misregulated enhancers involved in PD, we used hMeDIP-seq to profile hydroxymethylation genome-wide in neurons of PD patients and healthy control individuals (44 individuals: 21 PD, 23 controls).

first: Bryan

last: Killinger

first: Peipei

first: Elizabeth

last: Ensink

first: Wei

last: Cui

first: Katie

first: Juozas

last: Gordevicius

first: Matthew

last: Weiland

last: Jovinge

first: Viviane

last: Labrie


title: Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [PD_TET2_Bisulfite_Padlock_Seq]

overall_design: To identify epigenetically perturbations at the TET2 gene in PD, we performed a targeted bisulfite deep sequencing approach at the entire TET2 gene and surrounding genomic area (±300 kb) in isolated prefrontal cortex neuronal nuclei from PD patients and healthy control individuals (30 individuals: 20 PD, 10 controls).

first: Stefan


title: CRISPR-Assisted Detection of RNA-Protein Interactions in Living Cells

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

summary: Delineating the protein network associated with long non-coding RNAs (lncRNAs) is fundamental to understanding the functional mechanisms of lncRNAs. Current methods to identify lncRNA binding proteins either rely on crosslinking mediated complex co-precipitation or require extensive molecular engineering, leading to drawbacks such as loss of cellular context and low capture efficiency, and limiting their broad application. We develop a CRISPR-Assisted RNA-Protein Interaction Detection method (CARPID), which leverages CRISPR/CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific lncRNA in the native cellular context. Applied to the nuclear lncRNA XIST, CARPID captured a list of known interacting proteins and multiple previously uncharacterized   binding proteins. We generalize CARPID to explore binders of lncRNA DANCR and MALAT1, revealing its wide applicability in identifying RNA binding proteins.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design:
We did not observe significant change of gene expression in cells with over expression of dCasRx-BASU and gRNAs, confirming that CARPID did not alter the physiological function of transfected cells.
[GSM4285650-GSM4285655] We performed RNA-seq on immortalized mouse embryonic fibroblasts derived from a hybrid female mouse to further confirm the role of TAF15 on XCI. The hybrid mouse was a crossing of a Mus musculus (129S1/SvImJ) female and a Mus castaneus (CAST/EiJ) male. We generated RNA-seq data from this cell line in two replicates with no treatment (NT), upon 5-aza treatment, and upon 5-aza treatment in Taf15-knockdown cells [processed data: allelicExpr.readCount.matrix.csv].

first: Wenju

last: Sun

first: Wenkai

last: Yi

first: Xi

last: Wang


title: Reduced left atrial cardiomyocyte PITX2 and elevated circulating BMP10 predict atrial fibrillation after ablation

city: Birmingham

first: Jasmeet

middle: S

last: Reyat

address: Vincent Drive

institute: University of Birmingham

summary:
Background: Genomic and experimental studies suggest a role for PITX2 in atrial fibrillation (AF). To assess whether this association is relevant for recurrent AF in patients, we tested whether left atrial PITX2 affects recurrent AF after AF ablation.
Methods: mRNA concentrations of PITX2 and its cardiac isoform, PITX2c, were quantified in left atrial appendages (LAA) from patients undergoing thoracoscopic AF ablation, either in whole LAA tissue (n=83) or in LAA cardiomyocytes (n=52), and combined with clinical parameters to predict AF recurrence. Literature suggests bone morphogenetic protein 10 (BMP10) as a PITX2-repressed, atrial-specific, secreted protein. BMP10 plasma concentrations were combined with eleven cardiovascular biomarkers and clinical parameters to predict recurrent AF after catheter ablation in 359 patients.
Results: Reduced cardiomyocyte PITX2 concentrations, but not whole LAA tissue PITX2, were associated with AF recurrence after thoracoscopic AF ablation (16% decreased recurrence per 2-(ΔΔCt) increase in PITX2). RNA sequencing, qPCR and Western blotting confirmed BMP10 as one of most PITX2-repressed atrial genes. Left atrial size (hazard ratio per mm increase, HR [95%CI] 1.055 [1.028, 1.082], non-paroxysmal AF (HR 1.672 [1.206, 2.318]) and elevated BMP10 (HR 1.339 [CI 1.159, 1.546] per quartile increase) were predictive of recurrent AF. BMP10 outperformed eleven other cardiovascular biomarkers in predicting recurrent AF.
Conclusions: Reduced left atrial cardiomyocyte PITX2 and elevated plasma concentrations of the PITX2-repressed, secreted, atrial protein BMP10 identify patients at risk of recurrent AF after ablation.

overall_design: Left atrial tissue samples from WT and Pitx2+/- mice

first: Paulus

last: Kirchhof


title: Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [TET2i_Bisulfite_Padlock_seq]

overall_design: To explore the capacity for TET2 to induce epigenetic changes at cytosine sites associated with PD in neurons, we depleted TET2 mRNA levels by siRNA in an in vitro neuronal cell model, SH-SY5Y cells. DNA isolated from TET2 inhibited and non-targeting control were then used for targeted bisulfite deep sequencing (16 samples: 8 TET2 siRNA, 8 non-targeting control).

last: Li


title: Resident peritoneal macrophage exhibit marked sexual dimorphism in gene expression

city: Edinburgh

first: Stephen

middle: John

last: Jenkins

state: Midlothian

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: Resident CD102+ peritoneal and plueral macrophages were FACS-sorted from unmanipulated male and female C57BL/6 mice and compared by RNAseq.

overall_design: Population-level transcriptomic data are presented from single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+ peritoneal and pleural macrophages from male and female C57BL/6 mice.

first: Calum

last: Bain

first: Nichlolas

last: Steers


title: Oxidant Alterations in Adipocyte mRNA Expression: Role of the Na,K-ATPase Oxidant Amplification Loop

status: Public on Jun 18 2020

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

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

overall_design: Refer to individual Series


title: Seminal Plasma-Derived Extracellular-Vesicle Fractions from HIV-Infected Men Exhibit Unique MicroRNA Signatures and Induce a Proinflammatory Response in Cells Isolated from the Female Reproductive Tract

city: San Francisco

first: Nadia

last: Roan

state: California

address: 1650 Owens Street

institute: University of California at San Francisco

summary: The continuing spread of HIV/AIDS is predominantly fueled by sexual exposure to HIV-contaminated semen. Seminal plasma (SP), the liquid portion of semen, harbors a variety of factors that may favor HIV transmission by facilitating viral entry into host cells, eliciting the production of pro-inflammatory cytokines, and enhancing the translocation of HIV across the genital epithelium. One important and abundant class of factors in SP is extracellular vesicles (EVs), which in general are important intercellular signal transducers. Although numerous studies have characterized blood plasma-derived EVs from both uninfected and HIV-infected individuals, little is known about the properties of EVs from semen of HIV-infected individuals. We report here that fractionated SP enriched for EVs from HIV-infected men induce potent transcriptional responses in epithelial and stromal cells that interface with luminal contents of the female reproductive tract. Compared to semen EV fractions from uninfected individuals, those from acutely-infected individuals induced a more pro-inflammatory signature. This was not associated with any observable differences in the surface phenotypes of the vesicles. However, miRNA expression profiling analysis revealed that EV fractions from infected individuals exhibit a broader and more diverse profile. Taken together, our data suggest that SP EVs from HIV-infected individuals exhibit unique miRNA signatures and exert potent pro-inflammatory transcriptional changes in cells of the female reproductive tract, which may facilitate HIV transmission.

overall_design: The seminal plasma-derived microvesicle fractions (from 15 acutely-infected individuals and from 15 uninfected individuals) were assessed for their effects on endometrial stromal fibroblasts (n=3 donors) and endometrial epithelial cells (n=3 donors) by RNAseq.

first: Erika

middle: G

last: Marques de Menezes

first: Karen

last: Jang

first: Ashley

middle: F

last: George

first: Mette

last: Nyegaard

first: Jason

last: Neidleman

first: Heather

middle: C

last: Inglis

first: Ali

last: Danesh

first: Xutao

last: Deng

first: Amirali

last: Afshari

first: Young

middle: H

last: Kim

first: Jean-Noël

last: Billaud

first: Kara

last: Marson

first: Christopher

middle: D

last: Pilcher

first: Satish

middle: K

last: Pillai

first: Phillip

last: Norris

middle: R


title: Mucin-type O-glycosylation controls pluripotency in mouse embryonic stem cells via Wnt receptor endocytosis

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Bioinformatics

institute: Soka University, Graduate School of Engineering

summary: Mucin-type O-glycosylation regulates mouse embryonic stem cells pluripotency by directly modulating the endocytosis of the Wnt receptor Frizzled-5, finely tuning Wnt signaling outcome.

overall_design: RNA-seq to examine galectins and Znrf3/Rnf43 expression in 1 technical and biological replicate of WT R1 mouse ESC cell line

first: Federico

last: Pecori

first: Yoshihiro

last: Akimoto

first: Hisatoshi

last: Hanamatsu

first: Jun-ichi

last: Furukawa

first: Yasuro

last: Shinohara

first: Yuzuru

last: Ikehara