title: The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

institute: Imperial College

summary: Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. We confirm and extend prior results showing that T. acidophilum harbours a HU family protein, HTa, that protects part of the genome from MNase digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization behaviour. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

sample_organism:
Escherichia coli
Thermoplasma acidophilum
synthetic construct

overall_design: Examination of Mnase digestion products along the course of T.acidophilum growth phase, In E.coli cells expressing Hta. Digestion of T.acidophilum and E.coli genomic DNA by MNase. Relative migration of DNA oligo in EMSA-seq assay using purified HTa.

first: Antoine

last: Hocher


title: MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [CLIP-Seq]

status: Public on Oct 03 2019

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

country: China

institute: Southern Medical University

summary: Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. We demonstrate the critical role of MyoD in activating eRNAs production. Results from in depth dissection of two eRNAs transcribed from super enhancers (seRNA-1 and -2) suggest that seRNAs can promote myogenic differentiation in vitro and in vivo; the induction of the seRNAs is in coordination with the activation of the neighboring genes and seRNA loss largely impairs their expression. Mechanistically, we elucidate these seRNAs specifically bind to heterogeneous nuclear ribonucleoprotein L (hnRNPL) and modulate hnRNPL binding to the target promoter. A CAAA tract on the seRNA was identified to be essential in mediating the interaction between seRNA-1 and hnRNPL. Disruption of seRNA-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the target genes, in coincidence with the reduction of their expression. Furthermore, analyses of hnRNPL binding transcriptome-wide reveals its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction contributes to target mRNA activation.

overall_design: 2 RNA-seq, 1 hnRNPL CLIP-seq, 8 GRO-seq experiments performed.

first: Huating

last: Wang

first: Hao

last: Sun

first: Yu

last: Zhao

first: Liangqiang

last: He

first: Kun

first: Xiaona

last: Chen

first: Yuying

last: Li


title: MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation

type: Expression profiling by high throughput sequencing


title: Genetic networks regulating structure and function of the maize shoot apical meristem

status: Public on Oct 02 2019

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

country: Germany

institute: University of Tuebingen

summary:
The shoot apical meristem (SAM) of plants, a specialized stem cell niche at the growing shoot tip, integrates developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its activity throughout the plant's lifetime is tightly controlled. To gain insight into gene regulatory networks behind stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of distinct domains and cell types within the vegetative shoot apex of 14 day-old maize B73 seedlings using laser microdissection and RNA deep sequencing.
Data for 9 domains was previously released under SRA: SRP101301. This release adds data for biological duplicate samples collected for the SAM central zone, and the adaxial and abaxial sides of leaf primordia.

overall_design: Bulk RNA sequencing for maize shoot apices. 2x replicates center zone of shoot apex, 2x replicates abaxial sides of leaf primordia, and 2x replciates adaxial sides of leaf primordia


title: Generation of targeted homozygosity in the genome of human induced pluripotent stem cells

status: Public on Oct 01 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: When loss of heterozygosity (LOH) is correlated with loss or gain of disease phenotype, it is often necessary to identify which gene or genes are involved. Here, we generated a region-specific LOH-inducing system based on mitotic crossover in human induced pluripotent stem cells (hiPSCs). We first tested our system on chromosome 19. To detect homozygous clones generated by LOH, a positive selection cassette was inserted at the AASV1 locus of chromosome 19. LOHs were generated by the combination of allele-specific double-stranded DNA breaks introduced by CRISPR/Cas9 and suppression of Bloom syndrome (BLM) gene expression by the Tet-Off system. The BLM protein inhibitor, ML216, exhibited a similar crossover efficiency and distribution of crossover sites. We next applied this system to the short arm of chromosome 6 where human leukocyte antigen (HLA) loci are located. Genotyping and fluorescence-activated cell sorting analysis demonstrated that LOHs associated with chromosomal crossover occurred at the expected positions. Thus, HLA-homozygous hiPSCs generated from parental cells may help to mitigate a current shortcoming of hiPSC-based transplantation related to the immunological differences between donor and host. In conclusion, the system described in this study would greatly facilitate not only the genetic analysis of hiPSCs but also hiPSCs-based  regenerative medicine.

overall_design: RNA-sequencing analyses were performed in six fibroblast cells and one its-derived induced pluripotent stem cells.

first: Yasuhide

last: Yoshimura


title: GEF-H1 mediated gene expression changes in BMDCs in response to microtubule destabilization

city: Dallas

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

department: Medicine

country: USA

institute: University of Texas Southwestern Medical Center

summary: GEF-H1 controls transcriptional programs that mediate antitumor immuity upon microtubule destabilization.

overall_design: Transcriptional responses in BMDCs from WT and Arhgef2 deficient after 5 hours of microtubule destbilization.


title: GIRK1 triggers multiple cancer-related pathways in the benign mammary epithelial cell line MCF10A

city: Graz

first: Wolfgang

last: Schreibmayer

state: Styria

address: Neue Stiftingtalstrasse 6/D04

department: Biophysics

country: Austria

institute: Medical University of Graz

summary: Excessive expression of subunit 1 of GIRK1 in ER+ breast tumors is associated with reduced survival times, and increased lymph node metastasis in patients. To investigate possible tumor-initiating properties, benign MCF10A and malign MCF7 mammary epithelial cells overexpressing GIRK1 were engineered, neoplasia associated vital parameters and resting potentials were measured and compared to controls.  Presence of GIRK1 resulted in resting potentials negative to controls. Upon GIRK1 overexpression, several cellular pathways were sizably regulated towards pro-tumorigenic action as revealed by comparison of transcriptomes of MCF10AGIRK1 with control (MCF10AeGFP). According to transcriptome analysis, cellular migration was promoted while wound healing and extracellular matrix interactions were impaired. Vital parameters in MCF7 cells were affected akin the benign MCF10A lines, although to a lesser extent. Thus, GIRK1 overexpression will aid in classification of ER+ breast tumors and bears the potential to open a new window for the therapy of this detrimental disease.

overall_design: Transcriptomes of two MCF10A cell lines stably overexpressing KCNJ3 (GIRK1) and of two control MCF10A lines were assesed

first: Gebhard

last: Schratter

first: Thomas

last: Bauernhofer


title: A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

summary: Single cell RNA-sequencing of kidney, lung, and spleen tissue from young (7-8 months) and old (22-23 months) male C57Bl/6 mice.

overall_design: Kidney, lung, and spleen were extracted from each of 4 young (7-8 mo) and 3 old (22-23 mo) mice. Single cells were isolated from each tissue. Each tissue cell suspension from each animal was processed in 2 technical replicates (separate emulsion reactions in a 10x Chromium).

middle: C

first: Lolita

last: Penland

first: Nimrod

middle: D

last: Rubinstein

first: David

middle: G

last: Hendrickson

middle: R

last: Kelley

first: Adam

middle: Z

last: Rosenthal


title: Single cell transcriptome analysis of normal, Thalassemia and sickle cell donors' bone marrow CD34+ cells

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

summary: 4 normal, 3 thalassemia major and 5 sickle cell donors' bone marrow CD34+ cells were analyzed using 10X chromium platform and also Lineage depleted CD34+ cells from one normal sample


title: Next Generation Sequencing of Wild Type and Mice Knocked Out for Known Methionine Sulfoxide Reducatases

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: Methionine sulfoxide reductase (Msr) is an important antioxidant enzyme. The mammalian Msr family has four members: MsrA, MsrB1, MsrB2, and MsrB3. We generated a mouse strain with deletion of all four Msr proteins. Deletion was confirmed by Western blotting. The quadruple knockout mouse is viable, and growth, development, and fertility appear normal. However, they are unexpectedly resistanct to oxidative stresses. We therefore determined the RNA expression profile in liver and heart of wild-type and quadruple knockout mice.

overall_design: Cardiac and liver mRNA profiles of 3-6 month old wild type and quadruple knockout female mice were generated by deep sequencing, using Illumina Hiseq3000.

first: Lo

last: Lai

first: Rodney

middle: L

last: Levine


title: Gene expression data from early mouse prostate development

city: Gainesville

first: Tracie

last: Baker

state: FL

institute: University of Florida

summary:
Evaluation of gene expression changes corresponding to urogenital epithelial migration during early mouse prostatic development
We used microarrays to investigate the global programme of gene expression in early mouse prostate tissue and identified necessary mediators of urogenital epithemial migration and relation to SOX9

overall_design: Mouse urogenital sinuses of littermate controls and SOX9 knockouts were analyzed for phenotypic and gene expression changes. 6 Male wildtype, 6 Male SOX9 KO, 5 Female WT and 5 Female SOX9 KO.

first: Richard

middle: E

last: Peterson


title: Cx3cr1-deficient microglia exhibit a premature aging transcriptome

city: La Jolla

first: Christopher

middle: K

last: Glass

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CX3CR1, one of the highest expressed genes in microglia in mice and humans, is implicated in numerous microglial functions. However, the molecular mechanisms underlying Cx3cr1 signaling are not well understood. Here, we analyzed transcriptomes of Cx3cr1-deficient microglia under varying conditions by RNA-Seq. In 2 mos mice, Cx3cr1 deletion resulted in the downregulation of a subset of immune-related genes, without substantial epigenetic changes in markers of active chromatin. Surprisingly, Cx3cr1-deficient microglia from young mice exhibited a transcriptome consistent with that of aged Cx3cr1-sufficient animals, suggesting a premature aging transcriptomic signature. Immunohistochemical analysis of microglia in young and aged mice revealed that loss of Cx3cr1 modulates microglial morphology in a compatible fashion. Our results suggest that CX3CR1 may regulate microglial function in part by modulating the expression levels of a subset of inflammatory genes during chronological aging, making Cx3cr1-deficient mice useful for studying aged microglia.

overall_design: H3K27ac and Rpb2 ChIP-seq for microglia C57BL/6J mice and Cx3cr1-deficient mice.

first: Stefka

last: Gyoneva

first: Raghavendra

last: Hosur

last: Gosselin

first: Baohong

last: Zhang

first: Zhengyu

last: Ouyang

first: Anne

last: Cotleur

first: Michael

first: Norm

last: Allaire

first: Ravi

last: Challa

first: Patrick

last: Cullen

first: Chris

last: Roberts

first: Kelly

last: Miao

first: Taylor

last: Reynolds

first: Linda

last: Burkly

middle: M

last: Ransohoff


title: Ac4ManNAz enriched small RNAs

status: Public on Sep 30 2019

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary: Ac4ManNAz enriched small RNAs in HeLa and H9 ES cells

overall_design: RNA sequencing libraries from the small RNA fractions of Ac4ManNAz treated HeLa and H9. RNA samples were isolated from bulk small RNAs or Ac4ManNAz-enriched (via biotin-streptavidin pulldowns after Cu-free click to DBCO-biotin).


title: CAR T cells Overexpressing cJun Are Exhaustion-Resistant and   Mediate Enhanced Antitumor Activity

city: PALO ALTO

first: Hima

last: Anbunathan

address: 265 Campus Drive

summary: CAR T cells mediate antitumor effects in a small subset of cancer patients, but dysfunction due to T cell exhaustion is an important barrier to progress.  To investigate the biology of exhaustion in human T cells expressing CAR receptors, we used a model system employing a tonically signaling CAR, which induces hallmarks of exhaustion described in other settings.  Exhaustion was associated with a profound defect in IL-2 production alongside increased chromatin accessibility of AP-1 transcription factor motifs, and overexpression of numerous bZIP and IRF transcription factors that have been implicated in inhibitory activity. Here we demonstrate that engineering CAR T cells to overexpress c-Jun, a canonical AP-1 factor, enhanced expansion potential, increased functional capacity, diminished terminal differentiation and improved antitumor potency in numerous in vivo tumor models. We conclude that a functional deficiency in c-Jun mediates dysfunction in exhausted human T cells and that engineering CAR T cells to overexpress c-Jun renders them exhaustion-resistant, thereby addressing a major barrier to progress for this emerging class of therapeutics.

overall_design: RNAseq profiling of Naïve- and CM-derived GD2, CD19 or HA CAR T cells at days 7, 10, and 14 in culture and JUN overexpressed HA and CD19 CART.

first: Rachel

last: Lynn

first: Evan

middle: W

last: Weber

first: Elena

last: Sotillo

first: Zinaida

last: Good

first: Robert

last: Jones

first: Robbie

last: Majzner

first: Crystal

last: Mackall


title: RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

city: indianapolis

first: Rudong

last: Li

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their disease-causing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, we develop      the RegSNPs-intron algorithm based on a random forest classifier that integrates RNA splicing, protein structure and evolutionary conservation features. RegSNPs-intron shows excellent performance in evaluating the pathogenic impacts of iSNVs. Using a high-throughput functional reporter assay called ASSET-seq (ASsay for Splicing using ExonTrap and sequencing), we evaluate the impact of regSNPs-intron predictions on splicing outcome. Together, RegSNPs-intron and ASSET-seq enable effective prioritization of iSNVs for disease pathogenesis.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Sequencing of RNA products (amplified using PCR) generated from an Exontrap plasmid loaded with a fragment containing a part of real exon and intron harboring the reference or alternative allele of an intronic variant. Counts of spliced products with respect to a set of test variants were documented, in five replicates for each of three cell lines.

first: Joseph

last: Ipe


title: Hippo Pathway Deletion in Adult Resting Cardiac Fibroblasts Initiates a Cell State Transition with Spontaneous and Self-Sustaining Fibrosis

city: Cambridge

first: Matthew

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Cardiac fibroblasts (CFs) respond to injury by transitioning through multiple cell states, including resting CFs, activated CFs, and myofibroblasts. We report here that Hippo signaling cell-autonomously regulates CF fate transitions and proliferation, and non-cell-autonomously regulates both myeloid and CF activation in the heart. Conditional deletion of Hippo pathway kinases, Lats1 and Lats2, in uninjured CFs initiated a self-perpetuating fibrotic response in the adult heart that was lethally exacerbated by myocardial infarction (MI). Single cell transcriptomics showed that uninjured Lats1/2 mutant CFs spontaneously transitioned to a myofibroblast cell state. Through gene regulatory network reconstruction, we found that Hippo-deficient myofibroblasts deployed a network of transcriptional regulators of endoplasmic reticulum (ER) stress, and the unfolded protein response (UPR) consistent with elevated secretory activity. Moreover, we observed an expansion of myeloid cell heterogeneity in uninjured Lats1/2 CKO hearts with a striking similarity to cells recovered from infarcted control hearts. Integrated genome-wide analysis of Yap chromatin occupancy revealed that Yap directly activates myofibroblast cell identity genes, the proto-oncogene Myc, and an array of genes encoding pro-inflammatory factors through enhancer-promoter looping. Thus, our data indicate that Lats1/2 maintain the resting CF cell state through restricting the Yap-induced injury response.

overall_design: Using unbiased genomic approaches including high throughput single-cell transcriptomics, enhancer connectome profiling (H3K27ac HiChIP), CUT&RUN, and computational analysis to characterize CFs and myofibroblasts in unprecedented detail, we discovered that the Hippo signaling pathway acts as a repressor of pro-inflammatory signaling cascades, myofibroblast identity, and the global cardiac injury response. Remarkably, after deletion of the core Hippo signaling kinase components, Lats1 and Lats2, in uninjured mouse CFs, we observed massive organ-wide fibrosis that resembled, at the molecular and phenotypic levels, the control heart after MI. Furthermore, Hippo-deficient CFs challenged with myocardial infarction were unable to differentiate and generate a mature scar. Our data highlight an essential role for Lats kinases in cardiac tissue homeostasis and the regulation of the wound response through repression of the downstream effector Yap.


title: Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures

city: New York

first: Alice

middle: V

last: Easton

state: NY

address: 430 E 29th St

department: Microbiology

institute: NYU Langone

summary:
Purpose: Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system.

Methods: Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur.

Results: We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa.

Conclusions: There is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.

overall_design:
Cross-sectional and longitudinal samples from human study participants. Treatment consisted of 3 doses of albendazole 400mg/day, and post-deworming samples were collected approximately 3 weeks later.

Please note that the micronutient/diet characteristis are done 1x per person, thus same value shown at both time-points for people sampled twice

Raw data of microbial 16S rRNA sequencing has been deposited on Qiita (https://qiita.ucsd.edu/), with the study identifiers 11912 and 11913

first: Mei

middle: S

last: Tang

first: P'ng

last: Loke


title: Attenuated FGF signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae

city: Boston

first: John

last: Young

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

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

sample_organism:
Dromaius novaehollandiae
Gallus gallus

platform_organism:
Dromaius novaehollandiae
Gallus gallus

overall_design: Refer to individual Series


title: BAT Hi-C maps global chromatin interactions in an efficient and economical way

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary:
We describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops.
This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs.
The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time.

overall_design: BAT Hi-C data in Untreated mES cells. Reference: The SRA Study accession (SRP218781) and BioProject accession (PRJNA561038)

first: Jie

last: Huang

first: Yongpeng

last: Jiang


title: Attenuated FGF signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae (RNA-seq data)

summary: The evolutionary origin of powered flight was fundamental to the establishment and radiation of the avian clade, and it remains a salient feature of modern birds.  However, flight has been lost multiple times throughout the evolution of the avian lineage.  Ratites (flightless palaeognaths, including the emu, ostrich and other well-known groups) are perhaps the most notable flightless birds, and their convergent losses of flight often coincide with adaptations to a cursorial lifestyle, including robust legs, digit loss, and reduced wings. Although there is a wealth of comparative anatomical knowledge for several ratites, the underlying genetic mechanisms producing these changes remain debated. Here we use a multidisciplinary approach employing embryological, genetic, and genomic techniques to interrogate the mechanisms underlying the delay in forelimb development contributing to the diminution of the forelimb in emu embryos.  We show that the epithelial to mesenchymal transition (EMT) in the lateral plate mesoderm (LPM) and muscle precursor migration, the initiating events of limb formation, occur at equivalent stages in the emu and chick. However, the early emu forelimb fails to proliferate at HH18.  The unique emu forelimb expression of Nkx2.5, previously associated with diminished wing development, does not initiate until after this stage, concomitant with migration of myoblasts into the limb bud, and hence would not appear to be the proximal cause of limb reduction in this species.  In contrast, RNA-sequencing of HH18 limb tissues reveals significantly lower Fgf10 expression in the emu forelimb. Artificially increasing mesenchymal Fgf10 expression to the nascent emu wing induces ectodermal Fgf8 expression and results in a proliferative limb bud.  Analyzing open chromatin reveals differentially active regulatory elements near Fgf10 and Sall-1 in the emu wing compared to emu hindlimb and both chicken limbs.  Additionally, we show that the Sall-1 enhancer activity is dependent on an Ets transcription factor-binding site likely mediated by Fgf-signaling.  Taken together, our results support a model where regulatory changes result in lower expression of Fgf10 and a concomitant failure to induce the genes required for limb proliferation in the early emu wing bud at HH18.

overall_design: Comparison of different tissue between the emu and the chick

middle: J


title: EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA  methylation

first: Priscillia

last: Lhoumaud

address: 550 first avenue Smilow 307

department: Pathology

institute: NYU Langone Health

type: Methylation profiling by high throughput sequencing

summary: We developed a low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA.

overall_design: M-ATAC and CTCF-M-ChIP in mouse embryonic stem cells, M-ATAC and KLF4 M-ChIP in KLF4 KO mESC that reexpress either a WT or mutant version of KLF4 (R462A), and RNAseq

first: Jane

last: Skok


title: Physical and functional interaction between the SET1/COMPASS complex component CFP-1/CXXC and a Sin3S HDAC complex

status: Public on Sep 29 2019

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: The CFP1/CXXC protein targets SET1/COMPASS complexes to non-methylated CpG rich promoter regions to implement tri-methylation of histone H3 Ly4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss depend on chromatin context. Little is known about how CFP1 binding is coordinated with other chromatin factors. Using a proteomics approach, we establish a link between C. elegans CFP1 and a small Rpd3/Sin3 histone deacetylase (HDAC) complex (Sin3S). Mutants of CFP-1, SIN-3, and the catalytic subunit SET-2/SET1 have similar phenotypes and misregulate the expression of common genes. CFP-1 directly interacts with SIN-3 through a region including the conserved PAH1 domain, and contributes to recruitment of SIN-3 and the Sin3S subunit HDA-1 to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3 HDAC small complex at promoters, with implications for the coordinate regulation of gene expression by chromatin- associated complexes with distinct activities.

overall_design: ChIP-seq was used to profile H3K4me3, SIN-3, and HDA-1 in wild-type, cfp-1, and set-2 mutant C. elegans embryos

first: Przemyslaw

last: Stempor


title: Transcriptional control of lung alveolar type 1 cell development and maintenance by NK Homeobox 2-1 [ChIP-Seq]

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: The extraordinarily thin alveolar type 1 (AT1) cell constitutes nearly the entire gas exchange surface and allows passive diffusion of oxygen into the blood stream. Despite such an essential role, the transcriptional network controlling AT1 cells remains unclear. Using cell-specific knockout mouse models, genomic profiling, and three-dimensional imaging, we found that NK Homeobox 2-1 (NKX2-1) is expressed in AT1 cells and is required for the development and maintenance of AT1 cells. Without Nkx2-1, developing AT1 cells lose three defining features — molecular markers, expansive morphology, and cellular quiescence — leading to alveolar simplification and lethality. NKX2-1 is also cell-autonomously required for the same three defining features in mature AT1 cells. Intriguingly, Nkx2-1 mutant AT1 cells activate gastrointestinal genes and form dense microvilli-like structures apically. Single cell RNA-seq and whole lung ChIP-seq show NKX2-1 binding to 68% of genes that are downregulated upon Nkx2-1 deletion including 93% of known AT1 genes, but near-background binding to upregulated genes. Our results identify a key node in the AT1 cell transcriptional network and demonstrate remarkable plasticity of an otherwise terminally differentiated cell type.

overall_design: Whole lung ChIP-seq to examine NKX2-1 binding.

first: Jichao

last: Chen


title: Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from CTNNB1 gene (circ-CTNNB1)

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Circular RNAs (circRNAs), a subclass of noncoding RNAs characterized by covalently closed continuous loops, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating the Wnt/β-catenin signaling and cancer progression still remain elusive. We identify one intronic circRNA derived from CTNNB1 (circ-CTNNB1) as a novel driver of cancer progression. To investigate the mechanisms underlying the oncogenic functions of circ-CTNNB1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer AGS cells in response to stable over-expression of circ-CTNNB1. The results showed that stable over-expression of circ-CTNNB1 led to altered expression of 2230 human mRNAs, including 1244 up-regulated genes and 986 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-CTNNB1 over-expression in human cancer cells, and these findings will help us understand the pathogenesis of cancer progression.

overall_design: Total RNA of cells stably transfected with empty vector or circ-CTNNB1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: Effects of BPA, BPF and BPS treatments on mESC EB-based global and neural differentiations.

first: Francesco

last: Faiola

address: 18 Shuangqing rd

institute: Research Center foe Eco-Environmental Sciences, Chinese Academy of Sciences

summary:
Purpose: the goal of this study is to determine the changes in gene expression during EB differentiation after BPA, BPF and BPS treatments, as indications of potential developmental toxicity.
Methods: Transcriptomics profiling for EB samples treated with 100 nM BPA, BPF, BPS or DMSO control at different time points were generated by RNA-seq, using a BGISEQ-500 platform. Reads were filtered and aligned to the reference genome with Bowtie2.
Results: BPA, BPF and BPS disrupted many processes, during mESC global and neural differentiations, in very similar manners. In fact, analogous gene categories were differentially regulated by the three chemicals, at each time point, particularly the ones involved in cell-matrix and cell-cell adhesions, signal transduction pathways, and medical conditions such as cardiovascular diseases and cancer.

overall_design: Samples treated with 100 nM BPA, BPF, BPS or DMSO were collected at differentiation days 0, 4, 6, 9, 12 and 20 for global EB differentiation, and at days 0, 4, 8 and 10 during EB/NPC differentiation.


title: An Improved Platform for Functional Assessment of Large Protein Libraries in Mammalian Cells

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

summary: Multiplex genetic assays can simultaneously test thousands of genetic variants for a property of interest. However, limitations of existing multiplex assay methods in cultured mammalian cells hinder the breadth, speed, and scale of these experiments. Here, we describe a series of improvements that greatly enhance the capabilities of a Bxb1 recombinase-based landing pad system for conducting different types of multiplex genetic assays in various mammalian cell lines. We incorporate the landing pad into a lentiviral vector, easing the process of generating new landing pad cell lines. We also develop several new landing pad versions, including one where the Bxb1 recombinase is expressed from the landing pad itself, improving recombination efficiency more than 2-fold and permitting rapid prototyping of transgenic constructs. Other versions incorporate positive and negative selection markers that enable drug-based enrichment of recombinant cells, enabling the use of larger libraries and reducing costs. A version with dual convergent promoters allows enrichment of recombinant cells independent of transgene expression, permitting the assessment of libraries of transgenes that perturb cell growth and survival. Finally, we demonstrate these improvements by assessing the effects of a combinatorial library of oncogenes and tumor suppressors on cell growth. Collectively, these advancements make multiplex genetic assays in diverse cultured cell lines easier, cheaper and more effective, facilitating future studies probing how proteins impact cell function, using transgenic variant libraries tested individually or in combination.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: We created a molecular cloning framework that allows for combinatorial barcoding, expression, and sequencing of two distinct transgenes separated by a 2A element. Each transgene in each position was given a 16 nucleotide identifier sequence, separated by a 20 nucleotide constant region. Each 16 nucleotide identifier was composed of eight nucleotides of known sequence serving as a transgene identifier, flanked on either side by four degenerate nucleotides serving as unique plasmid identifier sequences. The plasmid preparation was sequenced in two seperate instances. We recombined the library into LLP-rEF1α cells (Fig 3a) and grew the cells for two weeks, enricheding recombined cells to ~40%. Genomic DNA was extracted from each cell pellet, and recombined plasmid barcodes were amplified and sequenced at high throughput. We performed a total of eight replicate experiments from two independent recombinations.

middle: A

first: Douglas

last: Fowler


title: Expression profile of human umbilical venous endothelial cells and human pluripotent stem cell-derived endothelial cells

status: Public on Sep 28 2019

city: Kyoto

first: Rio

last: Sugimura

state: KYOTO

address: 53 Shogoin

institute: CiRA

summary: We report that HUVEC-derived angiocrine factors amplify erythroblast. We took hPSC-EC as a reference

overall_design: Examination of gene expression in 2 cell types

first: Ryohichi

first: Daisuke

last: Okuzaki


title: An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

sample_organism:
Sarcophilus harrisii
Homo sapiens
Mus musculus


title: An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer [RNA-Seq]

summary: Loss of MHC class I (MHC-I) antigen presentation in cancer cells can lead to immunotherapy resistance. Using a genome-wide CRISPR/Cas9 screen we identify a critical role for polycomb repressive complex 2 (PRC2) in the coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP). This evolutionarily conserved function of PRC2 promotes evasion of T-cell mediated immunity, enabling tumour transmission to non-histocompatible recipients in small cell lung cancer (SCLC) and Tasmanian Devil Facial Tumour. MHC-I APP gene promoters in MHC-I low cancers harbour bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine induced MHC-I APP gene upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological silencing of MHC-I expression highlights a conserved mechanism by which cancers arising from these primitive tissues coopt PRC2 activity to enable immune evasion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Changes in gene expression following CRISPR KO of EED with/without IFNg treatment in K562 cells, and Mouse SCLC treated with IFNg and/or EZH2i

first: Marian

last: Burr

first: Enid

last: Lam


title: Region-wide subsets of AR, FOXA1 and H3K27ac ChIP-Seq within three primary prostate adenocarcinoma, three metastatic castratation-resistant and prostate cell-lines.

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Division of Oncogenomics

country: Netherlands

institute: NKI

summary: Supporting ChIP-Seq data for the article "The genomic landscape of metastatic castration-resistant prostate cancers" by Dessel et al. (Nat. Comm. 2019)  reveals multiple distinct genotypes with potential clinical impact

overall_design:
Examination of AR, FOXA1 and H3K27ac binding within the 7.5Mb region of four genes (AR, MYC, KLK3, TMPRSS2)
Note from submitter: Raw data files will be submitted at  the European Genome-phenome Archive (EGA) due to it being personally identifiable genetic and phenotypic data

first: Job

last: van Riet

first: Yanyun

last: Zhu

first: Harmen

last: van de Werken


title: Genome-wide maps of heterochromatin state (H3K9me2) in kinetochore and other centromere related mutants.

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

summary: We report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 maps of fission yeast mutants with either deletions of non-essential kinetochore genes or conditional inactivation (temperature sensitive, ts) mutations in essential ones. We find that the impairment of the kinetochore componnets cause various levels (from no to prominent) of heterochroamatin spreading into centromeric core regions. Hence, we conclude that the integrity of the inner kinetochore is required to maintain normal centromeric chromatin organization as well as distinct centromere identity.

overall_design: 2 outer kinetochore ts mutants, 7 inner kinetochore mutants and 4 mutants of genes encoding centromere-interacting proteins or histone chaperones were examined. All ts mutants are cultured under permissive condition (26 °C) and non-permissive condition (26 °C shifted to 36 °C for 3-4 h).  In anti-H3K9me2 ChIP-seq experiments, only mhf2∆ and cnp3∆fta6∆ had two biological replicates, the remaining samples were examined only once.

first: Xiangwei

last: He


title: Expression data from P14 Lgr5-2A-EGFP mouse uterus

status: Public on Sep 26 2019

city: Singapore

first: Ryo

last: Seishima

address: 8A Biomedical Grove

country: Singapore

institute: A*STAR Institute of Medical Biology

summary:
Epithelial gland development within the uterine lining during prepubertal period is important to ensure successful gestation in adults. Lgr5 expression in uterus becomes largely restricted to the tips of developing glands after birth. These Lgr5 highly expressing cells function as stem cells during gland development.
We used microarrays to detail the gene expression profilings and compare between Lgr5 highly and negatively expressing cells in developing uterus.

overall_design: Uteruses from Lgr5-2A-EGFP mice aged at P14 were used for RNA extraction and hybridization on Affymetrix microarrays. We sorted EGFP high and negative cells by FACS and proceeded for RNA extraction.

first: Yada

last: Swathi


title: Age-related dopaminergic innervation augments Th2 inflammation in the postnatal lung

first: Xingbin

last: Ai

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: The goal of this assay is to investigate the signaling pathways involved in dopamine's promotion on Th2 differentiation and proliferation and to clarify the role of dopaminergic nerve innervation in neonatal asthma pathogenesis, to help identifying potential targets for therapy. To do that, we isolated naïve CD4+ T cells from spleens of non-transgenic C57BL/6 mice according to established protocols, and we cultured them under Th0 condition with/without dopamine treatment. To obtain an unbiased view of gene regulation in mouse CD4+ T cells exposed to dopamine, we analyzed the transcriptome of untreated control CD4+ T cells ('Th0') and dopamine-treated CD4+ T cells ('Th0+Dopa') via explorative RNA-sequencing.

overall_design: Relative comparison of mRNA profile of mouse splenic naïve CD4+ T cells with different treatments: (1) naïve CD4+ T cells cultured under Th0 condition ('Th0'), (2) naïve CD4+ T cells cultured under Th0 condition with dopamine treatment ('Th0+Dopa'). The RNA sequencing was performed in Illumina HiSeq2500, with each sample split into 2 lanes. Data were generated in duplicate.

first: Wei

last: Wang

first: Matthew

last: Jones


title: Transcriptional profile of Tim-3+ and Tim-3- CD8+ T cells from trigeminal ganglion 8 days post HSV-1 infection

city: Pittsburgh

first: Anthony

last: St. Leger

state: PA

address: 203 Lothrop St.

department: Ophthalmology

institute: University of Pittsburgh

summary: The goal of this study was to compare the transcriptional profile between different subpopulations of CD8+ T cells in the trigeminal ganglion 8 days post HSV-1 infection. Within the HSV-1 infected TG, essentially all of the CD8+ T cells are virus specific and by using a tetramer for the immunodominant epitope from glycoprotein B (gB), we can separate the CD8+ T cell response into two populations: the gB-CD8+ T cells and the Subdom-CD8+ T cells. These populations have different levels of functionality during viral latency and express different checkpoint molecules that may influence this. Past work has shown that expression of PD-1 is associated with impaired functionality in this model and we are currently investigating the role of Tim-3, as there is little overlap in expression between Tim-3 and PD-1 and Tim-3 appears to mark functional cells when assessed by flow cytometry. By sorting cells first by using tetramer to create two populations of CD8+ T cells and then further separating these populations using expression of Tim-3 and PD-1, we have isolated subpopulations to assess what genes are up and downregulated in Tim-3+ cells compared to Tim-3- cells in each population.

overall_design: Trigeminal ganglion from 10-12 mice infected with HSV-1 were excised at 8dpi and pooled and CD8+ T cells were FACS sorted into a total of eight populations. To obtain these eight populations, the pooled sample was split into two and the CD8+ T cells were divided using a tetramer for the immunodominant gB epitope. One sample was used to obtain the gB tetramer positive cells (gB-CD8+ T cells) and the second sample was used to obtain the gB tetramer negative cells (Subdom-CD8+ T cells). These two subpopulations were each sorted into four populations based on Tim-3 and PD-1 expression (Tim-3+PD-1+, Tim-3+PD-1-, Tim-3-PD-1+, and Tim3-PD-1-). The sort was repeated twice for a total of three replicates.

first: Kate

last: Carroll


title: RORα is crucial for attenuated inflammatory response to maintain intestinal homeostasis.

city: Seoul

first: Dongha

last: Kim

address: 599 Gwanak-ro

country: South Korea

institute: Seoul National University

summary: A member of the nuclear receptors, retinoic acid-related orphan receptor a (RORa) is an important transcription factor for various biological processes including circadian rhythm, metabolic regulation, immune cell development and cancer. Here we found that RORa is important for intestinal homeostasis by negatively regulating the transcriptional activity of NF-kB, a major inflammatory regulator in intestinal epithelial cells. Intestinal Rora-deficient mice found were highly susceptible to DSS-induced injury. Transcriptome analysis showed that intestine-specific Rora deletion causes regulatory impairment of NF-kB signaling leading to excessive inflammatory responses. RORa specifically binds to the NF-kB target promoter and inhibits transcriptional activity for transcriptional repression of NF-kB activity via histone deacetylase 3 (HDAC3). Taken together, RORa plays a pivotal role in the homeostatic regulation of intestinal epithelial cells in inflammatory conditions. Therefore, therapeutic strategies designed to modulate RORa activity may be beneficial in the treatment of chronic inflammatory diseases such as Inflammatory bowel disease (IBD).

overall_design: Gene expression profiling of RORaf/f and intestine-specific Rora knock-out (RORaΔIEC) Intestinal Ephithelial Cell (IEC) untreated or treated with DSS.

first: Daechan

last: Park

first: Sung-Hee

last: Baek


title: The zingerone analog, acetyl zingerone, bolsters matrisome synthesis, inhibits MMPs, and represses IL-17A target gene expression [Experiment 2]

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary:
Zingerone (Z) is a phenolic alkanone derived from natural sources with anti-inflammatory and antioxidant effects. Acetyl zingerone (AZ) is a newly designed molecule that shares structural features with Z but is expected to have improved stability and antioxidant function. This study utilized microarrays to compare effects of Z and AZ on gene expression in reconstituted human epidermis. Both Z and AZ increased Notch pathway gene expression (NOTCH1, MAML3) and decreased expression of genes linked to extracellular matrix disassembly (MMP3, CTSV) and reactive oxygen species metabolism (PMAIP1, ARG2). Although Z and AZ each inhibited in vitro MMP-1, MMP-3 and MMP-12 activity, inhibition of MMP-3 and MMP-12 was greater with AZ. Moreover, AZ led to more consistent increases in the expression of genes encoding collagens (COL11A2), proteoglycans (VCAN) and ECM glycoproteins (SPARC). Finally, AZ opposed gene expression patterns associated with fibroblast senescence, keratinocyte differentiation, and IL-17A stimulation. These effects were AZ-specific and not replicated by Z. These results show that AZ improves extracellular matrix integrity with retinoid-like effects on differentiation and inflammation. Our findings provide rationale for clinical studies to understand benefits of AZ in the treatment or prevention of skin aging, or potentially, as a treatment for other human skin diseases.
Microarray analyses was performed to characterize global gene expression responses to acetyl zingerone (AZ) (50 μg/ml) in EpiDerm FT (RHE) tissue cultures.

overall_design: EpiDerm FT (RHE) tissues were treated with CTL or AZ for a 24 hour period. Water was used as the control and the AZ concentration was 50 μg/ml. RNA was then extracted and samples were then sent for DNA microarray analysis (Agilent microarrays, Human version 8X60K).

first: Krzysztof

last: Bojanowski

first: Ratan

last: Chaudhuri


title: The zingerone analog, acetyl zingerone, bolsters matrisome synthesis, inhibits MMPs, and represses IL-17A target gene expression

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

overall_design: Refer to individual Series


title: Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

status: Public on Sep 27 2019

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: The human bronchial epithelium is composed of multiple, distinct cell types that cooperate to defend against environmental insults. While studies have shown that smoking alters bronchial epithelial function and morphology, its precise effects on specific cell types and overall tissue composition are unclear. We used single-cell RNA sequencing to profile bronchial epithelial cells from six never- and six current smokers. Unsupervised analyses led to the characterization of a set of toxin metabolism genes that localized to smoker ciliated cells, tissue remodeling associated with a loss of club cells and extensive goblet cell hyperplasia, and a novel peri-goblet epithelial subpopulation in smokers that expressed a marker of bronchial premalignant lesions. Our data demonstrates that smoke exposure drives a complex landscape of cellular alterations that may prime the human bronchial epithelium for disease.

overall_design: Single-cell RNA-Seq was performed on cells isolated from bronchial brushings procured from healthy, volunteer never smokers (n=6) and current smokers (n=6).

first: Grant

last: Duclos

first: Joshua

last: Campbell

first: Jennifer

last: Beane


title: The zingerone analog, acetyl zingerone, bolsters matrisome synthesis, inhibits MMPs, and represses IL-17A target gene expression [Experiment 1]

summary:
Zingerone (Z) is a phenolic alkanone derived from natural sources with anti-inflammatory and antioxidant effects. Acetyl zingerone (AZ) is a newly designed molecule that shares structural features with Z but is expected to have improved stability and antioxidant function. This study utilized microarrays to compare effects of Z and AZ on gene expression in reconstituted human epidermis. Both Z and AZ increased Notch pathway gene expression (NOTCH1, MAML3) and decreased expression of genes linked to extracellular matrix disassembly (MMP3, CTSV) and reactive oxygen species metabolism (PMAIP1, ARG2). Although Z and AZ each inhibited in vitro MMP-1, MMP-3 and MMP-12 activity, inhibition of MMP-3 and MMP-12 was greater with AZ. Moreover, AZ led to more consistent increases in the expression of genes encoding collagens (COL11A2), proteoglycans (VCAN) and ECM glycoproteins (SPARC). Finally, AZ opposed gene expression patterns associated with fibroblast senescence, keratinocyte differentiation, and IL-17A stimulation. These effects were AZ-specific and not replicated by Z. These results show that AZ improves extracellular matrix integrity with retinoid-like effects on differentiation and inflammation. Our findings provide rationale for clinical studies to understand benefits of AZ in the treatment or prevention of skin aging, or potentially, as a treatment for other human skin diseases.
Microarray analyses was performed to characterize global gene expression responses to zingerone (Z) (50 μg/ml) in EpiDerm FT (RHE) tissue cultures.

overall_design: EpiDerm FT (RHE) tissues were treated with CTL or Z for a 24 hour period. Water was used as the control and the Z concentration was 50 μg/ml. RNA was then extracted and samples were then sent for DNA microarray analysis (Affymetrix Human Gene ST 2.1 strips). Samples were processed on 3 microarray strips.


title: A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signaling in monocyte-derived alveolar macrophages

city: Chicago

first: Alexander

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Pulmonary fibrosis is a heterogenous syndrome in which fibrotic scar replaces normal lung tissue. We performed single-cell RNA-seq on the lungs from mice exposed to fibrogenic particle (asbestos) and non-fibrogenic particle (TiO2) 14 days after the exposure to dissect cellular interactions unfolding during the early stages of the pulmonary fibrosis.

overall_design: Three months-old C57Bl/6 male mice were exposed to abestos or TiO2 (intratracheally) and 14 days later single cell suspension was prepared and single-cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).

first: Nikita

last: Joshi

first: Alexandra

last: McQuattie-Pimentel

first: Satoshi

last: Watanabe

first: GR

last: Budinger

first: Nikolay

last: Markov


title: Differential response to rotator cuff tear in C57BL/6J mice and MRL/MpJ mice

first: Christopher

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report RNA sequencing data from the infraspinatus muscles of 3-month old male C57BL/6J (Jackson Labs stock 000664) or MRL/MpJ mice (Jackson Labs stock 000486). Mice underwent a full-thickness infraspinatus tenectomy and denervation, and four weeks later muscles were collected for analysis. Comparisons are made to control male mice of the same strains who did not undergo infraspinatus tenectomy and denervation.

overall_design: Differential expression of mRNAs were evaluated between the infraspinatus muscles of C57BL/6J and MRL/MpJ mice that were either subjected to a infraspinatus tenectomy and denervation or who were unoperated controls.


title: The distinct immune-stimulatory capacities of Porphyromonas gingivalis strains 381 and 33277 are determined by the fimB allele and gingipain activity

city: Seattle

first: Jeffrey

last: McLean

state: WA

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

summary: The genomes of P. gingivalis strains 33277 and 381 are highly related phylogenetically.  However,  33277  displays a reduced capacity to stimulate HEK cell TLR2-dependent signaling and THP-1 cell-dependent IL-1β production compared to 381, suggesting strain-specific differences in the expression of one or more bacterial immune-modulatory cell surface molecules.  Genomic sequencing identified a single nucleotide polymorphism in the 33277 fimB allele (A>T), encoding a truncated FimB protein, relative to the 381 fimB allele. Gene exchange experiments indicated that the 33277 fimB allele contributes to the reduced immune-stimulatory capacity of this strain. Transcriptomic analyses determined that multiple genes related to carboxy-terminal domain (CTD) family proteins, including the gingipains, were upregulated in strain 33277 relative to strain 381.  A gingipain substrate degradation assay confirmed that cell surface gingipain activity is higher in 33277; and an isogenic mutant strain deficient for the gingipains exhibited an increased capacity to activate TLR2 signaling and induce IL-1β production. Furthermore, 33277 and 381 isogenic mutant strains devoid of CTD cell surface proteins displayed increased immune-stimulatory capacities compared to the wild-type parental strains, confirming an immune-suppressive role for the gingipains.  Collectively, our data indicate that the combination of an intact fimB allele and limited cell surface gingipain expression in strain 381 contributes to its relatively potent immune-stimulatory activity.  Conversely, a defective fimB allele and high levels of cell surface gingipains reduce the capacity of strain 33277 to elicit host cell innate immune responses.

sample_organism:
Porphyromonas gingivalis ATCC 33277
Porphyromonas gingivalis 381

overall_design: Transcriptional profiling of triplicate cultures of Porphyromonas gingivalis strains ATCC 33277 and 381.

first: Stephen

last: Coats

first: Nutthapong

last: Kantrong

first: Sumita

last: Jain

first: Erik

last: Hendrickson

first: Thao

middle: T

last: To

first: Caroline

last: Genco

first: Richard

middle: P

last: Darveau


title: An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer [ChIP-Seq]

first: Mark

last: Dawson

summary: Loss of MHC class I (MHC-I) antigen presentation in cancer cells can lead to immunotherapy resistance. Using a genome-wide CRISPR/Cas9 screen we identify a critical role for polycomb repressive complex 2 (PRC2) in the coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP). This evolutionarily conserved function of PRC2 promotes evasion of T-cell mediated immunity, enabling tumor transmission to non-histocompatible recipients in small cell lung cancer (SCLC) and Tasmanian Devil Facial Tumor. MHC-I APP gene promoters in MHC-I low cancers harbour bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine induced MHC-I APP gene upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological silencing of MHC-I expression highlights a conserved mechanism by which cancers arising from these primitive tissues coopt PRC2 activity to enable immune evasion.

platform_organism:
Sarcophilus harrisii
Homo sapiens
Mus musculus

overall_design: Changes in histone modifications and IRF1 binding with EZH2 inhibitor in mouse SCLC and human K562 cells

first: Marian

last: Burr

first: Enid

last: Lam


title: Physical and functional interaction between the SET1 complex component CFP-1/CXXC and the Sin-3S/HDAC complex in C. elegans embryos

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

summary: The highly conserved CFP1 CXXC zinc finger protein targets SET1 family complexes to promoter regions to implement methylation of histone H3 Ly4  (H3K4me), a mark that correlates with gene expression  depending on the chromatin context. Whether CFP1 physically interacts with additional chromatin modifying proteins on chromatin has not been investigated. By applying interaction proteomics coupled to mass spectrometry to identify factors that interact with C. elegans CFP-1, we establish a link between CFP-1 and the Rpd3/Sin3 histone deacetylase (HDAC) small complex (Rpd3/Sin3S) in embryos. We show that CFP-1 directly interacts with SIN-3 through a highly conserved C-terminal domain, and that the two proteins extensively colocalize with H3K4me3 at promoter regions genome-wide. Animals lacking sin-3, cfp-1 or the catalytic H3K4 methyltransferase subunit set-2/SET1 show misregulation of common genes in early embryos, reduction in fertility, and defects in the division of intestinal cells in adults, consistent with common developmental functions. Our results suggest that in addition to its well characterized role as a central subunit of the SET-2/SET1 complex, CFP-1 interacts with the Sin3S/HDAC complex at promoter regions to influence gene expression in a developmental context. This has implications for the coordinate regulation of gene expression by chromatin associated complexes with distinct activities.

overall_design: 3 replicates of 4 different embryonic C.elegans strains have been anayzed : wild-type strain (WT) was used as control and the 3 mutants strains are cfp-1(tm6369), sin-3(tm1276) and set-2(bn129)

first: Flore

last: Beurton

first: Matthieu

last: Caron

first: Cecile

last: Bedet

first: David

last: Cluet

first: Marion

last: Herbette

first: Helène

first: Yohann

last: Couté

first: Martin

last: Spichty

first: Przemysław

last: Stempor

first: Julie

last: Ahringer

first: Francesca

last: Palladino


title: A vasodilator Oxyfedrine Inhibits Aldehyde Metabolism and thereby Sensitizes Cancer Cells to Glutathione Depleting Agents

status: Public on Sep 25 2019

city: Shinjuku-ku

first: Yuji

last: Otsuki

state: Tokyo

address: 35 Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University

summary: The major antioxidant glutathione (GSH) protects cancer cells from oxidative damage leading to ferroptosis, an iron-dependent cell death. Therapy-resistant cancer cells often manifest high expression of the cystine-glutamate antiporter subunit xCT which enhances cystine uptake leading to GSH synthesis and thereby survive oxidative damage and ferroptosis. The use of GSH-depleting agents including xCT inhibitors might thus be expected to enhance the efficacy of cancer therapy. On the other hand, the efficacy of xCT-targeted therapy depends on the cellular metabolism affecting antioxidant system in cancer cells and metabolic reprograming might reduce the efficacy of cancer therapy using xCT inhibitors. Recently, to overcome the resistance to xCT-targeted therapy, we performed a library screening and identified an oral anesthetics dyclonine (DYC) as a sensitizing drug for xCT inhibitor sulfasalazine (SSZ). However, DYC is a local anesthetic and might not suitable for the systemic administration combined with SSZ in a clinical setting. In this study, we identified a vasodilator oxyfedrine (OXY) which is clinically used in systemic administration also acts as a sensitizing drug to GSH-depleting agents in multiple type of cancer cells. OXY and DYC share the motif required for the covalent inhibition of aldehyde dehydrogenases (ALDHs), and combined treatment with OXY and SSZ induced the accumulation of cytotoxic aldehyde 4-hydroxynonenal (4-HNE) and induce cell death in SSZ-resistant cancer cells. Furthermore, we found that OXY sensitizes cancer cells to radiation therapy which decreases intracellular GSH content. Our findings establish a rationale for repurposing of OXY as a sensitizing drug for xCT-targeted cancer therapy.

overall_design: HCT116 cells (2 × 106 cells per site) were implanted s.c. in the flank of athymic nude mice (CLEA Japan). The mice were then injected i.p. with physiological saline, Sulfasalazine, Oxyfedrine, or both drugs. Triple independent replicates were performed.

first: Juntaro

last: Yamasaki

first: Kentaro

last: Suina

first: Shogo

last: Okazaki

first: Naoyoshi

last: Koike

first: Hideyuki

last: Saya

first: Osamu

last: Nagano


title: Single nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

city: Houston

first: Qingnan

last: Liang

state: TX

address: One Baylor Plaza

department: HGSC

institute: Baylor College of Medicine

summary: We report a single-nuclei RNA-seq (snRNA-seq) transcriptomic study on human neural retinal tissue to identify transcriptome profile for individual cell types. Six retina samples from three healthy donors were profiled and RNA-seq data with high quality was obtained for 5873 single nuclei. All seven major retinal cell types were observed from the dataset and marker genes for each cell type were identified by differential gene express analysis.

overall_design: To globally characterize the transcriptomes of healthy human retina, we performed single nuclei RNA sequencing  of retinal tissues from three healthy donors.

first: Rachayata

last: Dharmat

first: Sangbae

last: Kim

first: Yumei

last: Li

first: Margaret

last: DeAngelis

first: Rui

last: Chen


title: Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]

city: Boston

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

summary: Silencers active in the Drosophila embryonic mesoderm were identified by reporter assays in dissociated embryonic cells. We find that, despite the presence of ChIP peaks for known transcriptional corepressors and marks of repressed chromatin, the only significantly enriched source of mesodermal silencers is non-mesodermal enhancers. We present evidence that a subset of silencers acts by looping to target promoters.

overall_design: We generated a population of Drosophila embryos in which GFP is driven by a strong, ubiquitous enhancer modified by the activity of a library of candidate silencers. We FACS-sorted embryonic mesodermal cells with reduced GFP expression and recovered mesodermal silencers by PCR and Illumina high-throughput sequencing.

first: Alexandre

last: Palagi

first: Jesse

last: Kurland

first: Julia

last: Rogers

first: Hakan

last: Ozadam

first: Ye

last: Zhan

first: Job

last: Dekker

first: Martha

last: Bulyk


title: The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells [dataset 5, MAVAN I]

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

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

type: Methylation profiling by genome tiling array

summary: The development of current biological markers of aging has primarily focused on adult samples. The epigenetic clock is one promising tool for measuring biological age that shows impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several agerelated phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as  compared to adults. To address this crucial gap, we aimed to develop a highly accurate, noninvasive biological measure age specific to pediatric samples by using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032) and the performance was assessed in a separate dataset (n = 689). The DNAm at 94 CpG sites was highly predictive of age in the test cohorts (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs (MAVAN I, dataset 5, n = 98, age range = 4.2-11.2 years). Buccal swabs were collected using Catch-All Swabs (Epicentre, Illumina, USA). Genomic DNA was extracted using the  Masterpure system (Epicentre, USA), quantified using a NanoPhotometer P300 (Implen, Germany) and subsequently purified and concentrated using DNA Clean & Concentrator  (Zymo Research, CA, USA).

first: Lisa

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

last: McGill

first: Rachel

middle: D

last: Edgar

first: Meaghan

last: Jones

last: MacIsaac

first: David

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

last: Kee

first: Torsten

last: Klengel

first: Nancy

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

middle: F

last: Giesbrecht

first: James

middle: N

last: Reynolds

first: Darina

last: Czamara

first: Jeffrey

last: Armstrong

first: Marilyn

last: Essex

first: Carolina

last: de Weerth

first: Roseriet

last: Beijers

first: Marieke

last: Tollenaar

first: Bekh

last: Bradley

first: Tanja

last: Jovanovic

first: Kerry

last: Ressler

first: Meir

last: Steiner

first: Sonja

last: Entringer

first: Pathik

last: Wadhwa

first: Claudia

last: Buss

last: Bush

first: Elisabeth

middle: B

last: Binder


title: The PedBE clock estimates DNA methylation age in pediatric buccal cells [dataset 10, MAVAN II]

first: Michael

last: Kobor

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs (MAVAN II, dataset 10, n = 265, age range = 5-11 years). This data is longitudinal with two-three samplings per individual, time range between samplings varied between 6 months and 2 years. Buccal swabs were collected using Catch-All Swabs (Epicentre, Illumina, USA). Genomic DNA was extracted using the Masterpure system (Epicentre, USA), quantified using a NanoPhotometer P300 (Implen, Germany) and subsequently purified and concentrated using DNA Clean & Concentrator (Zymo Research, CA, USA).

first: Lisa

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

middle: G

last: McGill

first: Rachel

last: Edgar

first: Meaghan

last: Jones

first: Julia

middle: L

last: MacIsaac

first: David

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

middle: Z

last: Kee

first: Torsten

last: Klengel

first: Nancy

middle: E

last: Adler

first: Ronald

last: Barr

last: Letourneau

last: Giesbrecht

middle: R


title: Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly-editable sites, including some human pathogenic C-to-T mutations. We further profile the accessibilities of twenty base editors to all possible pathogenic mutations in silico. Finally, we build the BEable-GPS (Base Editable prediction of Global Pathogenic SNVs) database for users to select proper base editors to model or correct disease-related mutations. This in-vivo comparison and in-silico profiling catalogs the availability of base editors and their broad applications in biomedical studies.

overall_design: Comparison of cytosine base editors on pathogenic and genomic sites

first: Jia

last: Chen

first: Bei

first: Ying

last: Wang

first: Runze

last: Gao

first: Jing

last: Wu

first: Yi-Chun

last: Xiong

last: Wei

first: Sipin

last: Zhang


title: Genome sequence of the Eastern woodchuck (Marmota monax) – a preclinical animal model for chronic hepatitis B

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Gene expression profiling by RNAseq of lung, thymus, heart, pancreas, kidney, spleen and liver tissues from woodchuck as a preclinical animal model for chronic hepatitis B

overall_design: In total 20 untreated reference samples  from 6 different organs

first: Tyler

last: Alioto

first: Fernando

last: Cruz

first: Jèssica

last: Gómez-Garrido

first: Miriam

last: Triyatni

first: Marta

last: Gut

first: Leonor

last: Frias

first: Anna

last: Esteve-Codina

first: Stephan

last: Menne

last: Kiialainen

first: Nadine

last: Kumpesa

first: Fabian

last: Birzele

first: Ivo

first: Olivia

last: Spleiss


title: E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [RNA-Seq]

city: Eugene

first: Jeffrey

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: We report the development of a versatile strategy for engineered nucleosome positoining across eukaryotic genomes.

overall_design: Transcription profiling data (Strand-specific RNA-seq from rRNA-depleted samples) from yeast containing engineered chromatin remodeling proteins

first: Drake

last: Donovan

first: Johnathan

last: Crandall

first: Orion

last: Banks

first: Devin

last: Dinwiddie

first: Vi

last: Truong

first: Zena

last: Jensvold

first: Laura


title: The PedBE clock estimates DNA methylation age in pediatric buccal cells [dataset 2, C3ARE]

first: Michael

last: Kobor

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs from the Gene Expression Collaborative for Kids Only (C3ARE, dataset 2, n = 89, age range = 3.6-5.8 years) cohort. This cohort is comprised of Canadian children from Vancouver, British Columbia. Buccal epithelial cells were collected with  using Isohelix Buccal Swabs (Cell Projects, Harrietsham, Kent, England) and stabilized per manufacturer’s instructions for storage at room temperature. Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects, Harrietsham, Kent, England), and then purified and concentrated using DNA Clean & Concentrator (Zymo Research, Irvine, CA).

first: Lisa

middle: M

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

last: McGill

first: Rachel

last: Edgar

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: David

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

last: Kee

first: Torsten

last: Klengel

first: Nancy

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

last: Giesbrecht

first: James

last: Reynolds

first: Darina

last: Czamara

last: Armstrong

first: Marilyn

last: Essex

first: Carolina

last: de Weerth

first: Roseriet

last: Beijers

first: Marieke

last: Tollenaar

first: Bekh

last: Bradley

first: Tanja

last: Jovanovic

first: Kerry

last: Ressler

first: Meir

last: Steiner

first: Sonja

last: Entringer

first: Pathik

last: Wadhwa

first: Claudia

last: Buss

last: Bush

first: Elisabeth

last: Binder


title: Attenuated FGF signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae (ATAC-seq data)

first: John

last: Young

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The evolutionary origin of powered flight was fundamental to the establishment and radiation of the avian clade, and it remains a salient feature of modern birds.  However, flight has been lost multiple times throughout the evolution of the avian lineage.  Ratites (flightless palaeognaths, including the emu, ostrich and other well-known groups) are perhaps the most notable flightless birds, and their convergent losses of flight often coincide with adaptations to a cursorial lifestyle, including robust legs, digit loss, and reduced wings. Although there is a wealth of comparative anatomical knowledge for several ratites, the underlying genetic mechanisms producing these changes remain debated. Here we use a multidisciplinary approach employing embryological, genetic, and genomic techniques to interrogate the mechanisms underlying the delay in forelimb development contributing to the diminution of the forelimb in emu embryos.  We show that the epithelial to mesenchymal transition (EMT) in the lateral plate mesoderm (LPM) and muscle precursor migration, the initiating events of limb formation, occur at equivalent stages in the emu and chick. However, the early emu forelimb fails to proliferate at HH18.  The unique emu forelimb expression of Nkx2.5, previously associated with diminished wing development, does not initiate until after this stage, concomitant with migration of myoblasts into the limb bud, and hence would not appear to be the proximal cause of limb reduction in this species.  In contrast, RNA-sequencing of HH18 limb tissues reveals significantly lower Fgf10 expression in the emu forelimb. Artificially increasing mesenchymal Fgf10 expression to the nascent emu wing induces ectodermal Fgf8 expression and results in a proliferative limb bud.  Analyzing open chromatin reveals differentially active regulatory elements near Fgf10 and Sall-1 in the emu wing compared to emu hindlimb and both chicken limbs.  Additionally, we show that the Sall-1 enhancer activity is dependent on an Ets transcription factor-binding site likely mediated by Fgf-signaling.  Taken together, our results support a model where regulatory changes result in lower expression of Fgf10 and a concomitant failure to induce the genes required for limb proliferation in the early emu wing bud at HH18.

overall_design: Bulk ATAC-seq from three tissues (HH18 forelimb somatopleure, HH18 flank somatopleure, and HH18 hindlimb somatopleure) from emu and chicken embryos.  Three biological replicates were generated for each tissue and species.

first: Phil

last: Grayson


title: VEGF-A drives TOX-dependent T cell exhaustion in anti–PD-1–resistant microsatellite stable colorectal cancers

city: Daejeon

first: Chang Gon

last: Kim

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

overall_design: Normal colon, MC38-OVA, Control siRNA transfected, TOX siRNA transfected CD8 T cell, Control CD8 T cell, VEGF-A treated CD8 T cell

first: Mi

last: Jang

first: Youngun

first: Galam

last: Leem

first: Kyung-Hwan

first: Hoyoung

last: Lee

first: Tae-Shin

first: Seong-Jin

last: Choi

first: Hyung-Don

first: Ji-Won

last: Han

first: Minsuk

last: Kwon

first: Jong-Hoon

first: Andrew J.

first: Su-Kyung

last: Nam

first: Seok-Joo

last: Bae

first: Sat-Byol

first: Sang-Joon

last: Shin

first: Joong-Bae

last: Ahn

first: Kang-Young

first: Sung-Ho

last: Park

first: Inkyung

last: Jung

first: Su-Hyung

first: Hoguen

first: Byung-Soh

last: Min

first: Eui-Cheol


title: E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [ChIP-Seq]

first: Jeffrey

last: McKnight

overall_design: ChIP-seq is used to track removal of Ume6-FLAG by action of engineered chromatin remodeling proteins in yeast. ChIP-seq is used to track acetylated H3K23 levels before and after Ume6 removal via action of engineered chromatin remodeling proteins in yeast

first: Drake

last: Donovan

first: Johnathan

last: Crandall

first: Orion

last: Banks

first: Devin

last: Dinwiddie

first: Vi

last: Truong

first: Zena

last: Jensvold

first: Laura


title: Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [Hi-C]

first: Stephen

last: Gisselbrecht

institute: Brigham and Women's Hospital

summary: We generated HiC data from sorted mesodermal and non-mesodermal cells from stage 11-12 Drosophila embryos to explore the distribution of genomic contacts of silencers and non-silencers (identified elsewhere in the manuscript).

overall_design: HiC data were generated genome-wide from sorted mesoderm and non-mesoderm, in duplicate, on an Illumina HiSeq 4000 platform with 50 bp paired-end reads.

middle: S

first: Alexandre

last: Palagi

first: Jesse

middle: V

last: Kurland

first: Julia

last: Rogers

first: Hakan

last: Ozadam

first: Ye

last: Zhan

first: Job

last: Dekker

first: Martha

last: Bulyk


title: E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning [MNase-Seq]

overall_design: Nucleosome positioning data (MNase-seq) from yeast containing engineered chromatin remodeling proteins


title: Functional loss of ATRX and telomerase activates Alternative Lengthening of Telomeres (ALT)

first: Mindy

middle: Kim

last: Graham

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

summary: The presence of ALT is strongly associated with recurrent cancer-specific somatic inactivating mutations in the ATRX-DAXX chromatin remodeling complex. Here, we generate an ALT-positive adenocarcinoma cell line following functional inactivation of ATRX and telomerase in a telomerase-positive carcinoma cell line.

overall_design: We used the CRISPR Cas9 nickase system to generate multiple ATRXKO clones in LAPC4 and CWR22Rv1. We used previously designed gRNAs that targeted the ATRX-DNMT3-DNMT3L (ADD) domain of ATRX. We generated three independent isogenic KO clones derived from LAPC-4 (LAPC-4 ATRXKO 1-3) and CWR22Rv1 (CWR22Rv1 ATRXKO 1-3) with sequence-confirmed frameshift mutations in ATRX and disrupted ATRX protein expression.

middle: K

first: Jiyoung

last: Kim

first: Joseph

last: Da

first: Jacqueline

last: Brosnan-Cashman

first: Anthony

last: Rizzo

first: Javier

last: Baena Del Valle

first: Lionel

last: Chia

first: Michael

last: Rubenstein

first: Christine

last: Davis

first: Leslie

last: Cope

last: Considine

middle: C

last: Haffner

first: Angelo

last: De Marzo

first: Alan

last: Meeker

first: Christopher

last: Heaphy


title: mRNA expression of Control or TRIB3-silenced MCF7 cells

city: Beijing

first: Jinmei

last: Yu

address: 1 Xian Nong Tan Street

institute: The Institute of Materia Medica

summary:
Investigation of whole genome gene expression level changes in TRIB3-silenced MCF7 cells as compared to Control MCF7 cells.
Analysis of activity changes of pathways for FOXO1 phosphorylation between TRIB3-silenced and Control MCF7 cells.

overall_design: Total RNA from MCF7 cells expressing Con-shRNA or TRIB3-shRNA were obtained. RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarrays were performed.


title: E-ChRPs: Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning

first: Jeffrey

last: McKnight

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

overall_design: Refer to individual Series


title: The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Circadian rhythmicity is a defining feature of mammalian metabolism that synchronizes metabolic processes to day-night light cycles. Here, we show that the intestinal microbiota programs diurnal metabolic rhythms in the mouse small intestine through histone deacetylase 3 (HDAC3).  The microbiota induced expression of intestinal epithelial HDAC3, which was recruited rhythmically to chromatin and produced synchronized diurnal oscillations in histone acetylation, metabolic gene expression, and nutrient uptake. HDAC3 also functioned non-canonically to coactivate estrogen related receptor a (ERRa), inducing microbiota-dependent rhythmic transcription of the lipid transporter gene Cd36 and promoting lipid absorption and diet-induced obesity. Our findings reveal that HDAC3 integrates microbial and circadian cues to regulate diurnal metabolic rhythms, and pinpoint a key mechanism by which the microbiota controls host metabolism.

overall_design: 1. RNAseq analysis of epithelial cell transcripts in Germ-free WT mice and conventional HDAC3fl/fl and HDAC3ΔIEC mice at 4 time points across a circadian cycle. Laser captured epithelial cells from 3 mice were pooled together for RNAseq at each time point. 2. ChIPseq analysis of epithelial cell H3K9ac and H3K27ac in Germ-free and conventional WT mice and conventional HDAC3fl/fl and HDAC3ΔIEC mice across a circadian cycle. Epithelial cells from 3 mice were pooled together for ChIPseq at each time point. 3. 16s sequencing analysis of fecal bacterial composition in HDAC3fl/fl and HDAC3ΔIEC mice before and after switching from chow diet to high-fat diet.

first: Yuhao

last: Wang

first: Yun

last: Li

first: Cunqi

last: Ye

first: Kelly

middle: A

last: Ruhn

first: Cassie

last: Behrendt

first: Eric

last: Olson

first: Lora

last: Hooper


title: The transcriptomic landscape of MAIT cell development in the thymus (NN41 RNAseq data set)

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

institute: Walter and Eliza Hall Institute of Medical Research

summary: We report the transcriptomic landscape of MAIT cell development by examining thymic immature stage 1 and mature stage 3 MAIT cells from mouse thymus, and thymic immature stage 1, stage 2  mature stage 3 MAIT cells from human thymus using RNAseq.

overall_design: We bulk-sorted (100 cell) each MAIT cell subset by flow cytometry and compared the differentially expressed genes (DEGs) between subsets.

first: Hui-Fern

last: Koay

first: Daniela

last: Zalcenstein

first: Tracey

last: Baldwin

first: Peter

last: Hickey

first: Shalin

last: Naik

first: Matthew

last: Ritchie


title: Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

summary: Transplantation of genetically corrected hepatocytes is an attractive alternative to liver transplantation but is hampered by the low amplification potential of these cells in vitro. Here, we describe a method for generating proliferative hepatic progenitor cells (iHPC) from human hepatocytes as an expandable cell source for liver therapy. Dedifferentiation of primary hepatocytes to iHPC was achieved in less than 7 days by culturing the cells in medium with a cocktail of growth factors and small molecules. In culture, iHPC expressed a combination of endoderm hepatic progenitor and mesenchymal stem cell markers and proliferated vigorously, allowing for their expansion by at least 104 times. RNA sequencing of iHPC demonstrated that they displayed far more subtle changes in both transcriptome and transposcriptome, compared to hepatocyte-derived iPSC. Finally, transplantation of iHPC into the liver of immuno-deficient mice showed iHPC differentiation potential in vivo, without triggering detectable tumor development.

overall_design: Transcriptome profiling of human primary hepatocytes from two different pediatric donors, de-differentiation timepoints to induced hepatic progenitor cells (iHPC), one iHPC clone per donor at different passages and two differentiation timepoints to hepatocyte-like cells (HLC).

first: Carmen

last: Unzu


overall_design: Transcriptome profiling of human primary hepatocytes from two different pediatric donors, reprogramming timepoints to induced pluripotent stem cells (iPSC) from one donor, two iPSC clones and differentiation timepoints to hepatocyte-like cells (HLC).


title: Migratory and Dancing Macrophage Subsets in Atherosclerotic Lesions

status: Public on Sep 24 2019

city: La Jolla

first: Klaus

last: Ley

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Macrophage heterogeneity within atherosclerotic plaques was explored with intravital imaging, flow cytometry, and RNA sequencing. 4 populations of cells were found with varying expression profiles and functions relevant to atherosclerosis and inflammation.

overall_design: Cells were sorted from the aortas and carotid arteries of atherosclerotic Apoe-/- Cx3cr1GFP Cd11cYFP mice fed Western Diet based on GFP and YFP expression. The expression profiles of the 4 subsets (GFP+, GFP+YFP+, YFP+, GFP-YFP-) were found using an Illumina HiSeq4000.

first: Sara

last: McArdle

first: Konrad

last: Buscher

first: Yanal

last: Ghosheh

first: Akula

last: Bala Pramod

first: Jacqueline

last: Miller

first: Holger

last: Winkels

first: Dennis

last: Wolf


title: The PedBE clock estimates DNA methylation age in pediatric buccal cells [dataset 3, GECKO]

first: Michael

middle: S.

last: Kobor

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs from the Gene Expression Collaborative for Kids Only (GECKO, dataset 3, n = 254, age range = 7-12 years) cohort. This cohort is comprised of Canadian children from British Columbia. Buccal epithelial cells were collected with Isohelix DNA buccal swabs using standard collection procedures and stabilized with Isohelix Dri-Capsules for storage at room temperature prior to genomic DNA extraction (Cell Projects Ltd., Kent, UK). Genomic DNA was purified and concentrated using a DNA Clean and Concentrator Kit (Zymo Research, CA, USA).

first: Lisa

last: McEwen

first: Kieran

middle: J

last: O’Donnell

first: Megan

last: McGill

first: Rachel

last: Edgar

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: David

middle: T

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

last: Kee

first: Torsten

last: Klengel

first: Nancy

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

last: Giesbrecht

first: James

last: Reynolds

first: Darina

last: Czamara

first: Jeffrey

last: Armstrong

first: Marilyn

last: Essex

first: Carolina

last: de Weerth

first: Roseriet

last: Beijers

first: Marieke

last: Tollenaar

first: Bekh

last: Bradley

first: Tanja

last: Jovanovic

first: Kerry

last: Ressler

first: Meir

last: Steiner

first: Sonja

last: Entringer

first: Pathik

last: Wadhwa

first: Claudia

last: Buss

last: Bush

first: Elisabeth

last: Binder


title: Deregulated pulmonary growth hormones after intrauterine smoke exposure

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Background: In utero smoke exposure is a recognized risk factor for impaired lung function development and a significant risk factor for airway disease. Despite intensive anti-tobacco campaigns the prevalence of smoking pregnant women has remained high requiring additional strategies to protect the offspring’s lung. To achieve this goal, it is critical to understand the mechanisms how disease risks are established in early life.
Objective: To develop an animal model that recapitulates clinical findings in prenatally exposed children to allow the investigation of early molecular changes in the lung.
Methods: Pregnant mice were exposed to active smoking from gestational day (GD) 2.5 until caesarean section or spontaneous delivery. After careful maternal characterization, we monitored weight development, lung function, and airway remodeling in offspring. mRNA/miRNA arrays were performed in fetal lungs (GD18.5), followed by network analyses, qPCR and histone analyses.

overall_design: We performed small RNA expression microarray analysis on fetal (E18.5) lung tissue derived from mothers exposed to smoke or from untreated mothers.

first: Stefan

last: Dehmel

first: Petra

last: Nathan

first: Hagen

last: Scherb

first: Sabine

last: Bartel

first: Katrin

last: Milger

first: Gerrit

last: John

first: Ali

middle: O

last: Yildirim

first: Machteld

last: Hylkema

first: Martin

last: Irmler

first: Arthur

last: Penn

first: Bianca

last: Schaub

first: Oliver

last: Eickelberg

first: Susanne

last: Krauss-Etschmann


title: The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells [dataset 16, GUSTO]

first: Michael

last: Kobor

summary: The development of current biological markers of aging has primarily focused on adult samples. The epigenetic clock is 1 promising tool for measuring biological age that shows impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several agerelated phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as  compared to adults. To address this crucial gap, we aimed to develop a highly accurate, noninvasive biological measure age specific to pediatric samples by using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032) and the performance was assessed in a separate dataset (n = 689). The DNAm at 94 CpG sites was highly predictive of age in the test cohorts (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in  understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.

overall_design: GUSTO (Growing Up in Singapore Towards Healthy Outcomes, dataset 16, n = 339), is a Singaporean cohort of pregnant women with human buccal epithelial swabs collected from children at 3, 9, and 48 months of age. The Illumina Infinium MethylationEPIC array was used to collect genome wide DNA methylation measures from each timepoint, however, we have only included the 3 and 9 month timepoints in the current study. DNA extraction was performed using the Isohelix DDK-50 kit.

first: Lisa

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

last: McGill

first: Rachel

middle: D

last: Edgar

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: David

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

last: Kee

first: Torsten

last: Klengel

first: Nancy

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

middle: F

last: Giesbrecht

first: James

middle: N

last: Reynolds

first: Darina

last: Czamara

first: Jeffrey

last: Armstrong

first: Marilyn

last: Essex

first: Carolina

last: de Weerth

first: Roseriet

last: Beijers

first: Marieke

last: Tollenaar

first: Bekh

last: Bradley

first: Tanja

last: Jovanovic

first: Kerry

last: Ressler

first: Meir

last: Steiner

first: Sonja

last: Entringer

first: Pathik

last: Wadhwa

last: Buss

middle: B


title: Gene expression data from human breast cancer MCF-7 cells treated with siRNAs targeting long non-coding RNA TMPO-AS1

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of long non-coding RNA TMPO-AS1 in breast cancer, MCF-7 cells were treated with siRNAs targeting TMPO-AS1 (siTMPO-AS1) or control siRNA (siControl). TMPO-AS1 was shown to closely associate with estrogen signaling pathway.

overall_design: Expression profiling of siControl and siTMPO-AS1 treated MCF-7 cells.

first: Yuichi

last: Mitobe

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Multileveled reduction of p21 expression by Linc-ASEN represses cellular senescence

city: Incheon

first: Donghee

last: Kang

address: 100 Inha-ro, Michuhol-gu

department: Medicine

institute: Inha University