summary: Purpose: we utilized a mouse model that permanently labels neurons activated throughout a specific experience to decipher the interplay between chromatin accessibility, 3D-chromatin architecture and transcriptional changes across different memory phases. Non activated (basal) and activated neurons during memory encoding (early), consolidation (late) and recall (reactivated) were sorted and subjected to nuclear RNA sequencing (nRNA-seq) to determine gene expression, ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to assess chromatin accessibility, chromosome conformation capture (Hi-C) to identify global 3D -genome architecture and promoter capture Hi-C to identify the long range promoter-enhancer interactions.  Results: Our differentially expressed gene (DEG) analysis revealed relatively low amount of changes in the early phase, when compared to basal-state neurons (Basal vs. Early). In contrast, neurons from late phase presented higher numbers of DEGs despite there being more similarity in chromatin accessibility at these time points (Early vs. Late; Late vs. Reactivated). Our studies illuminate for the first time the unique transcriptional landscape of reactivated engram cells where we observed up-regulation of genes involved in mRNA transport and local protein translation in synaptic compartments. These changes corresponded to morphological and functional changes in those neurons.

overall_design: To elucidate how changes in chromatin accessibility and promoter-enhancer interactions were affecting gene expression, we performed nuclear RNA-seq (nRNA-seq) from all the neuronal sub-populations. To obtain 10,000 nuclei per condition, we pooled the hippocampal tissue from multiple mice (10-12) and isolated each group of cells via fluorescence-activated cell sorting (FACS). Collected nuclei were subjected to nRNA-seq library preparation (SmartSeq2 protocol) in 3 biological replicates.


title: Divergent cell fates and functions between skeletal and soft tissue CD146+ pericytes

status: Public on Jun 22 2020

city: Baltimore

first: Jiajia

last: Xu

state: MD

address: 720 Rutland Avenue

department: Pathology-Surgical Pathology

country: USA

institute: The Johns Hopkins University School of Medicine

summary: Human pericytes demonstrate multilineage differentiation potential, and their descendants participate in tissue homeostasis and repair.  Increasing evidence from developmental biology and tissue engineering suggest that regional specification by tissue of origin exists among human pericytes.Here, we sought to define the differentiation of CD146+ human pericytes from skeletal and soft tissue sources.  Uncultured CD146+CD31-CD45- pericytes were derived by fluorescent activated cell sorting from human periosteum, adipose, or dermal tissue.  Periosteal CD146+CD31-CD45- cells retained canonical features of pericytes, including cell surface marker expression, multilineage differentiation potential, and paracrine induced tubulogenesis.  Periosteal pericytes demonstrated a striking tendency to undergo osteoblastogenesis, while soft tissue pericytes did not in vitro or in vivo. Microarray analysis demonstrated enrichment in CXCR4 and BMP signaling among periosteal pericytes in comparison to their soft tissue pericyte counterparts.  Signaling pathway manipulation of CXCR4 among soft tissue pericytes led to an increase in osteoblastogenesis and bone formation.  In sum, skeletal and soft tissue pericytes differ in their relative lineage differentiation potential and ability to form bone.  Plasticity exists, however, and manipulation of CXCR4 signaling pathway may ‘coax’ a soft tissue pericyte toward an osteoblastogenic cell fate.

overall_design: Pericyte were FAC sorted from periosteum, adipose and skin. Microarray analysis was used to identified the gene expression differences between pericytes in 3 different tissue.

first: Aaron

last: James

first: Chingyun

last: Hsu

first: Dongqing

last: Li


title: IMPLICON: a high-resolution method to uncover DNA methylation at imprinted regions

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is an epigenetic phenomenon leading to parental allele specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for a number of human disorders. Imprinted expression is dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although a number of approaches can be used for methylation inspection at ICRs, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a new high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold genomic coverage. We initially designed this method to look at ICRs in adult tissues of inbred mice. Then, we validated in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in naïve human embryonic and induced pluripotent stem cells.  We also provide rules and guidelines in which this method can be adapted to investigate the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: [IMPLICON]  Amplicon bisulfite libraries targetting imprinted control regions for mouse and human

first: Tajda

last: Klobučar

first: Elisa

last: Kreibich

first: Maria

last: Arez

first: Duarte

last: Pólvora-Brandão

first: Ferdinand

last: von Meyenn

first: Wolf

last: Reik

first: Simão

last: Teixeira da Rocha

first: Melanie

last: Eckersley-Maslin


title: Analysis of hepatic transcriptome modulation exerted by γ-conglutin from lupins in a streptozotocin-induced diabetes model

status: Public on Jun 20 2020

city: Guadalajara

first: Carmen

middle: Magdalena

last: Gurrola-Díaz

state: Jalisco

address: Sierra Mojada 950

department: Departamento de Biología Molecular y Genómica

country: Mexico

institute: Universidad de Guadalajara

summary: Lupinus albus γ-conglutin is proposed to positively affect glucose metabolism through inhibition of hepatic glucose production and insulin-mimetic activity; however, the action mechanism is not entirely known. Besides, most studies had focused on its effect on molecular targets directly related to glucose metabolism, and few studies have investigated how γ-conglutin may affect the liver gene expression or if it plays a role in other metabolic processes. Therefore, we investigated the influence of γ-conglutin on the liver transcriptome of streptozotocin-induced diabetic rats using DNA microarrays, ontological analyses, and quantitative PCR. Of the 22,000 genes evaluated, 803 and 173 were downregulated and upregulated, respectively. The ontological analyses of the differentially expressed genes revealed that among others, the mitochondria, microtubules, cytoskeleton, and oxidoreductase activity terms were enriched, implying a possible role of γ-conglutin on autophagy. To corroborate the microarray results, we selected and quantified, by PCR, the expression of two genes associated with autophagy (Atg7 and Snx18) and found their expression augmented two and threefold, respectively; indicating a higher autophagy activity in animals treated with γ-conglutin. Although complementary studies are required, our findings indicate for the first time that the hypoglycaemic effects of γ-conglutin may involve an autophagy induction mechanism, a pivotal process for the preservation of cell physiology and glucose homeostasis.

overall_design: A two-color microarrays experiment was performed. We separately pooled equal amounts of high-quality RNA from five diabetic rats of the treated (with γ-conglutin, n = 5) and non-treated (without γ-conglutin, n = 5) groups before carrying out the cDNA synthesis and hybridization. We also replicated the cDNA hybridization using the dye-swap replication technique in two separate two-color microarray slides. Each slide contained samples from both the control and treatment groups differentially stained.

first: Tereso

middle: J

last: Guzmán

first: Belinda

last: Vargas-Guerrero

first: Pedro

middle: M

last: García-López


title: Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

status: Public on Jun 18 2020

city: Boston

first: Jing

last: Zhang

state: MA

address: 610 Commonwealth Avenuce

institute: Boston University

type: Expression profiling by high throughput sequencing

summary: When performing a computation, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to measure part function and identify the origins of failures. Here, we take “snapshots” of a large genetic circuit in different states. RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts are parameterized. The circuit behaves as designed; however, it is riddled with errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons and a failed gate. While serendipitously not impacting function, they reduce prediction accuracy and could lead to failures when used in other designs. Finally, the cellular power (RNAPs and ribosomes) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.

overall_design: Transcriptome and translatome of E.coli DH10b cells carrying a genetic circuit 0x41 at different induction states were generated

first: Amin

last: Espah Borujeni

first: Hamid

last: Doosthosseini

first: Alec

middle: A

last: Nielsen

first: Christopher

last: Voigt


title: Structure of DNA methyltransferases DNMT3A/DNMT3B bound to a nucleosome [seq]

status: Public on Jun 17 2020

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CpG methylation by the de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes yet cannot methylate the DNA wrapped around the nucleosome core2, and favor the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-EM structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3, and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.

overall_design: We verified the catalytic activity of wildtype and mutant DNMT3A2/3B3 complex using bisulfite sequencing. We also used limited micrococcal nuclease (MNase) digestion followed by sequencing to map the binding of DNMT3A2/3B3 complex to in vitro assembled nucleosome.

first: Minmin

last: Liu

first: Ting-Hai

last: Xu

first: Edward

middle: X

last: Zhou

first: Gangning

last: Liang

first: Gongpu

last: Zhao

first: Eric

middle: H

first: Karsten

last: Melcher


title: Structure of DNA methyltransferases DNMT3A/DNMT3B bound to a nucleosome

type: Methylation profiling by genome tiling array

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Expression Analysis of Mouse Tumor and Metastatic Pancreatic Ductal Adenocarcinoma Organoids

status: Public on Jun 16 2020

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: This study used Illumina strand-specific, paired-end RNA-sequencing to examine gene expression differences between matched murine tumor- and metastasis-derived mouse pancreatic ductal adenocarcinoma (PDAC) cells grown as three-dimensional, organoid cultures. The study analyzed 16 organoid lines derived from matched primary PDAC tumors and PDAC metastases from 6 KPC (KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre) mice.

overall_design: RNA-sequencing analysis (Illumina sequencing) of the primary tumor- and metastasis-derived organoids from the KPC mouse model of pancreatic ductal adenocarcinoma

first: Lindsey

last: Baker

first: Astrid

last: Deschênes


title: Total RNA-seq on purified neutrophils from healthy humans

status: Public on Jun 29 2020

city: Bethesda

first: Luis

last: Franco

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The goal of this study was to analyze the transcriptome of circulating neutrophils from healthy human donors by high-throughput sequencing of total RNA samples obtained from neutrophils purified directly from whole blood (without density-gradient centrifugation or red blood cell lysis) by immunomagnetic negative selection.

overall_design: Twenty healthy volunteers were studied (10 males and 10 females). Whole blood was obtained from healthy human donors and was collected in EDTA tubes (BD Vacutainer). Neutrophil purification was performed with the EasySep Direct Human Neutrophil Purification Kit (STEMCELL Technologies, Cat. No. 19666).

first: Manasi

last: Gadkari

first: Katherine

middle: N

last: Howe


title: RNA-sequence of epithelial-specific active mTOR transgenic mouse lung

status: Public on Jun 13 2020

city: Tokyo

first: Minako

last: Saito

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

summary: The purpose of this study is to identify the roles of epithelial active mTOR in lung fibrosis. We generated Sftpc-mTOR transgeneic mice, in which active mTOR is conditionally expressed in alveolar epithelial type II cells (AECII). We obtained AECII from mice and performed RNA sequencing.

overall_design: We extracted mRNA of AECII from 14-week-old wild type and active mTOR conditional transgenic mice.

first: Akihisa

last: Mitani


title: SOAT1 knock-out downregulates the expression of mevalonate pathway genes in PDAC organoids

summary: One of the emerging cancer vulnerabilities is altered metabolism, and several metabolic pathways have been shown to promote pancreatic ductal adenocarcinoma (PDAC). Here we use genetic targeting to delete SOAT1 from murine PDAC metastasis organoids, and use RNA-seq to identify genes differentially regulated in normal and cholesterol-supplemented media conditions in the presence or absence of SOAT1.

overall_design: RNA-seq performed in complete and cholesterol media conditions with technical duplicates for each condition.

first: Tim

middle: D

last: Somerville

first: Giulia

last: Biffi

first: Yuan

last: Hao


title: Transcriptomic profiling in juvenile P23H Retinitis Pigmentosa mouse retinas

city: Irvine

first: Henri

last: Leinonen

state: California

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California, Irvine

summary: Neuronal plasticity of the inner retina has been observed in response to photoreceptor degeneration. Typically, this phenomenon has been considered maladaptive and may preclude vision restoration in the blind. However, several recent studies utilizing triggered photoreceptor ablation have shown adaptive responses in bipolar cell dendrites expected to support normal vision. Whether such homeostatic plasticity occurs during progressive photoreceptor degenerative disease to help maintain normal visual behavior is unknown. We addressed these issues in an established mouse model of Retinitis Pigmentosa caused by the P23H mutation in rhodopsin. We show robust modulation of the retinal transcriptomic network reminiscent of the neurodevelopmental state as well as potentiation of rod – rod bipolar cell signaling following rod photoreceptor degeneration. Additionally, we found highly sensitive night vision in P23H mice even when more than half of the rod photoreceptors were lost. The results implicate retinal adaptation leading to persistent visual function during photoreceptor degenerative disease.

overall_design: Bulk retina mRNA profiling in heterozygous P23H rhodopsin mutated mice (n=7) and their wild-type littermates (n=7) at postnatal day 30

first: Frans

last: Vinberg


title: Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

status: Public on Jun 23 2020

city: Rehovot

first: Asaf

last: Marco

address: Herzl 229

country: Israel

institute: The Hebrew University of Jerusalem


title: Strain-specific strategies of 2′-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697

status: Public on Jun 07 2020

city: Madison

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

summary: Human milk oligosaccharides (HMOs) function as prebiotics for beneficial bacteria in the developing gut, often dominated by Bifidobacterium spp. To understand the relationship between Bifidobacterium utilizing HMOs and how the metabolites that are produced could affect the host, we analyzed the metabolism of HMO 2’-fucosyllactose (2’-FL), 3-fucosyllactose (3FL and difucosyllactose (DFL) in Bifidobacterium longum ssp. infantis Bi-26 and ATCC15697. RNA-seq and metabolite analysis was performed on samples at early (A600=0.25), mid-log (0.5-0.7) and late-log phases (1.0-2.0) of growth.

overall_design: Bifidobacterium longum subsp. infantis strain Bi-26 and ATCC15697 was used in this study with 2'-FL, 3FL and DFL as the test carbon sources and lactose or no carbohytdrate added control, Samples were done in duplicate with samples taken at early phase (A600 ~0.2) mid log (0.5-1.1) and late log (1.1+). ATCC15697 only had mid-log samples taken.

first: Kara

middle: C

last: Evans


title: Sequencing of Nothobranchius furzeri brain in two age groups

status: Public on Jun 19 2020

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Comparison of gene expression and ribosome profiles from Nothobranchius furzeri brain of 2 age groups. The RNA-seq and ART-seq data comprise 2 groups: 6 and 26 weeks.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: RNA-seq and ART-seq of 8 samples in 2 groups: 6 weeks (4 Samples), 26 weeks (4 Samples)

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Bimodal Adenine and Cytosine CRISPR Base Editing on DNA

status: Public on Jul 02 2020

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Adenine and cytosine base editors (ABEs and CBEs) represent a new genome editing technology that allows the programmable installation of  A-to-G or C-to-T alterations on DNA. We engineered Streptococcus pyogenes Cas9-based adenine and cytosine base editor (SpACE) that enables efficient simultaneous introduction of A-to-G and C-to-T substitutions in the same base editing window on DNA.

overall_design: HEK293T cells were transfected with a variety of base editor constructs. nCas9 and GFP expressing cells were negative controls. ABEmax and miniABEmax-V82G served as a control for A-to-G base editing on DNA and A-to-I editing on RNA. Target-AID served as a control for C-to-T base editing on DNA and C-to-U editing on RNA. All base editor constructs co-translationally expressed GFP (P2A-EGFP).The Cells were sorted for GFP based on FITC signal. RNA-seq was performed to measure transcriptional changes associated with different constructs.

first: Julian

last: Grunewald


title: Comprehensive transcriptome profiling for response to phytohormone-induced signaling in Capsicum annuum L.

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

summary: We sought to investigate the scope of transcriptome analyses of peppers subjected to four major phytohormones. For this, At the 6-true-leaf stage, pepper plants were sprayed at underside of leaves with 5 mM sodium salicylate (SA), 100 μM methyl jasmonate (JA), 5 mM ethephone (ET), 100 μM (±)-ABA, or distilled water (mock). For RNA-seq library construction, the third or fourth leaves from four plants were harvested per replicate at 0, 1, 3, 6, 12, and 24 h after treatment. A total of 187.8 Gb of transcriptome data were generated using transcriptome analysis pipelines consisting of quality control, quantification, and differential gene expression analyses. The extensive transcriptome data obtained will provide valuable information for future studies of crops exposed to responsive of phytohormones.

overall_design: We performed the RNA-seq analyses of peppers treated with SA, JA, ET, and ABA at six different time points. A total of 78 RNA samples, containing three biological replicates per time point for each of the phytohormones and a mock control, were used for RNA-sequencing

first: Junesung

last: Lee

first: Jae-Young

last: Nam

first: Hakgi

last: Jang

first: Nayoung

last: Kim

first: Yong-Min

first: Won-Hee

last: Kang


title: Gene expression changes in REH following CDC42 inhibition

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

summary: ARHGEF4 expression is associated with t(12;21) acute lymphoblastic leukaemia (ALL). Our study investigated the substrate specificity of ARHGEF4, a member of the diffuse B-cell lymphoma (DBL) family of guanine nucleotide exchange factors (GEFs), in t(12;21) ALL REH cells. ARHGEF4 was found to activate the small guanine nucleotide binding protein (GTPase) CDC42. In order to determine the function of CDC42 in t(12;21) ALL cells, we performed RNAseq analysis on REH cells treated for 24 hours with DMSO vehicle control in comparison to 25uM ML141, a CDC42 inhibitor.

overall_design: Total cellular RNA was purified from DMSO and 25uM ML141 treated REH samples from three independent experiments

first: Clemence

last: Virely

first: Luca

last: Gasparoli

first: Jasper

last: de Boer


title: Next Generation Sequencing of Total RNA of Senescent WI38 Human Fibroblast with and without knockdown of G3BP1

status: Public on Jun 04 2020

city: Montreal

first: Amr

last: Omer

state: QUEBEC

address: 3655, Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

overall_design: WI-38 cells transfected with scrambled control siRNA (siCTLD8) or G3BP knockdown siRNA (siG3BP1D8) (2 replicates each).

first: Imed-Eddine

last: Gallouzi

first: Sergio

last: Di Marco


title: Molecular and cellular consequences of genetic knockout of Hdac2 and Hdac3 in striatal medium spiny neurons of Huntington's disease knock-in mice

status: Public on Jun 01 2020

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Somatic expansion of the Huntington’s disease (HD) CAG repeat drives the rate of a pathogenic process resulting in neuronal cell death. Although mechanisms of neuronal toxicity are not well delineated, transcriptional dysregulation is a likely contributor. Chromatin modifiers are implicated in both mechanisms of CAG instability and transcriptional dysregulation. Here, we tested whether histone deacetylase genes Hdac2 and Hdac3 modify molecular and cellular phenotypes in HttQ111 knock-in mice using conditional knockouts in striatal medium-spiny striatal neurons (MSNs) exhibiting extensive CAG expansion and exquisite disease vulnerability.  MSN-specific Hdac2 or Hdac3 knockout attenuated CAG expansion, with the Hdac2 knockout impacting nuclear huntingtin pathology. Hdac2 knockout resulted in a substantial transcriptional response that included reversal of transcriptional dysregulation elicited by the HttQ111 allele. Our results identify novel modifiers of CAG expansion in MSNs, providing testable mechanistic hypotheses, and a potentially complex relationship between Htt and Hdac2 with implications for targeting transcriptional dysregulation in HD.

overall_design: RNA sequencing in 35 mouse striatal tissues of four genotype groups: HttQ111/+ Hdac2+/+ , Htt+/+ Hdac2+/+  , HttQ111/+ Hdac2D/D , Htt+/+ Hdac2D/D

first: Marina

last: Kovalenko

first: Marissa

last: Andrew

first: Jason

last: St. Claire

first: Melissa

last: Shaughnessey

first: Leroy

last: Hubert

first: Joao

middle: L

last: Neto

first: Alexei

last: Stortchevoi

first: Daniel

last: Fass

first: Ricardo

last: Pinto

first: Stephen

last: Haggarty

first: John

last: Wilson

first: Michael

middle: E

last: Talkowski

first: Vanessa

last: Wheeler


title: C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor: RNA-seq dataset 1

status: Public on Jun 05 2020

city: Worcestor

first: Gabrielle

last: Giese

address: 368 Plantation St.

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: Vitamin B12 is an essential micronutrient that functions in two metabolic pathways: the canonical propionate breakdown pathway and the methionine/S-adenosylmethionine (Met/SAM) cycle. In Caenorhabditis elegans, low vitamin B12, or genetic perturbation of the canonical propionate breakdown pathway results in propionate accumulation and the transcriptional activation of a propionate shunt pathway. This propionate-dependent mechanism requires nhr-10 and is referred to as “B12-mechanism-I”. Here, we report that vitamin B12 represses the expression of Met/SAM cycle genes by a propionate-independent mechanism we refer to as “B12-mechanism-II”. This mechanism is activated by perturbations in the Met/SAM cycle, genetically or due to low dietary vitamin B12.  B12-mechanism-II requires nhr-114 to activate Met/SAM cycle gene expression, the vitamin B12 transporter, pmp-5, and adjust influx and efflux of the cycle by activating msra-1 and repressing cbs-1, respectively. Taken together, Met/SAM cycle activity is sensed and transcriptionally adjusted to be in a tight metabolic regime.

overall_design: C. elegans RNA-sequencing of three experiments. All animals contain the Pacdh-1::GFP transgene and a deletion in nhr-10.  Parent, mthf-1 point mutant, sams-1 point mutant, metr-1 point mutant, and mtrr-1 point mutant  all treated with 20 nM vitamin B12 on an E. coli OP50 diet for 48 hours in biological duplicate.

first: Albertha

last: Walhout


title: C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor


title: C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor: RNA-seq dataset 2

overall_design: C. elegans RNA-sequencing of two experiments. All animals in both experiments contain Pacdh-1::GFP transgene. Experiment 1: wild type and nhr-114 deletion treated with nothing or 25 mM methionine and fed E. coli OP50  for 48 hours in biological duplicate. Experiment 2 - wild type, metr-1 deletion,  and metr-1 point mutant containing a deletion in nhr-10 were all grown on 20 nM vitamin B12 and treated with either vector or nhr-114 RNAi for 48 hours in biological duplicate.


title: Enhancer activation during tumor progression in the KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mouse model of pancreatic ductal adenocarcinoma.

first: David

last: Tuveson

summary: Murine pancreatic ductal adenocarcinoma tumor organoids (T6 and T23) were generated from primary tumors from KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre mice. At the first passage, cells in Matrigel were overlaid with mouse complete medium alone or supplemented with 10 uM Nutlin-3a to select for cells that have undergone loss-of-heterozygosity (LOH) for the wild-type (wt, "+") allele of Trp53. Organoids were cultured for 3 passages in the presence or absense of Nutlin-3a, and then culturing was continued in unsupplemented mouse complete medium. H3K27ac ChIP-sequencing (ChIP-seq) was performed to identify regions differentially enriched for H3K27ac binding in Trp53-LOH vs. wt tumor organoids.

overall_design: ChIP-sequencing to map peaks of H3K27ac enrichment in 2 pairs of Trp53-R172H/+ and Trp53-R172H/LOH organoids.

first: Claudia

last: Tonelli

first: Lindsey

last: Baker


title: Human iPSC-derived astrocytes from ALS patients with mutated C9ORF72 show increased oxidative stress and neurotoxicity

city: Jerusalem

first: Benjamin

last: Reubinoff

state: Jerusalem

address: Kiryat Hadassah

department: The Goldyne Savad Institute of Gene Therapy

institute: Hadassah  University Medical Center

summary: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that affects motor neurons (MNs). It was shown that human astrocytes with mutations in genes associated with ALS, like C9orf72 (C9) or SOD1, reduce survival of MNs. Astrocyte toxicity may be related to their dysfunction or the release of neurotoxic factors. We used human induced pluripotent stem cell-derived astrocytes from ALS patients carrying C9orf72 mutations and non-affected donors. We utilized these cells to investigate astrocytic induced neuronal toxicity, changes in astrocyte transcription profile as well as changes in secretome profiles. We report that C9-mutated astrocytes are toxic to MNs via soluble factors. The toxic effects of astrocytes are positively correlated with the length of astrocyte propagation in culture, consistent with the age-related nature of ALS. We show that C9-mutated astrocytes downregulate the secretion of several antioxidant proteins. In line with these findings, we show increased astrocytic oxidative stress and senescence. Importantly, media conditioned by C9-astrocytes increased oxidative stress in wild type MNs. Our results suggest that dysfunction of C9-astrocytes leads to oxidative stress of themselves and MNs, which probably contributes to neurodegeneration. Our findings suggest that therapeutic strategies in familial ALS must not only target MNs but also focus on astrocytes to abrogate nervous system injury.

overall_design: We used human induced pluripotent stem cell-derived astrocytes from two ALS patients carrying C9orf72 mutations and two non-affected donors. We utilized these cells to investigate the changes in astrocyte transcription profile.

first: Anastasya

last: Birger

first: Israel

last: Ben-Dor

first: Tikva

last: Turetsky

first: Yaniv

last: Gil

first: Eithan

last: Galun

first: Eva

last: Feldman

first: Oded

last: Behar


title: A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood stage samples

status: Public on Jun 02 2020

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Here we have designed a full processing pipeline of P. falciparum RNA that innclues RNA preservation, extraction, cDNA synthesis and amplification, globin depletion and final transcriptome readout. To validate the protocol we have analyzed transcriptomes of  P. falciaprum samples derived from filed studies as well as 3D7 lab strains.

overall_design: Samples were extracted using high-throughput techniques adied by automatics liquid handlers, cDNA was amplified and resulted transcriptomes were analyzed and validated using RNA-seq platform. Some samples were globin depeted in vitro using novel CRISPR-Cas9 depletion method.

first: Jaishree

last: Tripathi

first: Michal

last: Kucharski

first: Sourav

last: Nayak

first: Lei

last: Zhu


title: Retrieval of germinal zone neural stem cells from the cerebrospinal fluid of premature infants with intraventricular hemorrhage

city: Sevilla

first: Luis

last: Lopez Navas

state: Sevilla

address: c/ Americo Vespucio, 15, Ed. S-2

department: Preclinical Research

country: Spain

institute: Red Andaluza de diseño y traslación de Terapias Avanzadas

summary: Intraventricular hemorrhage is a common cause of morbidity and mortality in premature infants. The rupture of the germinal zone into the ventricles entails loss of neural stem cells and disturbs the normal cytoarchitecture of the region, compromising late neurogliogenesis. Here we demonstrate that neural stem cells can be easily and robustly isolated from the hemorrhagic cerebrospinal fluid obtained during therapeutic neuroendoscopic lavage in preterm infants with severe intraventricular hemorrhage. Our analyses demonstrate that these neural stem cells, although similar to human fetal cell lines, display distinctive hallmarks related to their regional and developmental origin in the germinal zone of the ventral forebrain, the ganglionic eminences that give rise to interneurons and oligodendrocytes. These cells can be expanded, cryopreserved, and differentiated in vitro and in vivo in the brain of nude mice and show no sign of tumoral transformation 6 months after transplantation. This novel class of neural stem cells poses no ethical concerns, as the fluid is usually discarded, and could be useful for the development of an autologous therapy for preterm infants, aiming to restore late neurogliogenesis and attenuate neurocognitive deficits. Furthermore, these cells represent a valuable tool for the study of the final stages of human brain development and germinal zone biology.

overall_design: 29 samples in total from different cell types and sources. Biological replicates are included. Our aim was to demonstrate that cerebrospinal fluid derived NSCs display distinctive hallmarks related to their regional and developmental origin in the ganglionic eminences of the ventricular zone. Other cell types are used to further characterization of NSCs through a comparative transcriptomic analysis

first: Beatriz

last: Fernández-Muñoz

first: Rosario

last: Sanchez-Pernaute


title: Activation of the myeloid checkpoint inhibitor LILRB3 (ILT5) elicits profound immununomodulation

status: Public on Jun 03 2020

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Purpose:To investigate the potential immunomodulatory function of a new panel of LILRB3-specific monoclonal antibody

overall_design: Human peripheral blood monocytes were isolated from freshly prepared PBMCs taken from healthy donors. ). Cells were incubated in CTL medium supplemented with 100 U/ml Penicillin-Streptomycin, 2 mM Glutamine and HEPES buffer and treated with 10 µg/ml of an isotype control or an agonistic LILRB3 mAb (clone A1; hIgG1). 18 hours later, cells were lysed in RLT lysis buffer and total RNA extracted using the RNeasy micro kit for RNAseq.

first: Ali

last: Roghanian


title: Gene expression data from T47D human breast ductal carcinoma cells treated with prolactin and/or NIM811

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1101 E Marshall St

department: Pathology

institute: Virginia Commonwealth University

summary:
The hormone prolactin is implicated in the pathogenesis of breast cancer, and a subset of prolactin-induced gene expression is mediated by CypA activity.
The non-immunosuppressive prolyl isomerase inhibitor, NIM811, is an inhibitor of CypA. We used NIM811 in combination with prolactin treatment in T47D cells to determine differential expression under these conditions.

overall_design: T47D cells were serum starved for 24 hours prior to treatment with NIM811 and/or prolactin, and subsequent RNA extraction.

first: Charles

middle: V

last: Clevenger


title: CXCL4 links inflammation and fibrosis through transcriptional and epigenetic reprogramming of inflammatory monocyte-derived cells

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

summary:
Fibrosis is a condition shared by numerous inflammatory diseases. The molecular mechanisms underlying fibrosis have remained incompletely understood severely hampering drug development. CXCL4 is associated with the onset and extent of fibrosis development in systemic sclerosis (SSc), a prototypic inflammatory and fibrotic disease. Here, we integrated 65 paired sequential whole genome transcriptional and methylation profiles from monocyte-derived cells as they respond to CXCL4 exposure. Using data-driven gene regulatory network analyses, we demonstrate that CXCL4 dramatically alters monocyte differentiation trajectory inducing a novel pro-inflammatory and pro-fibrotic phenotype mediated via key regulators such as CIITA and IRF8. Importantly, these CXCL4 exposed pro-inflammatory cells trigger a fibrosis cascade by directly producing ECM molecules and by inducing myofibroblast differentiation. Underscoring the computationally identified gene regulatory network, inhibition of CIITA mimicked CXCL4 inducing pro-inflammatory and pro-fibrotic phenotype. Our study uncovers CXCL4 as the endogenous ligand driving innate immune training and forming the long-sought link between inflammation and fibrosis.

This SuperSeries is composed of the SubSeries listed below.

Correspondence to: Prof. Timothy RDJ Radstake (T.R.D.J.Radstake@umcutrecht.nl) and Dr. Aridaman Pandit (A.Pandit@umcutrecht.nl)

overall_design: Refer to individual Series


title: CXCL4 links inflammation and fibrosis through transcriptional and epigenetic reprogramming of inflammatory monocyte-derived cells [RNA-seq]

summary:
Fibrosis is a condition shared by numerous inflammatory diseases. The molecular mechanisms underlying fibrosis have remained incompletely understood severely hampering drug development. CXCL4 is associated with the onset and extent of fibrosis development in systemic sclerosis (SSc), a prototypic inflammatory and fibrotic disease. Here, we integrated 65 paired sequential whole genome transcriptional and methylation profiles from monocyte-derived cells as they respond to CXCL4 exposure. Using data-driven gene regulatory network analyses, we demonstrate that CXCL4 dramatically alters monocyte differentiation trajectory inducing a novel pro-inflammatory and pro-fibrotic phenotype mediated via key regulators such as CIITA and IRF8. Importantly, these CXCL4 exposed pro-inflammatory cells trigger a fibrosis cascade by directly producing ECM molecules and by inducing myofibroblast differentiation. Underscoring the computationally identified gene regulatory network, inhibition of CIITA mimicked CXCL4 inducing pro-inflammatory and pro-fibrotic phenotype. Our study uncovers CXCL4 as the endogenous ligand driving innate immune training and forming the long-sought link between inflammation and fibrosis.

Correspondence to: Prof. Timothy RDJ Radstake (T.R.D.J.Radstake@umcutrecht.nl) and Dr. Aridaman Pandit (A.Pandit@umcutrecht.nl)

overall_design: Monocytes were collected from 5 healthy donors. To systematically study the effects of CXCL4 on cell differentiation, we obtained sequential RNA-seq profiles at day 0 (monocytes), day 2, 4, and 6, for monocyte differentiation into both moDCs and CXCL4-moDCs. To further study the effects of CXCL4 on cell maturation, at day 7 moDCs were stimulated with the toll-like receptor 3 ligand polyI:C. The transcriptional profiles at day 7 (before stimulation), 4 hours and 24 hours (day 8) after stimulation were studied(Fig. 1A).  In total, we obtained 65 samples for RNA-seq.

first: Sandra

last: Silva-Cardoso

first: Weiyang

last: Tao

first: Chiara

last: Angiolilli

first: Ana

middle: P

last: Lopes

first: Cornelis

last: Bekker

first: Abhinandan

last: Devaprasad

first: Barbara

last: Giovannone

first: Jaap

last: van Laar

first: Marta

last: Cossu

first: Wioleta

last: Marut

first: Erik

last: Hack

first: Rob

last: de Boer

first: Marianne

last: Boes

first: Timothy

middle: R

last: Radstake


title: RNA sequencing reveals the genetic relationship between TOPPs and its regulatory subunit PP1R3 in Arabidopsis thaliana

status: Public on Jun 09 2020

city: FuZhou

first: Jing

last: Zhang

state: Fujian Province

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

country: China

institute: Fujian Agriculture and Forestry University

summary: We identified a new regulatory subunit PP1R3 of type 1 protein phosphatase in Arabidopsis by immunoprecipitation coupled with liquid chromatography-mass spectrometry.Through RNA sequencing, it was found that there are few differentially expressed genes (DEGs) between pp1r3-2 and topp septuple mutants (topp-7m).Moreover, the DEGs of pp1r3-2 compared to the wild type (Col) have a great overlap with the DEGs of topp-7m compared to Col, and the change trend of gene expression is very similar.At the same time, we also found that pp1r3-2 can partially restore the gene expression changes in the dominant negative mutant topp4-1.And, the DEGs of pp1r3-2 and pp1r3-3 topp4-1 are less than one hundred, which is less than one-tenth of the number of DEGs of pp1r3-2 compared to Col.These results reveal a strong genetic interaction between PP1R3 and TOPPs at the gene expression level.

overall_design: 3-week greenhouse-grown  wild type Col and mutants pp1r3-2, topp-7m, topp4-1 and pp1r3-2 topp4-1

first: Suiwen

last: Hou


title: CXCL4 links inflammation and fibrosis through transcriptional and epigenetic reprogramming of inflammatory monocyte-derived cells [DNA methylation]

first: Aridaman

last: Pandit

overall_design:
Monocytes were collected from 5 healthy donors. To systematically study the effects of CXCL4 on cell differentiation, we obtained sequential DNA methylation profiles at day 0 (monocytes), day 2, 4, and 6, for monocyte differentiation into both moDCs and CXCL4-moDCs. To further study the effects of CXCL4 on cell maturation, at day 7 moDCs were stimulated with the toll-like receptor 3 ligand polyI:C. The trDNA methylationanscriptional profiles at day 7 (before stimulation), 4 hours and 24 hours (day 8) after stimulation were studied (Fig. 1A).  In total, we obtained 65 samples for DNA methylation profiling.

Please note that one sample (moDC differentiation sample from donor 4 on day 2) did not pass the quality check, and was removed from the subsequent analysis (i.e. total 64 samples represented in the GEO records). The complete raw data file that includes this failed sample is available at the foot of this record: signal_intensities_with_D20M_4.csv


title: Transcriptome analysis of cucumber in response to high temperature stress

status: Public on May 23 2020

city: Shandong

first: Zhonghai

last: Ren

address: Daizong Road No.61,Taian

department: College of Horticulture Science and Engineering

institute: Shandong Agricultural University

summary: In order to find out the genes involved in the heat shock response of cucumber, the seedlings of '9930', a North China type cucumber variety, were treated with high temperature at 42℃, and the leaves of the seedlings were taken after 0, 3 and 6 hours of treatment for transcriptome sequencing to analyze the differential expression genes of cucumber in response to high temperature stress. The results showed that compared with the control (heat treatment at 0h), there were 6 082 genes differentially expressed after heat treatment for 3 h and 6 h, of which 3245 were up-regulated and 2 388 were down-regulated. The results of enrichment analysis of GO and KEGG showed that these differentially expressed genes were mainly involved in metabolic pathway and protein synthesis pathway. Among the differentially expressed genes, there are many Hsp family genes, including Hsp20, HSP70 and Hsp90, which are up-regulated by heat stress, indicating that these genes may play a positive regulatory role in heat shock response of cucumber. In addition, many transcription factors, including AP2, MYB, WRKY, bHLH and HSF, were also induced by heat.

overall_design: mRNA profile of cucumber after heat treatment for 0,3,6 hours

first: Xueqian

last: Chen

last: Han


title: setd2 knockout zebrafish is survivable and fertile: differential and developmental-stress-related requirements for Setd2 and histone H3K36 trimethylation in different vertebrate animals

status: Public on May 27 2020

city: Shanghai

first: Dianjia

last: Liu

address: Room 807, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology，State Key Laboratory of Medical Genomics

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Setd2 is the only enzyme that catalyzes histone H3 lysine 36 trimethylation (H3K36me3) on virtually all actively transcribed protein-coding genes, and this mechanism is evolutionarily conserved from yeast to human. Setd2 and H3K36me3 have been revealed to be involved in many important biochemical mechanisms, including DNA repair, alternative mRNA splicing and transcription elongation. However, physiological function of Setd2 in the context of zebrafish development remains elusive. Here we generated zebrafish setd2 mutant lines through disrupting the majority of the protein. And mRNA profiles of wild-type (WT), Setd2(+/-) and Setd2(-/-) zebrafish embryos at 36hpf were generated by deep sequencing, providing an opportunity to uncover molecular programs and functions of Setd2.

overall_design: Zebrafish embryos mRNA profiles of wild type (WT), Setd2+/-, Setd2-/- at 36hpf.

first: Dian

first: Xiao

last: Sun


title: Adaptable durable human endothelial cells for organogenesis and tumorigenesis

status: Public on May 21 2020

first: David

last: Redmond

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: ETV2 resets endothelial cells' fate, confering them with vascular mallebility, which results in long-term stable vessel formation (R-VEC). R-VECs adapt to normal colon organoids and maladapt to  colorectal cancer organoids

overall_design: Single cell RNA-sequencing analysis of ETV2 reset endothelial cells (R-VEC) co-cultured with human normal colon organoids (hCO) or  human colorectal cancer organoids (hCRCO) utilizing  10x Chromium platform

first: Brisa

last: Palikuqi

first: Shahin

last: Rafii


title: A multicenter phase II study of pazopanib in patients with unresectable dermatofibrosarcoma protuberans

status: Public on May 19 2020

city: Paris

first: Julie

last: Delyon

address: 1 avenue Claude Vellefaux

department: Dermatology

country: France

institute: Hopital Saint-Louis

summary: Dermatofibrosarcoma protuberans (DFSP) is a soft-tissue sarcoma characterized by a high risk of local infiltration. The identification of the COL1A1-PDGFB t(17;22) translocation activating the PDGF pathway led to the use of imatinib in unresectable DFSP, with a response rate of 36-80%. Pazopanib is a multitarget tyrosine kinase inhibitor approved for soft tissue sarcomas. We conducted a phase II study of patients with unresectable DFSP to evaluate the efficacy and safety of pazopanib. Patients received 800 mg pazopanib daily. The primary endpoint was the objective response rate defined as the reduction of the largest diameter of the tumor ≥30% at 6 months or at surgery assessed by physical examination. Twenty-three patients, including one pre-treated with imatinib, were enrolled. With a median follow-up of 6.2 months (interquartile range 5.6-7.8 months), 5 patients (22%, 95% CI: 7-22%) had a partial response to pazopanib. The best objective response rate was 30% (95% CI 13-53%) using RECIST. One patient with metastatic DFSP previously treated with imatinib died after 2.4 months. Nine (39%) patients discontinued the treatment due to adverse events. Pharmacodynamics analyses of tumor samples were conducted: the enrichment of EGF and the EGFR-associated gene panel was associated with resistance, suggesting that EGFR-targeted therapies could be a therapeutic option to explore in DFSP.

overall_design: tumor samples were tested at baseline and during treatment with pazopanib for the mRNA expression of 302 genes involved in cell cycle, angiogenesis, apoptosis, proliferation (duplicate)

first: Samia

last: Mourah

first: Celeste

last: Lebbe


title: The chromatin state in WT and HPK1KO tumor specific T cells

status: Public on May 16 2020

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary: We then investigated how HPK1 induces new changes by comparing the open chromatin regions (OCRs) with WT control and founded that the ATAC-seq tracks were aligned with the previously reported OCRs of exhausted . HPK1 knockout induced loss of peaks in loci enriched in exhausted T (Tex) cells (e.g., PD-1, TIM-3, LAG-3, and TOX locus), indicating that HPK1 knockout could overcome some negative effects caused by TME,  ameliorate T cell exhaustion and thus extend their effector function (Figure S2F). Moreover, we also found that more accessible regions in HPK1-knockout CD8+TILs showed significant enrichment for pathways associated with cell cycle, antigen processing and presentation, T cell receptor signaling, Glyoxylate and dicarboxylate metabolism, AMPK pathway, and C-type lectin receptor signaling pathway (Figure S2G). It has been demonstrated that many peak changes were unique to either the early dysfunctional or functional state and included TCR signaling and cytokine production pathway genes. Pauken and the colleagues identified two metagenes in anti-PD-L1–treated exhausted T cell (TEX) compared to control TEX; one corresponding to leukocyte activation and one to cell cycle. The anti-PD-L1–treated TEX metagenes displayed some overlap with effector T cells (TEFF), largely driven by cell cycle pathways, but minimal overlap with Memory T cell (TMEM). Thus, we concluded that HPK1-/- TILs are prone to be effort T cells defined according to the chromatin states.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing to analyze the chromatin state in WT and HPK1KO tumor specific T cells.

first: Jingwen

last: Si


title: Unifying Developmental Programs for Embryonic and Post-Embryonic Neurogenesis in the Zebrafish Retina

first: Baijie

last: Xu

address: 320 Yue Yang Road

institute: Institute of Neuroscience, CAS

summary: It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post-embryonic neurogenic programs in the vertebrate retina.

overall_design: Retinal samples from 4 developmental stages and 1 post-embryonic stage

first: Xia

last: Tang

first: Hui

first: Lei

last: Du

first: Jie

last: He


title: Comparative transcriptome of cancer cells with enhanced brain tropism

status: Public on May 15 2020

city: Kanazawa

first: Eishu

last: Hirata

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

summary: Comparative transcriptome analysis of WM266.4 versus WM266.4-BrM3 human melanoma cells and PC9 versus PC9-BrM4 human lung cancer cells

overall_design: mRNAs extracted from WM266.4, WM266.4-BrM3, PC9 and PC9-BrM4 were sequenced by Illumina HiSeq 2500 in duplicate

first: Shinji

last: Kohsaka

first: Sinya

last: Kojima


title: Single cell RNA sequence of brain metastastic WM266.4 human melanoma cells

summary: WM266.4 human melanoma cells metatsasized to the brain of nude mice were subjected to single cell RNA sequencing.

overall_design: 96 cells extracted from the brains were sequenced by Illumina HiSeq 2500

first: Shinya


title: Essential functions of glycans in human epithelia dissected by a CRISPR/Cas9-engineered human organotypic skin model

city: Copenhagen N

first: Hans

middle: H.

last: Wandall

state: Denmark

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: We used RNA_Seq to quantify cellular transcripts in human immortalized N/TERT-1 keratinocytes upon knock out of genes delineating key subtypes of glycosylation pathways in humans.

overall_design: 2 different knock out clones of each B4GALT5, C1GALT1, C1GALT1C1, MGAT1, POFUT1, and POGLUT1, as well as 2 technical replicates of wild type.

first: Sally

last: Dabelsteen

first: Emil

last: Pallesen

first: Ieva

last: Bagdonaite


title: Genes regulated by DNMT1 in WM266.4 human melanoma cells

summary: Gene expression data of WM266.4-Luc-mEGFP cells treated with siCtrl or siDNMT1

overall_design: mRNAs extracted from WM266.4 cells treated with siCtrl or siDNMT1 were sequenced by Illumina HiSeq 2500 in triplicate


title: Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes

status: Public on May 31 2020

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: Due to breakthroughs in RNAi and genome editing methods in the past decade, it is now easier than ever to study fine details of protein synthesis in animal models. However, most of our understanding of translation comes from unicellular organisms and cultured mammalian cells. In this study, we demonstrate the feasibility of perturbing protein synthesis in a mouse liver by targeting translation elongation factor 2 (eEF2) with RNAi. We were able to achieve over 90% knockdown efficacy and maintain it for 2 weeks effectively slowing down the rate of translation elongation. As the total protein yield declined, both proteomics and ribosome profiling assays showed robust translational upregulation of ribosomal proteins relative to other proteins. Although all these genes bear the TOP regulatory motif, the branch of the mTOR pathway responsible for translation regulation was not activated. Paradoxically, coordinated translational upregulation of ribosomal proteins only occurred in the liver but not in murine cell culture. Thus, the upregulation of ribosomal transcripts likely occurred via passive mTOR-independent mechanisms. Impaired elongation sequesters ribosomes on mRNA and creates a shortage of free ribosomes. This leads to preferential translation of transcripts with high initiation rates such as ribosomal proteins. Furthermore, severe eEF2 shortage reduces the negative impact of positively charged amino acids frequent in ribosomal proteins on ribosome progression.

overall_design: 8 cell culture transcriptomes (4 control and 4 eef2 knockdowns); transcriptomes from 12 mouse livers (control, 7, 9 and 12 days; three animals in each group); 6 ribo-seq libraries prepared from the same tissues (matched within animal)

first: Mikhail

last: Nesterchuk

first: Elena

last: Smekalova

first: Timofei

last: Zatsepin

first: Daniel

last: Anderson

first: Vadim

last: Gladyshev

first: Viktor

last: Kotelianskii


title: Expression data from murine lymphatic endothelial cells with angiotensin II treated

status: Public on May 13 2020

city: Dalian

first: Qiuyue

last: Lin

address: No. 193, Lianhe Road, Dalian

department: First Affliated Hospital of Dalian Medical University

summary: Proliferation and migration of lymphatic endothelial cells (LECs) are essential for lymphatic vessel growth (also known as lymphangiogenesis), which plays a critical role in regulating the tissue fluid balance and immune cell trafficking in physiological and pathological conditions.

overall_design: In this study, murine LECs were stimulated with Ang II (500 nM) or saline for 12 or 24 hours. Cell proliferation and migration were determined. The gene expression profiles and signaling pathways were detected by time series microarray analysis.

first: Qiu-Yue

last: Bai


title: Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity [Conv]

city: New York

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Kinase inhibitors (KIs) represent an important class of anti-cancer drugs. Although cardiotoxicity is a serious adverse event associated with several KIs, the reasons remain poorly understood and its prediction remains challenging. Here, we perform transcriptomic profiling of human heart-derived primary cardiomyocyte cell lines treated with a panel of 26 FDA-approved KIs and classify their effects on subcellular pathways and processes. Individual cardiotoxicity patient reports for these KIs, obtained from the FDA Adverse Event Reporting System, are used to compute relative risk scores. These are then combined with cell line-derived transcriptomic datasets through elastic net regression analysis to identify a gene signature that can predict risk of cardiotoxicity. We also identify relationships between cardiotoxicity risk and structural/binding profiles of individual KIs. We conclude that acute transcriptomic changes in cell-based assays combined with drug substructures are predictive of KI-induced cardiotoxicity risk, and that they can be informative for future drug discovery.

overall_design: Cells were treated with one of 4 protein kinase inhibitors or vehicle control for 48 hours, and gene expression levels of all samples were measured by conventional random-primed mRNA sequencing using paired-end reading to obtain the genome-wide expression profiles for each sample.

first: J

middle: G

last: Coen van Hasselt

first: Rayees

last: Rahman

first: Jens

last: Hansen

first: Alan

last: Stern

first: Jaehee

last: Shim

first: Yuguang

last: Xiong

first: Amanda

last: Pickard

first: Gomathi

last: Jayaraman

first: Bin

last: Hu

first: Milind

last: Mahajan

first: James

last: Gallo

first: Joseph

last: Goldfarb

first: Eric

last: Sobie

first: Marc

last: Birtwistle

first: Avner

last: Schlessinger

first: Evren

middle: U

last: Azeloglu


title: Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity

first: Ravi

last: Iyengar

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

overall_design: Refer to individual Series


title: CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [GRO-Seq]

status: Public on May 11 2020

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

summary: RAG endonuclease initiates V(D)J recombination in progenitor (pro)-B cells. Upon binding a recombination center (RC)-based JH, RAG scans upstream chromatin via loop extrusion, potentially mediated by cohesin, to locate Ds and assemble a DJH-based RC. CTCF looping factor-bound elements (CBEs) within the IGCR1 element upstream of the Ds impede RAG-scanning; but their inactivation allows scanning to proximal VHs where additional CBEs activate rearrangement and impede scanning any further upstream. Distal VH utilization is thought to involve diffusional RC access following large-scale Igh locus contraction. Here, we test the potential of linear RAG-scanning to mediate distal VH usage in G1-arrested, v-Abl-pro-B cell lines, which undergo robust D-to-JH rearrangement, but little VH-to-DJH rearrangement, presumably due to lack of locus contraction. Through an auxin-induced approach, we degrade cohesin-component Rad21 or CTCF in these G1-arrested lines, which maintain substantial viability throughout four-day experiments. Rad21 degradation eliminated all V(D)J recombination and RAG-scanning-associated interactions, except RC-located DQ52-to-JH joining in which synapsis occurs by diffusion11. Remarkably, while CTCF degradation suppressed most CBE-based chromatin interactions, it promoted robust RC interactions with, and VH-to-DJH joining of, distal VHs, with patterns similar to those of "locus-contracted" primary pro-B cells. Thus, down-modulation of CTCF-bound scanning-impediment activity promotes cohesin-driven RAG-scanning across the 2.7Mb Igh locus.

overall_design: We performed LAM-HTGTS V(D)J-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in BM pro-B cells and v- Abl transformed pro-B cells and its various mutant derivatives to study roles of Rad21 and CTCF in long-range cohesin-driven V(D)J recombinational scanning

first: Ba

last: Zhaoqing

first: Lou

last: Jiangman


title: TBR-760, a Dopamine-Somatostatin Compound, Arrests Tumor Growth of Aggressive Non-Functioning Pituitary Adenomas in Mice

status: Public on Jun 06 2020

city: CAMBRIDGE

first: Jeong

last: Rih

address: 650 East Kendall Street

institute: IPSEN Bioscience

summary: TBR-760 (formerly BIM-23A760) is a chimeric dopamine (DA)-somatostatin (SST) compound with potent agonist activity at both DA type 2 (D2R) and SST type 2 (SSTR2) receptors. Non-functioning pituitary adenomas (NFPAs) express both D2R and SSTR2 and, consequently, may respond to TBR-760. We utilized a mouse model with the pro-opiomelanocortin (POMC) gene knocked-out that spontaneously develops aggressive NFPAs. Both genomic microarray and DA and SST receptor mRNA expression analysis indicate that POMC KO mouse tumors and human NFPAs have similar expression profiles, establishing POMC KO mice as a valid model for study of NFPAs. Treatment with TBR-760 for 8 weeks resulted in nearly complete inhibition of established tumor growth, whereas tumors from vehicle-treated mice increased in size by 890 ± 0.7%. These results support the development of TBR-760 as a therapy for patients with NFPA.

overall_design: Transcriptomic analysis was performed on the pituitary tissues from 2 normal mouse, 2 homozygous POMC gene knock-out mouse,  8 heterozygous POMC gene knock-out mouse. The analysis of whole mRNA transcript expression was done by Affymetrix Mouse Genome 430 2.0 Array, a Robust Multichip Analysis was performed on the CEL files, and differential analysis were done with GeneSpring software.

first: Heather

middle: A

last: Halem

first: Michael

last: Culler

first: Ute

last: Hochgeschwender

first: Arunthi

last: Thiagalingam


title: CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [3C-HTGTS]


title: CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [ChIP-Seq]


title: Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers

status: Public on May 08 2020

first: Matthieu

last: Dos Santos

state: Paris

address: 24 rue du Faubourg Saint Jacques

institute: Institut Cochin

summary: Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium.

overall_design: Single nuclei RNA-seq and single nuclei ATAC-seq

first: Pascal

last: Maire


title: Liver transcriptomics during malaria

status: Public on May 12 2020

city: Stanford

first: Michelle

last: Lissner

state: CA

address: 299 Campus Drive Fairchild D333

institute: Stanford University

summary: We performed RNA-seq on samples of liver tissue collected from Plasmodium chabaudi-infected C57BL/6-Crl mice.

overall_design: 8-12 week-old female C57BL/6-Crl mice were infected with 100,000 red blood cells infected with Plasmodium chabaudi AJ

middle: M

first: David

middle: S

last: Schneider


title: Small RNA sequencing of Zika virus-infected human umbilical cord mesenchymal stem cells

status: Public on May 07 2020

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

institute: Korea Univ.

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA profiles of hUCMSCs infected with ZIKV using Illumina small RNA sequencing platform

overall_design: Investigation of the differential expression patterns of miRNAs in response to ZIKV infection

first: Ok

first: Jae

middle: K

last: Lee

first: Rak-Kyun

last: Seong


title: RNA-Sequence analysis of enteroids incubating with Bifidobacterium longum

status: Public on May 01 2020

first: Xue

last: Fang

address: No.168, Changhai Road,Yangpu District 200433

department: Department of Gastroenterology

institute: Changhai Hospital

summary: Although oral administration of Bifidobacterium longum (B. longum) relieves irritable bowel syndrome (IBS) symptoms in a clinical setting, the underlying mechanisms remain undetermined. Herein, we confirmed that B. longum ameliorated defecation habits and alleviated visceral hypersensitivity in water avoidance stress (WAS) rats. Further analysis revealed that B. longum enhanced mucosal repair, promoted the production of lysozyme, and ameliorated microbiota dysbiosis in WAS rats. These activities are all closely correlated with Paneth cell function. In vitro, we incubated primary cultured enteroids with B. longum and found that this bacterium promoted the proliferation of these organoids, which may be attributed to the up-regulated expression of the stem niche factors WNT3A and TGF-β which are serected by the Paneth cells. On the basis of our findings, we propose that B. longum relieves IBS by restoring the antimicrobial activity and stem niche maintenance functions of Paneth cells.

overall_design: 2 samples of 3 biological replicates

first: Chun-hua

last: Zhou

first: Jia-Jia

last: Xu

first: Jun

last: Gao

first: Ling

last: Zhang

first: Jiu-Long

last: Zhao

first: Yu-Ting

last: Meng

first: Wei

first: Xu

last: Han

first: Yu

last: Bai

first: Zhao-Shen

last: Li

first: Duo-Wu

last: Zou


title: Adaptable durable human endothelial cells for organogenesis and tumorigenesis

first: Brisa

last: Palikuqi

address: 1300 York Ave

summary: ETV2 resets endothelial cells' fate, confering them with vascular mallebility, which results in long-term stable vessel formation.

overall_design: ETV2 reset endothelial cells (R-VEC) were compared in various conditions with matched CTRL-EC by bulk RNA-seq

first: Shahin

last: Rafii


title: Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation

status: Public on May 05 2020

city: Fort Collins

first: Michelle

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary: Characterization of genome-wide chromatin accessibility in bovine oocytes and preimplantation embryos using ATAC-seq

overall_design: ATAC-seq libraries were prepared from bovine GV oocytes and in vitro produced preimplantation embryos (2-cell, 4-cell, 8-cell, and morula-stage embryos). For each developmental stage, ATAC-seq libraries were prepared for three biological replicates (cells derived from three separate oocyte collections). A subset of embryos from each collection were concurrently cultured in the presence of a transcriptional inhibitor (α-amanitin), to interrogate the causal relationship between embryonic transcription and chromatin remodeling.

first: Pablo

middle: J

last: Ross


title: CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning [LAM-HTGTS]

first: Frederick

last: Alt

state: MA

overall_design: We performed LAM-HTGTS V(D)J-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in v- Abl transformed pro-B cells and its various mutant derivatives to study roles of chromatin loop extrusion mediated RAG scanning in IgH V(D)J recombination.

first: Ba

last: Zhaoqing

first: Lou

last: Jiangman


title: CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning


title: Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity [DGE]

first: Ravi

last: Iyengar

state: NY

first: J

last: Coen van Hasselt

first: Rayees

last: Rahman

first: Jens

last: Hansen

first: Alan

last: Stern

first: Jaehee

last: Shim

first: Yuguang

last: Xiong

first: Amanda

last: Pickard

first: Gomathi

last: Jayaraman

first: Bin

last: Hu

first: Milind

last: Mahajan

first: James

last: Gallo

first: Joseph

last: Goldfarb

first: Eric

last: Sobie

first: Marc

last: Birtwistle

first: Avner

last: Schlessinger

first: Evren

last: Azeloglu


title: A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysis

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

type:
Other
Third-party reanalysis

summary: Large-scale epigenomic projects have mapped hundreds of thousands of potential regulatory sites in the human genome, but only a small proportion of these elements are proximal to transcription start sites. It is believed that the majority of these sequences are remote promoter-activating genomic sites scattered within several hundreds of kilobases from their cognate promoters and referred to as enhancers. It is still unclear what principles, aside from relative closeness in the linear genome, determine which promoter(s) is controlled by a given enhancer; however, this understanding is of great fundamental and clinical relevance. In recent years, C-methods have become a powerful tool for the identification of enhancer-promoter spatial contacts that, in most cases, reflect their functional link. Here, we present data on spatial interactions of 867 promoters in HeLa cells. This data is obtained with a new hybridization-based promoter Capture-C protocol that makes use of biotinylated dsDNA probes and allows high-resolution promoter interactome description.

overall_design:
Spatial interactome of 867 promoters in HeLa cells was probed with PCHi-C technique. Two alternative PCHi-C protocols were used.

Raw data:  Due to patient privacy concerns, raw fastq files were submitted to SRA via dbGAP (study phs000640, substudy phs002014).

Third-party reanalysis:  Four Rao samples from dbGAP study phs001010.

first: Dmitrii

last: Abashkin

first: Nikolay

last: Kondratyev

first: Sergey

last: Razin

first: Alexey

last: Gavrilov

first: Vera

last: Golimbet


title: Chloroplast redox status modulates genome-wide plant responses during drought

status: Public on Apr 29 2020

city: Rosario

first: Juan

middle: José

last: Pierella Karlusich

state: Santa Fe

address: Esmeralda y Ocampo - Predio CONICET

country: Argentina

institute: Instituto de Biología Molecular y Celular de Rosario (IBR)

summary: Down-regulation of reactive oxygen species build-up in chloroplasts by expression of a plastid-targeted flavodoxin protects potato leaves under drought conditions. To better understand these effects we compared the transcriptomic alterations in a pre-symtomatic stage of drought treatment on leaves of Fld-expressing potato plants and their wild-type siblings.

overall_design: Gene expression in potato leaves was measured 3 days after water withdrawal under growth chamber conditions. Control conditions corresponds to continued watering. The analysed potato line was  transgenic  Stpfld252, which expresses flavodoxin in their chloroplasts, and their wild type siblings (S. tuberosum cv Solara). Two pooled biological replicates were used for each treatment and line.

first: Néstor

last: Carrillo

first: Mohammad-Reza

last: Hajirezaei

first: Uwe

last: Sonnewald

first: Sophia

first: Fahimeh

last: Shahinnia

first: Matías

middle: D

last: Zurbriggen

first: Rocío

last: Arce


title: Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans

status: Public on Apr 30 2020

city: PACIFICA

first: Hiten

last: Madhani

institute: UCSF

summary: Qsp1 is a secreted quorum sensing peptide required for virulence of the fungal meningitis pathogen Cryptococcus neoformans. Qsp1 functions to control cell wall integrity in vegetatively growing cells and also functions in mating.  Rather than acting on a cell surface receptor, Qsp1 is imported to act intracellularly via the predicted oligopeptide transporter Opt1. Here, we identify a transcription factor network as a target of Qsp1. Using whole-genome chromatin immunoprecipitation, we find Qsp1 controls the genomic associations of three transcription factors to genes whose outputs are regulated by Qsp1. One of these transcription factors, Cqs2, is also required for the action of Qsp1 during mating, indicating that it might be a shared proximal target of Qsp1. Consistent with this hypothesis, deletion of CQS2 impacts the binding of other network transcription factors specifically to Qsp1-regulated genes. These genetic and genomic studies illuminate mechanisms by which an imported peptide acts to modulate eukaryotic gene expression.

overall_design: RNA-seq and ChIP-seq to investigate the influence of Qsp1 on a network of transcription factors in C. neoformans

first: Diana

last: Summers


title: A broad response to intracellular long-chain polyphosphate in human cells

status: Public on Apr 22 2020

city: Ottawa

first: Michael

last: Downey

state: Ont

address: 451 Smyth Rd.

institute: University of Ottawa

summary: Polyphosphates (polyP) are ancient molecules comprised of inorganic phosphates joined by high energy phosphoanhydride bonds in chains of 3-1000 units in length. In this study, we describe a system to produce polyP in mammalian cells by ectopic expression of the E. coli ppk1+ gene. Production of the EcPpk1 protein results in polyP accumulation throughout the cell, including the nucleus. Using transcriptomic and proteomic analyses, we demonstrate a broad impact of polyP on diverse pathways, including activation of the ERK1/2-EGR1 signaling axis. PolyP accumulation also results in redistribution of several chromatin bound proteins and a translation initiation factor from the nucleus to the cytoplasm. Our work will serve as a novel resource to interrogate polyP biology in higher eukaryotes.

overall_design: In total, 6 samples were analyzed by RNA-sequencing, 3 control (CTRL) samples (cells transfected with empty pcDNA3.1-) and 3 Ppk1 samples (cells transfected ppk1+ expression plasmids (pcDNA3.1-ppk1+). Each control sample and PPK1 sample are matched biological replicates, generating 3 biological replicates for the experiment in total (CTRL B and PPK1 B, CTRL C and PPK1 C, CTRL D and PPK1 D).

first: Emma

last: Bondy-Chorney

first: Iryna

last: Abramchuk

first: Rawan

last: Nasser

first: Charlotte

last: Holinier

first: Alix

last: Denoncourt

first: Kanchi

last: Baijal

first: Mireille

last: Khacho

first: Mathieu

last: Lavallee-Adam


title: Transcriptome profiling of rat brain samples in two age groups in responding to intracerebral hemorrhage

status: Public on Apr 27 2020

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Aging-induced decline of endogenous neuroprotection has been shown to aggravate intracerebral hemorrhage (ICH)-induced acute brain injury, however, the underlying mechanisms in brain are still little known. In this study, we applied a rat ICH model to study the transcriptional responses in the early and late aging (13-month and 22-month old) rats that show substantial differences in brain damage and recovery. Transcriptome analysis (RNA-seq) reveals that brain expression of neuroinflammation genes is similarly and selectively upregulated in ICH, which includes genes in the cellular response to interferon gamma function. We show that the anti-IFN-γ treatment effectively reduces ICH-induced acute brain injury.

overall_design: Rats from two age groups, including 13-month and 22-month, were selected to perform experiments. Left brains of rats were treated with intracerebral hemorrhage, while right brains were as control. Three biological replicates were used to perform RNA-seq experiments. A total of 12 RNA-seq samples were obtained.

first: Yi

last: Zhang

first: Qingwu

last: Yang


title: Microarray profiling analysis of microRNAs expression in glioblastoma cells

status: Public on Apr 17 2020

city: Shenyang

first: Wei

last: Wang

state: Liaoning

address: 155 Nanjing North Street

department: Department of Neurosurgery

institute: the First Affiliated Hospital of China Medical University

summary: Although growing evidence has revealed that ZEB2 was correlated with grades and outcome of glioma positively, the mechanisms underlying ZEB2/miRNAs-mediated gliomas development remain largely unknown. Here the authors revealed that ZEB2 raised in glioblastoma samples compared to the lower-grade gliomas. Besides, miR-637 increased to the most extent per the miRNA array analysis of cells with- or without ZEB2. ZEB2 captured the promoter of miR-637 directly and suppressed miR-637 transcription. In the absence of ZEB2, overexpressed miR-637 targeted WNT7A and repressed the WNT/β-Catenin signaling pathways subsequently, which inhibited the expression of Cyclin D1 and Vimentin. Importantly, the combination of β-Catenin-specific inhibitor LGK974 and temozolomide hampered cell proliferation synergistically in cells expressing miR-637. In line with the expectation, the inhibition of miR-637 counteracted sh-ZEB2-caused tumor regression in U251 xenograft models. The current study evaluated a novel mechanism that the association of ZEB2/miR-637/WNT7A contributed to regulate glioblastoma cell proliferation and migration in a β-Catenin-dependent manner. The results may provide new rationales to optimize the trial designs, which try to select the ideal glioblastoma patients to receive β-Catenin-targeted therapy and chemotherapy.

overall_design: Three U251 sh-NC clones and three U251 sh-ZEB2 clones were generated in the present study. Microarray based miRNA expression profiles were obtained with miRCURY LNA miRNA custom probe PCR assays.

first: Di

last: Wu


title: Homeostatic mini-intestines through scaffold-guided organoid morphogenesis

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

summary: Epithelial organoids, such as those derived from stem cells of the intestine, have great potential for modelling tissue and disease biology. However, the approaches that are used at present to derive these organoids in three-dimensional matrices result in stochastically developing tissues with a closed, cystic architecture that restricts lifespan and size, limits experimental manipulation and prohibits homeostasis. Here, by using tissue engineering and the intrinsic self-organization properties of cells, we induce intestinal stem cells to form tube-shaped epithelia with an accessible lumen and a similar spatial arrangement of crypt- and villus-like domains to that in vivo. When connected to an external pumping system, the mini-gut tubes are perfusable; this allows the continuous removal of dead cells to prolong tissue lifespan by several weeks, and also enables the tubes to be colonized with microorganisms for modelling host-microorganism interactions. The mini-intestines include rare, specialized cell types that are seldom found in conventional organoids. They retain key physiological hallmarks of the intestine and have a notable capacity to regenerate. Our concept for extrinsically guiding the self-organization of stem cells into functional organoids-on-a-chip is broadly applicable and will enable the attainment of more physiologically relevant organoid shapes, sizes and functions.

overall_design: 10x single cell RNA-seq of mini-guts (mouse small intestinal organs on a chip) at 10 and 20 days of differentiation in ENR after propagation in ENRCV (E=EGF, N=Noggin, R=R-Spondin, C=CHIR99021, V=Valproate), as well as Cryptosporidium parvum infected mini-guts and control organoids differentiated in ENR for 10 days in 3D culture in matrigel. See Nikolaev et al. 2020 for detailed protocols.

first: Mikhail

last: Nikolaev

first: Matthias

last: Lutolf


title: miR396e-OsGRF7 module controls rice plant architecture (RNA-Seq)

status: Public on Apr 19 2020

city: Wuhan

first: Yunping

last: Chen

address: No. 299, Ba Yi Road, Wuchang

institute: Wuhan university

summary: Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the differential expressed genes between GRF7OE and WT plants.

overall_design: Examination of different expressed genes between WT and GRF7OE.

first: Zhiwu

last: Dan


title: AID-ChIP-seq Analysis of diffuse large B-cell lymphoma

status: Public on Apr 08 2020

city: Little Rock

first: PIROON

last: JENJAROENPUN

state: AR

address: 4301 W Markham Slot 782

country: USA

institute: University of Arkansas for Medical Sciences

summary:
Purpose: The goals of this study are to identify AID targets in DLBCL and investigate the overlapping of AID peaks and predicted G4 forming sequences (PQS) and the B-cell super enhancer (SE)
U2932 DLBCL cells obtained from the American Type Culture Collection were grown in RPMI 1640 medium (Corning) supplemented with 10% FBS (Atlanta Biiologicals) and 1% Pen/Strep (Gibco). For each immunoprecipitation reaction, 4x106 chromatin cell equivalent were incubated overnight with either an AID antibody (Abcam, ab59361) or a rabbit IgG negative control antibody, subjected to protein A/G magnetic bead binding, IP elution and DNA recovery. The ChIP DNA was used to generate ChIPseq libraries with the ChIP-Seq sample preparation kit (Illumina) for sequencing at the Arkansas Children’s Research Institute Genomics Core. The sequence reads that passed quality filters were aligned to the human genome (hg19) using BWA-MEM and peakcalled using MACS2.
Results: Using an optimized data analysis workflow, we mapped about 10-20 million sequence reads per sample to the human genome (build hg19) and identified 4,573 AID peaks which were filtered out if they overlap with the mock pull-down peaks and the blacklist (ENCODE blacklisted regions). We observed the intersection of AID peaks with PQS and SEs are significantly higher than expected by chance in all cases of comparisons supporting that the number of AID peaks sharing PQS and/or SEs is not a random event.
Conclusions: Sequencing analyses reveal AID targets in both activated B-cells and lymphoma are highly enriched for G4 elements and validation studies confirm a representative set of these sequences form characteristic, stable G4 structures.

overall_design: ChIP-seq of AID, IgG, and Input were generated by deep sequencing using Illumina NextSeq 500.

first: Samantha

last: Kendrick

first: Ying-Zhi

last: Xu

first: Piroon

last: Jenjaroenpun


title: RNA-Seq analysis of Pseudomonas aeruginosa response to testosterone

status: Public on Apr 21 2020

city: Singapore

first: Micheal

last: Mac Aogain

address: 308232, 11 Mandalay Rd, Singapore

department: Lee Kong Chian School of Medicine

institute: Nanyang Technological University

summary: Transcriptional response of P. aeruginosa grown in the presence of 2.5 micromolar testosterone.

overall_design: mRNA profiles of P. aeruginosa PAO1 cultures exposed to  2.5 microbolar testosterone were compared to vehicle controls (EtOH) following 24 hour exposure.

first: Celine

last: Vidaillac


title: RNA-seq to characterize estrogen receptor alpha mutation in the female rat right ventricle with pressure overload

status: Public on Apr 11 2020

city: Madison

first: Naomi

last: Chesler

state: Wisconsin

address: 2146 Engineering Centers Building, 1550 Engineering Drive

department: Biomedical Engineering

institute: University of Wisconsin-Madison

summary:
Purpose: While women are more susceptible to pulmonary arterial hypertension (PAH) than men, their right ventricular (RV) function is better preserved. Experimental studies have identified estrogen receptor alpha (ERα) as a likely mediator for estrogen protection in the RV. However, the role of ERα in preserving RV function and remodeling during pressure overload remains poorly understood. We hypothesized that loss of functional ERα removes female protection from adverse remodeling and is permissive for development of a maladapted RV phenotype.
Methods: Male and female rats with a loss-of-function mutation in ERα (ERαMut) and wildtype (WT) littermates, while at their surgical plane of anesthesia, underwent RV pressure overload by pulmonary artery banding (PAB) or a sham surgery.
Results: At 10 weeks post-PAB, WT and ERαMut demonstrated RV hypertrophy. Single beat analysis and Tau Weiss calculation from RV pressure waveforms (collected during surgical plane of anesthesia) demonstrated uncoupling of the RV-pulmonary vascular circuit and diastolic dysfunction, respectively, in female, but not male, ERαMut PAB rats. Similarly, female, but not male, ERαMut exhibited increased RV fibrosis, comprised primarily of stiffer collagen type I, suggesting RV stiffening by collagen type I accumulation. RNA-sequencing in female WT and ERαMut RV revealed Kallikrein related-peptidase 10 (Klk10) and Jun Proto-Oncogene (Jun) as possible mediators of female RV protection during PAB.
Conclusions: ERα in females is protective against RV-pulmonary vascular uncoupling, diastolic dysfunction, and fibrosis in response to pressure overload. ERα appears to be dispensable for RV adaptation in males. ERα may be a mediator of superior RV adaptation in female patients with PAH.

overall_design: 20-21 week old female wildtype (WT) and ERalpha -/- rats

first: Tik

middle: C

last: Cheng


title: Lineage-specific chromatin binding of FOXA1 is regulated by LSD1-mediated demethylation

city: Boston

first: Changmeng

last: Cai

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

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

overall_design: Refer to individual Series


title: The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

status: Public on Apr 28 2020

city: NEW YORK

first: Jennifer

last: Diaz

state: New York

address: 69 E 97TH ST, APT 17

institute: Icahn School of Medicine at Mount Sinai

summary: Our ability to predict the effects of drug combinations is limited, in part by limited understanding of how the transcriptional response of two monotherapies results in that of their combination. We performed the first analysis of matched time course RNAseq profiling of cells treated with both single drugs and their combinations. The transcriptional signature of the synergistic combination we studied had unique gene expression not seen in either constituent monotherapy. This can be explained mechanistically by the sequential activation of transcription factors in time in the gene regulatory network. The nature of this transcriptional cascade suggests that drug synergy may ensue when the transcriptional responses elicited by two unrelated individual drugs are correlated. We used these results as the basis of a simple prediction algorithm attaining an AUROC of 0.77 in the prediction of synergistic drug combinations in an independent dataset.

overall_design: RNAseq of MCF7 and LNCaP cells each treated with DMSO, 3 drugs, and the 3 combinations of the 3 drugs, in triplicate, well as a triple combination in LNCaP, at 0, 3, 6, 9, 12, and 24 hours

middle: E

first: Mehmet

last: Ahsen

first: Gustavo

last: Stolovitzky


title: Structure of DNA methyltransferases DNMT3A/DNMT3B bound to a nucleosome [array]

status: Public on Jun 17 2020

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

summary:
CpG methylation by the de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes yet cannot methylate the DNA wrapped around the nucleosome core2, and favor the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-EM structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3, and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.
CpG methylation by the de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes yet cannot methylate the DNA wrapped around the nucleosome core2, and favor the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-EM structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3, and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.

overall_design: To test whether the acidic patch interaction is important for reestablishing DNA methylation patterns in vivo, we analyzed DNA methylation patterns in DKO8 cells expressing wildtype and mutant DNMT3B3 using a DNA methylation array (Infinium MethylationEPIC BeadChip) at 56 days after infection.

first: Minmin

last: Liu

first: Ting-Hai

first: Edward

middle: X

last: Zhou

first: Gangning

last: Liang

first: Gongpu

last: Zhao

first: Eric

middle: H

first: Karsten

last: Melcher


title: DNA methylation analysis of HCT116 after disruption of methyllysine reading and writing.

status: Public on Apr 05 2020

first: Scott

last: Rothbart

address: 333 Bostwick Ave NE

summary: The chromatin-binding E3 ubiquitin ligase Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) maintains DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri- methylation on DNA ligase 1 (LIG1K126me2/me3). However, the functional significance and selectivity of these interactions remains unclear. In this study, we used protein domain microarrays to search for additional readers of LIG1K126me2, the preferred methyl state bound by the UHRF1 TTD. We show that the UHRF1 TTD binds LIG1K126me2 with high affinity and selectivity compared to other known methyllysine readers. Notably, and unlike H3K9me2/me3, the UHRF1 plant homeodomain (PHD) and its N-terminal linker (L2) do not contribute to multivalent LIG1K126me2 recognition along with the TTD. To test the functional significance of this interaction, we designed a LIG1K126me2 cell-penetrating peptide (CPP). Consistent with LIG1 knockdown in somatic cells, uptake of the CPP had no effect on the DNA methylation maintenance function of UHRF1. Further, we did not detect changes in bulk DNA methylation after chemical or genetic disruption of lysine methyltransferase activity. Collectively, these studies identify UHRF1 as a selective reader of LIG1K126me2 in vitro, implicate the UHRF1 TTD as a dispensable domain for DNA methylation maintenance, and call into question existing models of methyllysine-dependent DNA methylation maintenance in somatic cancer cells.

overall_design: HCT116 or HeLa cells were incubated for 7 days with high concentration (20 μM) of indicated methylated LIG1 peptides or water (- control). HCT116 cells were also treated with DMSO (control) or UNC0638 (1 uM) for 48 hrs. HCT116 cells were also passaged for 10 days with either H3.3 WT or H3.3 K9M transgene incorporation. Cells we were passaged to avoid confluence and peptide was refreshed at each passage. FAM, 6-carboxyfluorescein; CPP, cell penetrating peptide (-polyethylene glycol-kkkrkv). Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip.

first: Robert

last: Vaughan

middle: B


title: Bone morphogenetic protein 8b (bmp8b) in non-alcoholic steatohepatitis (nash), acute hepatic damage and liver regeneration

status: Public on Apr 01 2020

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: TGFβ/BMP family member Bone Morphogenetic Protein 8b (Bmp8b) is upregulated in NASH (Western Diet -WD- Model), acute liver damage (CCl4 model) and by Partial Hepatectomy (PH). Absence of Bmp8b reduces liver inflammation and fibrosis in the NASH model (WD). In the acute (3days) CCl4 model, absence of Bmp8b impacts acute inflammatory responses, hepatic stellate cells (HSC) activation, and compensatory hepatocyte proliferation; defective inflammatory pathways and hepatocytes proliferation is also observed in the Partial hepatectomy model. BMP8b is thus a pathophysiologically relevant target to modulate the responses to damage in acute and chronic liver disease.

overall_design: Male C57BL/6J mice (WT littermates and/or Bmp8b KO mice - WD experiment: 9 weeks old; CCl4 & PH: 16 weeks old) were challenged with: A) Western (Teklad, TD88137) or Low Fat Control (Teklad, TD08485) Diet for 32 weeks; B) IP injection of 2ul/g body weight of olive Oil (OO) or CCl4:olive oil [1:1 (v/v)] mix; Mice were culled 3 days after IP injection; or C) Partial Hepatectomy; Mice were culled 3 days after surgery.

first: Michele

last: Vacca

first: Antonio

last: Vidal-Puig

middle: Y

first: Marcella

last: Ma


title: EPR (BC030870) ChIP-Seq analysis in NMuMG mouse mammary gland

status: Public on Apr 07 2020

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: EPR, a lncRNA present in the chromatin fraction of NMuMG cells, controls proliferation and fate determination in mammary gland cells. We wanted to define if EPR overexpression in NMuMG cells affects the landcape of two histone activation marks (H3K4me3 and H3K27ac).

overall_design: Examination of 2 epigenetic modifiers in Triplicate NMuMG-mock and NMuMG-EPR

first: Roberto

last: Gherzi

first: Gabriele

last: Bucci


title: Adaptable durable human endothelial cells for organogenesis and tumorigenesis

status: Public on Mar 31 2020

city: New York

first: Ying

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: ETV2 resets endothelial cells' fate, confering them with vascular mallebility, which results in long-term stable vessel formation.

overall_design: Examination of ETV2, histone modifications K4me3, K27me3, and K27ac in different cell types.

first: Brisa

last: Palikuqi

first: Shahin

last: Rafii


title: High-throughput RNA sequencing of basilar artery smooth muscle cells in wild type and high-salt diet induced hypertension rats

status: Public on Apr 02 2020

city: Hefei

first: Lesha

last: Zhang

state: Anhui

address: 81 Meishan road

department: Physiology

institute: Anhui Medical University

summary: We utilized high-throughput sequencing and subsequent signaling pathway analyses to find 2 fold change or greater upregulated expression of 230 transcripts and downregulated expression of 165 transcripts in basilar artery smooth muscle cells derived from rats fed a high-salt diet compared with those from control rats.

overall_design: The RNA sample libraries of basilar artery smooth muscle cells in wild type and high-salt diet induced hypertension rats were established and sequenced using the high-throughput Illumina HiSeq 2500 sequencing platform, with a sequencing length of 150 base pairs. Then the RNA sequencing (RNA-Seq) Fastq raw data were pruned using Trimmomatic to remove adaptors and lower mass reads. The quality of clean data was assessed using FastQC software, following with GO and KEGG pathway enrichment analyses, PPI network integration and module analyses.

first: Bing

last: Shen