title: Lipopolysaccharide-mediated chronic inflammation promotes tobacco carcinogen-induced lung tumorigenesis

city: Pittsburgh

first: Chia-Hsin

last: Liu

state: PA

address: 130 Desoto Street, GSPH-A419

institute: University of Pittsburgh

summary: We developed a two-staged lung cancer mouse model, which mimics the smoking carcinogen-induced, and chronic obstructive pulmonary disease (COPD)-related airway inflammation promoted lung cancers. We used the carcinogen 4-(methylnitrosamino)-1-(3- pyridyl)-1-butanone (NNK) to induce lung cancer and in parallel to repeated Lipopolysaccharide (LPS) installation to induce chronic lung inflammation. To identify genes associated with chronic inflammation promoting lung tumorigenesis, we have performed whole genome microarray expression profiling of mice exposed to Phosphate-Buffered Saline (PBS), NNK, LPS, and combined NNK and LPS.

overall_design: Expression profiles of 12 samples in mice treated with  PBS (n=3), LPS (n=3), NNK (n=3), and LPS/NNK (n=3)


title: Expression data from transdetermined Drosophila eye antennal imaginal disc by vestigial and simjang overexpression.

status: Public on Dec 31 2020

city: Sendai

first: Keita

last: Masuko

address: Aoba 6-3, Aramaki, Aoba-ku,

department: Pharmaceutical Science

country: Japan

institute: Tohoku University

summary:
Drosophila imaginal disc cells exhibit a remarkable ability to switch cell fates under various perturbations, a phenomenon known as transdetermination (TD). The process of cell reprogramming seems to be regulated in stochastic manners. Ectopic expression of the master transcription factor of wing identity, vestigial, in eye progenitor cells induces eye-to-wing TD, but the frequency of the TD is low. We found that the overexpression of simjang gene dramatically enhanced eye-to-wing TD frequency. Gene network controlling this process, however, is largely unclear.
We used microarray to detail the global gene network underlying simj-mediated facilitation of eye-to-wing TD.

overall_design: Third instar larval eye imaginal discs were dissected for RNA extraction and hybridization on Affymetrix microarray. Flies from each genotype were used (I: eyeless-Gal4; UAS-lacZ, UAS-lacZ, II: ey-GAL4; UAS-lacZ, UAS-simj, III: ey-Gal4; UAS-vg, UAS-lacZ, IV: ey-Gal4 UAS-vg; UAS-simj. Two biologic replicates were obtained for each.

first: Shoichiro

last: Kurata


title: Expression data from senescence-inducible Suv39h1-ERT2 primary mouse Emu-myc B-cell lymphoma

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

summary:
Treatment-induced senescence (TIS) is a DNA damage-triggered stress-response program, resulting in terminal arrest of affected cells. TIS plays an important role in cancer therapy, as many tumor cells would undergo TIS instead of apoptosis when exposed to standard chemotherapy regimens. The contribution of TIS to overall disease outcome is, however, unclear. To address this, we use lymphoma cells with conditional expression of the senescence-essential factor Suv39h1 (regulatable by 4-hydroxi-tamoxifen). Only cells with active Suv39h1 would undergo TIS in response to chemotherapy. Suv39h1 inactivation during the chemo-treatment would prevent TIS induction, while inactivation in fully senescent cells would allow outgrowth from the TIS cell cycle arrest. Such post-senescent cells (PS) show very different biological behavior than the cells growing in senescence-incompetent setting - never senescent (NS). The molecular characteristics of each of these treatment conditions are analyzed here by assessing global transcriptome data.
We used global gene expression profiling by microarrays to gain insight in the molecular programme underlying the chemotherapy response in primary Emu-myc transgenic B-cell lymphomas.

overall_design: Primary Eµ-myc lymphomas with genetic deletion of Suv39h1 were retrovirally transduced with a Suv39h1-ERT2 fusion protein, enabling 4-OH-tamoxifen inducible activation of Suv39h1 function. In addition, all cells were transduced with anti-apoptotic factor Bcl2 in order to prevent apoptosis and potentiate senescence as a main stress-response mechanism to DNA-damaging therapy. Three biological replicates were used and treated in vitro with chemo-drug Adriamycin (ADR), with or without Suv39h1 activation (i.e. with or without 4-OHT treatment). After 5 days, the cells were transferred in ADR/4-OHT-free medium and cultivated for another 14 days (outgrowth populations).

first: Clemens

middle: A

last: Schmitt

first: Michael

last: Hummel

first: Dido

last: Lenze

first: Lisec

last: Jan


title: Expression data from SH-SY5Y neuroblastoma cells treated with the protein disulfide isomerase inhibitor origamicin

city: Copenhagen

first: Dennis

last: Özcelik

address: Universitetsparken 2

country: Denmark

institute: University of Copenhagen

summary:
Protein disulfide isomerase (PDI) is associated with many diseases including neurodegenerative disorders like Alzheimer’s disease and, hence, is considered a promising drug target. In this study, we investigate the abscisic acid (ABA)-derived PDI inhibitor origamicin for its neuropharmacological potential.
We used microarrays to analyze the global change in gene expression as a result of PDI inhibition in the human neuroblastoma cell line SH-SY5Y

overall_design: We treated SH-SY5Y cells with the PDI inhibitor Origamicin (30 uM) for 24 h and then extracted the global RNA. We subjected the RNA to an Affymetrix® Human Gene 2.0 ST Array

first: John

middle: P

last: Pezacki


title: DNA methylation profiling of whole blood from Han Chinese individuals: identification of age-related CpG sites for forensic use

city: Wuhan

first: Daixin

last: Huang

state: Hubei province

address: No. 13, Hangkong Road

department: Department of Forensic Medicine

country: China

institute: Huazhong University of Science and Technology

summary: Age-related CpG (AR-CpG) sites are currently the most promising molecular markers for age estimation. However, AR-CpG sites for the Han Chinese population have not yet been systematically identified. Besides, there may be high-performance AR-CpG sites beyond the coverage of the commonly used Illumina HumanMethylation450 BeadChip that covers over 450,000 CpG sites (450K), which accounts only 1.6% of CpG sites in the human genome. Therefore, we initiated a project to perform genome-wide methylation analysis on whole blood samples from 42 healthy Han Chinese individuals (21 males and 21 females, 18–62 years) using the newly developed Illumina Infinium MethylationEPIC array that assesses over 850,000 CpG sites (850K) to identify AR-CpG sites for forensic use systematically. The 850K methylation array contains > 90% of 450K CpG sites but adds 413,745 CpG sites. As expected, we not only replicated several high-performance AR-CpG sites previously discovered using the Illumina 450K BeadChip, such as cg16867656 (ELOVL2), cg22454769 (FHL2), and cg10501210 (C1orf132), but also identified 41 (60.3%), 34 (22.5%), and 382 (48.7%) novel AR-CpG sites from the methylation profiles of 21 males, 21 females, and all individuals, respectively.

overall_design: DNA extraction, bisulfite conversion, microarray hybridization, and chip data analysis were performed by Genergy Inc. (Shanghai, China), with the experimental procedures following the respective manufacturers' instructions. Briefly, genomic DNA was extracted from whole blood using QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany), quantified with Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, MA, USA), and tested for its integrity on agarose gels. DNA samples that passed the quality control were treated with bisulfite using EZ DNA Methylation Kit (Zymo Research, CA, USA). Bisulfite converted DNA from the 42 samples were hybridized to the Illumina Infinium MethylationEPIC Beadchip v1.0. Methylation arrays were imaged with an Illumina iScan using standard settings. The methylated and unmethylated intensities of the images were extracted using R package ChAMP v2.8.9. Methylation levels of CpG sites are expressed as beta values.

first: Chao

last: Xiao

first: Shaohua

last: Yi


title: Mediator12 and 13 act as conditional anti-silencing factors in Arabidopsis

city: Beijing

first: Qikun

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

institute: Peking University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tet2 is required for Socs activation in immune response cells [RRBS]

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

type: Methylation profiling by high throughput sequencing

summary: Purpose: We have previously established an in vitro murine model that recapitulates the transformed phenotype of primary Tet2-/- mast cells expressing the Kit kinase domain mutant allele, D816V, that is both an oncogene and characterises patients with mastocytosis. To better understand the molecular basis of this cooperation and to further our understanding of role of Tet2 during inflammation and in other immune system disorders, we used this same in vitro primary cell system for genome wide studies to identify genes and genomic loci that are deregulated when these two mutations cooperate in mast cells.

overall_design: RRBS was performed on biological replicates for 4 paired samples: 1) GFP-negative/control and 2) GFP-positive/KitD816V infected Tet2+/+ mast cells, and 3) GFP-negative/control and 4) GFP-positive/KitD816V infected Tet2-/- mast cells. Biological replicates constitute primary mast cell cultures derived from two individual mice of each genotype, cultured in parallel.

last: Weber


title: MiRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular gland

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

type: Non-coding RNA profiling by high throughput sequencing


title: Tet2 is required for Socs activation in immune response cells [ChIP-seq]

overall_design: ChIP-seq was performed on biological replicates with each ChIp antibody on 4 paired samples: 1) GFP-negative/control and 2) GFP-positive/KitD816V infected Tet2+/+ mast cells, and 3) GFP-negative/control and 4) GFP-positive/KitD816V infected Tet2-/- mast cells. Biological replicates constitute primary mast cell cultures derived from two individual mice of each genotype, cultured in parallel.

first: Patrice

last: Dubreuil

first: Rabie

last: Chelbi

first: Ghislain

last: Bidaut

first: Erinn

last: Soucie


title: Mediator12 and 13 act as conditional anti-silencing factors in Arabidopsis [ChIP-seq]

last: Liu

summary: Mediator is a multi-protein complex which facilitates the initial steps of gene transcription. Mediator 12 (MED12) and MED13 are components of a module that reversibly associates with the core Mediator complex, and both positively and negatively regulates gene expression. Here, in an Arabidopsis mutant screen for factors that can bypass repressive epigenetic marks, we identified MED12 and MED13 as anti-silencing factors. Both are preferentially required for the expression of genes in the absence of H3K4me3, an activating chromatin mark. Thus, MED12 and MED13 respond to specific epigenetic states and can act as conditional positive gene regulators in Arabidopsis.

overall_design: GFP-wt_H3K4me3 was normalized to GFP-wt_H3. GFP-morc1_H3K4me3 was normalized to GFP-morc1-H3. GFP-ddc_H3K4me3 was normalized to GFP-ddc_H3. MED12-YFP-FLAG was normalized to columbia-0_FLAG.

first: Steven

middle: E

last: Jacobsen


title: Gene expression data from UMUC-14 following FGFR3 knock-down using FGFR3 siRNAs

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

summary: To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of  UMUC-14 cell lines, which endogenously expressed a mutated activated form of FGFR3 (FGFR3-S249C), the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.

overall_design: UMUC-14 cells were transfected or not  with siRNA FGFR3. mRNA was extracted after 40h and gene expression analysis was assessed using the U133plus2.0 array

first: Mingjun

last: Shi

first: Aura

last: Moreno-Vega

last: Chapeaublanc

first: Isabelle

last: Bernard-Pierrot

first: David

last: Gentien


title: Development of gene signatures for doxorubicin resistance and cancer stem cell CD44+, CD24-/low ALD+ isolated from canine mammary adenocarcinoma cell line (mRNA)

city: Serdang

first: Gayathri

middle: Thevi

last: Selvarajah

state: Selangor

address: University Putra Malaysia

department: Faculty of Veterinary Medicine

country: Malaysia

institute: University Putra Malaysia

summary: CMT-Stylo is a canine mammary gland adenocarcinoma cell line. From this cell line, a doxorubicin resistant subline called CMT-Star was developed by culturing the cells in the presence of doxorubicin from low concentration to 100 nM doxorubicin (to induce drug resistance). The CMT-Stylo cells were maintained in Dulbecco’s modified eagles medium (DMEM) supplemented with 10% Foetal bovine serum (FBS) and 1% Penicillin-Streptomycin (ThermoFisher Scientific, USA) in 5% CO2 at 370C. The CMT-Star cell line was maintained in additional 5 nM doxorubicin to maintain its resistant phenotype.

overall_design: We set out to identify differentially expressed messenger RNAs between the CMT-Stylo cells and CMT-Star cells using canine specific cDNA microarrays. Additionally, we isolated cancer stem cells from the cell line and its doxorubicin resistant subline using flow cytometry ( CD44+, CD24-/low and ALDH+ cells sorted using FACS sorter) and using microarray, we identified differentially expressed messenger RNAs between each cell line and its cancer stem cells. At a fold change of 2 and p-value of p < 0.05, a total of 26652 messenger RNA entities were identified as dysregulated between CMT-Stylo cells and CMT-Star cells. Similarly, we identified 28614 messenger RNA entities as differentially expressed between CMT-Stylo cells and their cancer stem cells, and 1808 messenger RNAs entities between CMT-Star cells and their cancer stem cells, using the same parameters.

middle: T

first: Kabiru

last: Sahabi


title: Tet2 is required for Socs activation in immune response cells

last: soucie

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CD160+ NK cells from intratumoral and peritumoral tissues

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary: Purified NK cells from human intratumoral and peritumoral tissues tissues were first enriched by MACS using NK Cell Isolation Kit (Miltenyi Biotec, German) and CD96+/- hepatic NK cells were isolated by FACS Aria cell sorter (BD Biosciences, United States) to attain a purity greater than 95%.

overall_design: 1 intratumoral and 2 peritumoral tissues


title: Next Generation Sequencing Facilitates Quantitative Analysis of FZD2 Knockdown/Control SNU449 Cell Line Transcriptomes

city: Guangzhou

first: Dinghua

last: Yang

address: 1838 North Guangzhou Avenue

institute: Nanfang Hospital

summary: We report evidence that FZD2 is a driver for EMT, cancer stem cell (CSC) property, and vasculogenic mimicry (VM) in hepatocellular carcinoma. To further examine the transcriptional changes in response to FZD2 depletion, we performed RNA-seq with FZD2 knockdown and control SNU449 cells by BGISEQ-500.

overall_design: mRNA profiles of FZD2 knockdown and control SNU499 cells were generated by deep sequencing, using BGISEQ-500.

first: Huohui

last: Ou


title: Hepatic RNA expression profile analysis of antibiotics treated and untreated Clonorchis sinensis-infected mice

city: Xuzhou

first: Bo

last: Zhang

state: Jiangsu Province

address: 209 tongshan road, yunlong district.

department: Jiangsu Key Laboratory of Immunity and Metabolism

institute: Xuzhou Medical University

summary: Study whether IL-33 participates in the cholangiopathies during C. sinensis infection,and whether the gut microbiota participates in the pathogenesis of clonorchiasis

overall_design: we performed transcriptional profiling analysis by RNA sequencing of liver RNA isolated from antibiotics treated and untreated 35 days post C. sinensis-infected WT and IL-33-/- mice,in quadruplicate,using Illumina HiSeq X-TEN

first: Yugang

last: Wang


title: Genome-wide maps of SMAD3-binding sites in SW480 and their derivative cells.

city: Haining

first: Wei

last: Guo

state: Zhejiang

address: 718 South Tan Road

department: ZJU-UoE Institute

institute: Zhejiang University

summary: We report that nuclear PTEN negatively regulates DNA-binding activity of SMAD3. We compared SMAD3 binding activity in colorectal tumor cells without or with a nuclear PTEN (C124S) mutant.

overall_design: ChIP-seq analysis of SMAD3 binding activity in colorectal tumor cells SW480, SW480 with PTEN knockout (SW480 KOEMT), and PTEN-negatvie SW480 reconstituted with a nuclear PTEN (C124S) mutant (SW480 KOEMT + nuclear PTEN [C124S]).

first: Qiujun

last: Xu


title: Genome-wide maps of upregulated or downregulated genes in reconstituted SW48O KOEMT cells without or with a nuclear PTEN (C124S) mutant

summary: We report that nuclear PTEN negatively regulates DNA-binding activity of SMAD3. We compared upregulated or downregulated genes in colorectal tumor cells without or with a nuclear PTEN (C124S) mutant.

overall_design: RNA-seq analysis of upregulated or downregulated genes in colorectal tumor cells SW480, SW480 with PTEN knockout (SW480 KOEMT), and PTEN-negatvie SW480 reconstituted with a nuclear PTEN (C124S) mutant (SW480 KOEMT + nuclear PTEN [C124S]).


title: Heat stress induced transcriptomic profiling in Paulownia elongata

city: Northridge

first: Chhandak

last: Basu

state: CA

address: 18111 Nordhoff Street

department: Biology

country: USA

institute: California State University

summary: We analyzed the heat-induced gene expression at the transcriptomic levels using RNA-sequencing and bioinformatic analysis for Paulownia elongata plants.

overall_design: Differential expression analysis for heat stress treatment in Paulownia elongata (3 replicates (40 degrees) and 3 control (temp 25 degrees)) using Illumina MiSeq

first: Niveditha

last: Ramadoss

first: Neerja

last: Katiyar

first: Dinesh

last: Gupta

last: Wu

first: Suman

last: Pakala

first: Kerry

last: Cooper


title: CD160+ and CD160- NK cells from human livers

summary: Purified NK cells from human liver tissues were first enriched by MACS using NK Cell Isolation Kit (Miltenyi Biotec, German) and CD160+/- hepatic NK cells were isolated by FACS Aria cell sorter (BD Biosciences, United States) to attain a purity greater than 95%.

overall_design: three healthy donors were pooled for each cell type


title: Expression data from Arabidopsis thaliana seedings treated with scutellarin

city: Kunming

first: Xudong

state: Yunnan

address: 132# Lanhei Road, Heilongtan

institute: Kunming Institute of Botany, Chinese Academy of Sciences

summary:
Maintenance of the root-meristem is determined by polar auxin transport (PAT) and asymmetric cell division (ACD). We find that flavonoids scutellarin and scutellarein, which both have 6-hydroxyl group that differs in its structure from all known-flavonoid PAT inhibitors, promote PAT and ACD in Arabidopsis thaliana root tip, and increase root length.
We used microarrays to detail the global programme of gene expression under scutellarin and mock (DMSO) treatment and identified distinct classes of genes regulated by scutellarin.

overall_design: The total RNA of 10-day-old Arabidopsis thaliana seedlings was extracted using RNAiso Plus reagent (TAKARA). Three RNA samples from mock- or 100 M scutellarin-treated plants for 10 days were harvested from three independent experiments including 100 whole seedlings of each sample. cDNA preparation and hybridization with an Arabidopsis ATH1 Genome Array were performed (Affymetrix).

first: Xing

last: Huang

first: Yan

last: Li

first: Faqing

last: Tao

first: Qinshi

last: Zhao

first: Weiqi


title: Comprehensive analysis of differentially expressed genes responsed to mechanical stretch in human corneal keratocytes.

city: Taiyuan

first: Jie

last: Song

state: Shanxi

address: NO. 79, Yingze West Road

institute: Taiyuan University of Technology

summary: Mechanical stimulation is an important factor for the development of complications after LASIK, but the molecular mechanism still remains unclear. In this study, we have employed whole genome microarray expression profiling as a discovery platform to identify genes responded to mechanical stretch in human corneal keratocytes. Furthermore, the specific signal transduction pathways were discussed. Mechanical stretch regulated gene expression was measured in human corneal keratocytes subjected to cyclic stretch (0-15% elongation, 0.5 Hz, sine waveform) for 0, 1 and 6 hours, respectively. Totally, 840 differentially expressed genes were identified in keratocytes under mechanical stretching, among which 493 genes were up-regulated and 388 genes were down-regulated. Theses differential genes were mainly involved in cytokine-cytokine receptor interaction, ECM-receptor interaction, Focal adhesion, TNF signaling pathway, and MAPK signaling pathway.

overall_design: Mechanical stretch regulated gene expression was measured in human corneal keratocytes subjected to cyclic stretch (0-15% elongation, 0.5 Hz, sine waveform) for 0, 1 and 6 hours, respectively. Three independent experiments were performed for each stretch time (0, 1 or 6 hours).


title: Arabidopsis thaliana wild-type vs. cotyledon-less laterne (= pid enp homozygous)  mutant

city: Wien

first: Thomas

last: Nussbaumer

address: Althanstraße 14

country: Austria

institute: Computational Systems Biology

summary:
Transcriptional profiling of cotyledon transcriptomics at the seedling stage (6 d)  by comparison of wild-type vs. cotyledon-less laterne (= pid enp) homozygous mutant.
The goal was to determine the transcriptomic profile of a cotyledon. The experiment took advantage of the endogenously caused lack of cotyledons instead of dissecting these organs, which would cause wound-induced expression.This was achieved by comparing seedlings of the Arabidopsis thaliana  pid enp double mutant, which is incapable to generate cotyledons. This is caused by the loss of apical cell polarisation of the auxin efflux carrier PIN1 in epidermal cells during embryogenesis.

overall_design: Two-color experiments with four independent biological replicates no1-4. The experiments were repeated with reversed colors as technical replicates.

first: Ramon

last: Torres-Ruiz

first: Michaela

last: Matthes


title: Human monocyte-derived macrophages polarized by GM-CSF (M1) or M-CSF (M2) in the presence or absence of 5 micromolar methotrexate

city: Madrid

first: Amaya

last: Puig

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital Gregorio Marañón

summary: Identification of genes differentially expressed between human monocyte-macrophages generated in the presence of either GM-CSF (termed M1) or M-CSF (termed M2) and in the presence (+MTX) or absence (-) of methotrexate

overall_design: Human peripheral blood monocytes from three independent healthy donors (d1, d4 and d7) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were exposed to 5 micrmolar methotrexate (MTX) and cultured for 7 days in RPMI 10% FCS containing either GM-CSF (M1) or M-CSF (M2). Total RNA from each condition was extracted and purified using the RNeasy kit (Qiagen). Labelled RNA was used as hybridization probes on human Agilent human whole genome array (G4845A). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned with a GenePix 4000B (Axon Instruments) scanner. Scanned images and raw data were pre-processed with GeneSpring v12 (Agilent).

last: Kröger

first: Blanca

middle: S

last: Palacios


title: Barley gene expression during compatible and incompatible infection with the smut fungus Ustilago hordei

city: Summerland

first: Guus

last: Bakkeren

state: BC

department: Summerland Research and Development Centre

country: Canada

institute: Agriculture & Agri-Food Canada

summary: Ustilago hordei is a basidiomycete fungus that infects barley and oats. It has a narrow host range and can infect only germinating seedlings. Symptoms do not occur until heading of the mature plants when the fungus has proliferated in meristematic tissue and replaces kernels with masses of black teliospores. Incompatibility is due to the presence of an avirulence effector product, UhAVR1, expressed in the fungus upon infection and secreted into the host, which is subsequently recognized by the barley plant resistance gene product RUH1 in cultivar Hannchen, leading to plant cell death, fungal growth arrest, and no disease. We have identified UhAvr1, and the transcriptome response of the barley plant to strains with and deleted for this gene was assessed using the 22K Affymetrix barley array. Incompatibility and cell death is apparent at 48 hrs after inoculation, so the transcriptome was assessed at this time point. For comparison, the transcriptome of barley cultivar Odessa, which lacks resistance gene Ruh1, during a compatible interaction was also assessed.

overall_design:
Three biological repeats of a mock infection (coleoptiles brushed with water: "MC", mock control), U. hordei teliospores from a wild-type cross (Uh362 Uhavr1 x Uh364 UhAvr1, "58"), and teliospores from a cross with a UhAvr1 deletion mutant (cross Uh362 Uhavr1 x Uh364 ΔUhAvr1, "116") were analyzed on barley cultivar Hannchen (Ruh1). Teliospore samples "58" and "116" were also assessed, each in triplicate, on cultivar Odessa (ruh1).

Citation: Ali, S, Laurie, J. D., Linning, R., Cervantes-Chavez, J. A., Gaudet, D. and Bakkeren, G. An immunity-triggering effector from the barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution.

first: G


title: Expression data from primary mouse Emu-myc B-cell lymphoma

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

institute: Charite University Medicine, Berlin

summary:
We are interested in genetic programs and mutations which impact on tumor development and sensitivity to anticancer therapies. Utilizing Emu-myc transgenic mice, which spontaneously develop aggressive B-cell lymphomas, we aimed here to study the effects of drug responses in vivo, in particular genetic and biochemical components presented a priori in therapy-naive tumor cells, which determine the susceptibility of lymphoma cells to respond to standard chemotherapeutic drugs.
We used global gene expression profiling by microarrays to gain insight into the molecular program underlying the chemotherapy response potential in primary Emu-myc transgenic B-cell lymphomas.

overall_design: Immunocompetent recipient mice, transplanted with an aliquot of primary lymphoma cells explated from transgenic Emu-myc mice, were exposed to a single dose of Cyclophosphamide (CTX), a standard component of chemotherapeutic regimens used to treat human B-cell lymphomas. After obtaining long-term therapy response data in mice, therapy-naive aliquots of these same lymphomas were used for generating global expression profiles. This submission includes the therapy-naive lymphoma samples.

first: Clemens

last: Schmitt

first: Julia

last: Kase

first: Michael

last: Hummel

first: Dido

last: Lenze

first: Jan

middle: R

last: Dörr


title: Global expression profiling of Emu-myc lymphomas

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

overall_design: Refer to individual Series


title: Differential expression of genes in Listeria monocytogenes under thermo-tolerance condition of heat shock

city: Dallas

first: Palmy

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Previous studies have shown the increased thermo-tolerance of pathogenic bacteria if pre-exposed to temperatures above their optimal levels prior to a particular heat treatment. It was unclear, however, whether there was a direct relationship between the different gene expression and the induced thermo-tolerance. Microarray analysis was performed to identify the differentially expressed genes during heat stress by comparing the transcriptome of L. monocytogenes under optimal temperature (37°C), and thermo-tolerance inducing (48°C for 30 minutes. A majority of the differentially expressed genes were up-regulated at heat shock as compared to those that were down-regulated when the cells were exposed to thermo-tolerance inducing conditions. Though many of the differentially expressed genes could be tentatively classified based on the current functional classification of genes (COG) per the NCBI database, many of the gene loci could not been attributed to a specific function due to the current limited knowledge on the functional genomics of L. monocytogenes.

overall_design: A total of 5 microarray slides were used. Two arrays for each biological replicate that including dye swap method.

first: Réka

last: Ágoston

first: Scot

last: Dowd

first: Suresh

middle: D

last: Pillai


title: Global expression profiling of treatment-induced senescence in mouse Emu-myc B-cell lymphomas

summary: Therapy-induced senescence (TIS) is a DNA damage-triggered irreversible cell-cycle block that terminates further expansion of (pre-)malignant lesions. Utilizing the Eµ-myc transgenic mouse lymphoma model (apoptosis protected by retroviral Bcl2-overexpression), we sought to elucidate the biological properties, long-term fate of senescent tumor cells and their impact on the microenvironment. We used global gene expression profiling by microarrays to gain insight into the molecular program underlying the treatment-induced senescence in Emu-myc transgenic B-cell lymphomas (apoptosis protected by Bcl2 overexpression), which robustly enter senescence in response to DNA-damaging anticancer agents such as Adriamycin (ADR).

overall_design: We used primary lymphoma cells isolated from lymph nodes of Emu-Myc transgenic mice. In this model, the c-Myc oncogene is constitutively expressed in the cells of the B-cell lineage, leading to spontaneous development of aggressive B-cell lymphomas, resembling Burkitt lymphoma in humans. In order to bring up the senescence as the main fail-safe mechanism, primary lymphoma cells are protected from apoptosis by retroviral over-expression of Bcl2. These cells (Myc;Bcl2) massively undergo senescence upon DNA-damaging treatment. Adriamycin (ADR) is a cytostatic drug, used as a standard part of several lymphoma treatment regimens. In this study, transcriptional profiles of matched pairs of untreated vs. 5 days ADR-treated Myc;Bcl2 lymphomas were analysed.

first: Yong

last: Yu


title: Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats

status: Public on Dec 30 2020

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

summary:
Phosphine (PH3) is a highly toxic, corrosive, flammable, heavier-than-air gas that is a commonly used fumigant.  Although the mechanism of toxicity is unclear, PH3 is thought to be a metabolic poison.  PH3 exposure induces multi-organ toxicity and no effective antidotes or therapeutics have been identified.
To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations.  PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.

overall_design: Following whole body exposure to phosphine, RNA was isolated from tissues and blood from adult male Sprague-Dawley rats at 1, 3, 6, or 24 hours post-exposure and processed for hybridization to affymetrix microarrays. The concentration x time products for phosphine exposure was 15,480 ppm x min corresponding to 0.67 x LCt50 (low dose exposure).

middle: M

first: Benjamin

last: Wong


title: RNA-Seq analysis of melanoma cells, B16F10, in the presence of hypochlorous acid (HOCl)

city: Houston

first: David

last: Piwnica-Worms

address: 1881 East Road, Unit 1907

department: Cancer Systems Imaging

institute: The University of Texas MD Anderson Cancer Center

summary: We evaluated the changes in the transcriptome of a melanoma cell line, B16F10, and spleen isolated murine T cells when in the presence of hypochlorous acid (HOCl) using RNA-sequencing technologies.

overall_design: mRNA profile changes comparing B16F10 cells without or in the presence of 600 uM HOCl and T cells without or in the presence of 600 uM HOCl

first: Tracy

middle: W

last: Liu

first: Seth

last: Gammon


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells [scRNA-seq]

city: suwon

first: DAEUN

last: KIM

address: World cup-ro

country: South Korea

institute: Ajou university

summary: Telomere maintenance is indispensable for perpetuated cell division, but telomeres are not necessarily composed of a fixed sequence. Here we report the establishment of a model for alternative lengthening of telomeres (ALT) in mouse embryonic stem cells (mESCs) in which telomeres are reconstructed with an internal ALT template. Longitudinal whole-genome analyses of ALT mESCs showed that pre-amplification of the template into a telomeric region was a prerequisite for ALT activation, and that extensive copy number variations became concentrated in subtelomeric regions. Epigenomic analysis revealed the heterochromatic structure of the ALT telomeres, except for an insulator region within the ALT template. Quantitative proteomics followed by single-cell RNA-sequencing and functional assays revealed that HMGN1 protected new telomeres by regulating telomere repeat-containing RNA transcription and R loop formation in ALT mESCs. These findings implicate an evolutionarily conserved ALT mechanism driven by an internal template and provide a molecular basis underlying telomere evolution.

overall_design: Open chromatin profiling of Terc knock-out mouse Embryonic Stem Cell (mESC) by passage doubling

first: Chuna

last: Kim

first: Sanghyun

last: Sung

first: Yoonseok

last: Jung

first: Jenny

middle: J

last: Seo

first: V

middle: N


title: Climate warming and nutrient enrichment jointly affect microbial functional potentials important to nutrient cycling in shallow-lake mesocosms

first: Lijuan

last: Ren

address: 601 Huangpu Avenue West, Guangzhou, China

institute: JinanUniversity

summary: Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: In our study, we selected 16 fully mixed, outdoor, flow-through mesocosms (diameter 1.9 m, water depth 1 m, retention time ~2.5 months) combining two temperature scenarios (ambient temperature and warming scenario simulating the IPCC A2 + 50% with temperatures 4–5 °C higher than the ambient) and two nutrient levels with four replicates. Approximately 400 to 500 ml of the collected water was used for microbial Geochip analyses.

first: Qinglong

middle: L

last: Wu

first: Erik

last: Jeppesen


title: Single cell sequencing reveals that constitutive activation of cellular immunity underlies the evolution of resistance to infection

city: Cambridge

first: Frank

last: Jiggins

address: Downing Street

country: United Kingdom

institute: Department of Genetics, University of Cambridge

summary:
Goal: Natural populations of Drosophila melanogaster vary widely in their capacity to resist infection by the parasitic wasp Leptopilina boulardi. To date, little is known about the genetic, cellular and molecular basis underpinning the variation in susceptibility to parasitic wasps. In D.melanogaster populations artificially selected for parasitoid resistance, an increase in the number of circulating hemocytes (blood cells) is observed. One possibility is that this is accompanied by changes in hemocyte activation state, resulting in a successful defence response when exposed to parasitic wasps. We tested this possibility by generating populations that are highly resistant and highly susceptible to the parasitic wasps. We generated these populations after 26 generations of experimental evolution, starting from a single interbred wild caught population. Here, we study how selection for resistance to the parasitic wasp L. boulardi changes the number and type of circulating hemocytes in D. melanogaster larvae using scRNA-seq.
Methods: Wild caught D. melanogaster females were collected from Cambridge, UK, to establish an outbreed population. From this, three replicated populations were selected for resistance to L. boulardi strain NSRef for 26 generations (Selection). Another three populations were maintained in the laboratory for 26 generations without being exposed to parasitoid-associated selection pressures (No Selection). At generation 26, second instar D. melanogaster larvae (48-63 hours after fertilization) from each population were infected with L. boulardi for three hours (Infection) or maintained without infection (No infection). 48 hours after, circulating hemocytes from third instar D. melanogaster larvae (96-111 hours after fertilization) from each population were collected in PBS and cleaned in OptiPrep solution (1.09g/ml). 10X Single Cell GEX v2 libraries were prepared and sequenced. CellRanger v2 was used to generate sample cell count matrices. Seurat v3 was used to integrate, normalise and cluster the cell types.
Results: We identified novel plasmatocyte cell types, immature and mature lamellocytes and crystal cells. We identify a single lineage of cellular differentiation starting from a self-cycling plasmatocyte population, enriched for genes involved in extracellular matrix organisation, and ending in a mature lamellocyte population that has enriched expression of genes involved in signalling, hemostasis and gluconeogenesis. Immature lamellocytes were overrepresented in populations selected for resistance to parasitoids. Infection with parasitoid resulted in an increase in both immature and mature lamellocytes in circulation.
Conclusions: Selection for resistance to the parasitic wasps resulted in the constitutive activation of the D. melanogaster immune system, where plasmatocytes differentiate into immature lamellocytes even where they are not exposed to parasitic wasps. We speculate these constitutive changes assist in mounting a successful defence response when exposed to parasitic wasps.

overall_design: Two selection regimes (Selection and No selection) and two infection treatments (Infection and No infection), three samples for each condition (12 total). All 12 samples were multiplexed on each lane of NovaSeq 6000 S1. Two lanes were sequenced in total, i.e. each sample was sequenced over two lanes at 1/12 depth in each lane.

first: Alexandre

last: Leitão

first: Arunkumar

last: Ramesh

first: Jon

last: Day


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (WGS)

overall_design: Genome profiling of Terc knock-out mouse Embryonic Stem Cell (mESC) by passage doubling


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (RNA-seq)

overall_design: Gene expression profiling of Terc knock-out mouse Embryonic Stem Cell (mESC) by passage doubling


title: Transcriptome analysis of meiotic prophase spermatocytes in Zfp541 +/-  and Zfp541 KO mice

status: Public on Dec 29 2020

city: Chuo-ku

first: Kei-ichiro

last: Ishiguro

state: Kumamoto

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto university

summary: ZFP541 is one of the candidates for a transcriptional regulator during mouse meiotic prophase. In order to address the role of ZFP541, transcriptomes of meiotic prophase-enriched population were compared between Zfp541 +/- and Zfp541 KO testes by RNA-seq. The meiotic prophase-enriched population was isolated from Zfp541 +/-  and Zfp541 KO testes at postnatal day 18 (P18), on the Rec8-3FH-GFP KI background by fluorescent sorting of GFP positive cells.

overall_design: GFP positive cells from Zfp541 KO and the control heterozygous on the  Rec8-3xFLAG-HA-p2A-GFP knock-in background testis were sorted using SH800S cell sorter. (RNA-seq for 1 testis from  Zfp541 +/-: Rec8-3FH-GFP KI hetero,  1 testis from Zfp541 +/-: Rec8-3FH-GFP KI homo,  2 individual testes from Zfp541 KO: Rec8-3FH-GFP KI homo). Total RNAs were prepared by Trizol and quality of total RNA was confirmed by BioAnalyzer 2100 (RIN > 8). Library DNAs were prepared according to the Illumina Truseq protocol using Truseq Standard mRNA LT Sample Prep Kit (Illumina) and sequenced by Illumina NextSeq 500 (Illumina) using Nextseq 500/550 High Output v2.5 Kit (Illumina) to obtain single end 75 nt reads.

first: Shingo

last: Usuki

first: Kumi

last: Matsuura

first: Kenichi

last: Horisawa

first: Yuki

last: Takada


title: Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens BS-Seq]

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

summary: Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. We discovered that specific elimination of CG methylation is fully complemented by non-CG methylation but not vice versa. Between the symmetrically-methylated sites, CHG methylation silenced transposons stronger than CG methylation did. Finally, non-CG methylation revealed as crucial for the silencing of CG depleted transposons. Our results suggest that non-CG methylation evolved to silence transposons due to functional limitations and/or rapid mutability of methylated-CGs.

overall_design: Whole-genome bisulfite sequencing of two P. patens DNMT double mutants: met/dnmt3b and cmt/dnmt3b

first: Aviva

last: Katz

first: Rafael

last: Yaari

first: Efrat

last: Kaizler

first: Vu

last: Hoang Nguyen

first: Uyen

last: Vu Thuy Hong

first: Ofir

last: Griess

first: Keith

last: Harris

first: Karina

last: Gitin Heskiau

first: Nir

last: Ohad

first: Assaf

last: Zemach


title: Non-CG methylation is more potent than CG methylation in moss genome regulation

sample_organism:
Physcomitrium patens
Arabidopsis thaliana


title: Aging-associated alterations in mammary epithelia and stroma revealed by single-cell RNA sequencing

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Aging of the mammary gland is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations within this organ. Here we leveraged the power of high-throughput single-cell RNA-sequencing (scRNA-seq) to generate a detailed transcriptomic atlas of young and aged murine mammary tissues, including both epithelial and stromal cell types. This analysis identified altered proportions and distinct gene expression patterns in multiple cell populations as a consequence of aging, independent of history of pregnancy and hormone cycle. In addition, we detected a rare luminal cell type that expresses both hormone-sensing and alveolar lineage markers as well as a unique gene expression signature. In addition, these cells exhibit a significant decrease in relative abundance with age. Overall, this high-resolution transcriptomic landscape reveals the effects of aging on normal mammary gland physiology and can serve as a valuable resource for understanding aging-associated susceptibility to breast cancer.

overall_design: Single-cell RNA-seq (scRNA-seq) analysis of mammary tissues of 3 young mice (3-4 months of age) and 4 aged mice (13-14 months of age) using the 10X Chromium v2 platform.

first: Carman

last: Li

first: Hana

last: Shapiro

first: Christina

last: Tsiobikas

first: Laura

last: Selfors

first: Huidong

last: Chen

first: Jennifer

last: Rosenbluth

first: Kaitlin

last: Moore

first: Kenneth

last: Gray

first: Yaara

last: Oren

last: Guerriero

first: Luca

last: Pinello

first: Aviv

last: Regev


title: The Effect of Synonymous Single-Nucleotide Polymorphisms on an Atypical Cystic Fibrosis Clinical Presentation

status: Public on Dec 28 2020

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: Synonymous single nucleotide polymorphisms (sSNPs), which change a nucleotide, but not the encoded amino acid, are perceived as neutral to protein function and thus, classified as benign. We report a patient who was diagnosed with cystic fibrosis (CF) at an advanced age and presented very mild CF symptoms. The sequencing of the whole cystic fibrosis transmembrane conductance regulator (CFTR) gene locus revealed that the patient lacks known CF-causing mutations. We found a homozygous sSNP (c.1584G>A) at the end of exon 11 in the CFTR gene. Using sensitive molecular methods, we report that the c.1584G>A sSNP causes cognate exon skipping and retention of a sequence from the downstream intron, both of which, however, occur at a relatively low frequency. In addition, we found two other sSNPs (c.2562T>G (p.Thr854=) and c.4389G>A (p.Gln1463=)), for which the patient is also homozygous. These two sSNPs stabilize the CFTR protein expression, compensating, at least in part, for the c.1584G>A-triggered inefficient splicing. Our data highlight the importance of considering sSNPs when assessing the effect(s) of complex CFTR alleles. sSNPs may epistatically modulate mRNA and protein expression levels and consequently influence disease phenotype and progression.

overall_design: RNA sequencing and gene expression analysis of rectal organoid of mild cystic fibrosis patient homozygous for c.1584G>A sSNP

first: Giovana

last: Bampi

first: Anabela

last: Ramalho

first: Leonardo

last: Santos


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells

first: DAEUN

last: KIM


title: Transcriptome profiling of spinal cord vascular fragments of healthy mice that were either treated with imatinib or PBS

status: Public on Dec 25 2020

city: Solna

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

country: Sweden

institute: Karolinska Institute

summary: The purpose was to determine if imatinib has an effect on the BBB transcriptome in healthy mice.

overall_design: We analysed the transcriptome of vascular fragments of healthy mice treated with imatinib or PBS (n=3 for each condition), respectively. We compared PBS versus imatinb.


title: The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here we show that the Paf1C positively regulates RNAPII pause-release at both protein-coding genes and at enhancers in mouse embryonic stem cells (mESC). Our analyses reveal extensive Paf1C binding at mESC enhancers, in particular at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that mESC self-renewal depends on Paf1C-mediated positive regulation of pluripotency enhancers.

overall_design: RNA-Seq transcriptome profiling of murine ES-E14 and NIH-3T3 cells, as well as ChIP-Seq based examination of Ctr9 binding sites and H3K27ac histone modifications in both cell lines.

first: Ding

last: Li


title: Transcriptomic profiling of human gingiva in health and disease

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

institute: King's College London

summary: sc-RNAseq performed on gingival tissue isolated from healthy and periodontitis patients.

overall_design: 4 samples

first: Ana

last: Caetano

first: Paul

last: Sharpe


title: Transcriptional profiling of shoot of OsPI1 knockdown rice

city: Higashi-Hiroshima

first: Jun

last: Wasaki

state: Hiroshima

address: Kagamiyama 1-7-1

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary:
OsPI1 was isolated from rice and revealed to belong to the TPSI1/Mt4 family, a phosphorus deficiency responsive gene family. The importance of this family gene for phosphorus deficiency responses of plants had been already reported, though its actual role is still unclear. To understand the plants response mechanisms for phosphorus deficiency and the role of OsPI1 in it, we constructed a OsPI1 RNAi line (ospi1-2) for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the shoots and roots of ospi1-2 and Oryza sativa L. cv. Kitaake wild type (WT) rice plants under constitutive and phosphorus deficiency at seedling stage.
Keywords: Influences of OsPI1 knockdown

overall_design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice plant tissues during phosphorus deficiency. We used an OsPI1 knockdown line (ospi1-2) and wild type (WT). Plants were grown in growth chambers and treated in nutrient solutions with or without 32 μM NaH2PO4 for 9 d. Three plants were harvested for one replication and each sample was divided into roots and shoots. Two replications of microarray experiments using two biological replications were carried out by hybridizing the RNA from ospi1-2 and WT plants on the same slide.

first: Tomo

last: Nishiyama

first: SangJa

last: Choi

first: Sachihiro

last: Kuroda

first: Susumu

last: Ito

first: Takuro

last: Shinano

first: Mitsuru

last: Osaki


title: Gene expression profiling of Fah-deficient mouse livers upon short-term nitisinone discontinuation

status: Public on Dec 23 2020

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

summary:
Hereditary tyrosinemia type 1 (HT1) is a severe genetic disorder that affects the liver due to a defective fumarylacetoacetate hydrolase (Fah) enzyme in hepatocytes. The drug nitisinone (NTBC) has offered a life-saving treatment for HT1 patients by inhibiting the upstream enzyme 4-hydroxyphenylpyruvate dioxygenase (HPD).
We used microarray analyses to define the impact of short-term (ie. seven days) NTBC therapy discontinuation on the gene expression profile of liver tissue of Fah-deficient mice. Consequently, we investigated the modulation of canonical pathways related to oxidative stress, glutathione metabolism and liver regeneration.

overall_design: FRG mice (C57Bl/6J background) are characterized by a triple knockout of Fah−/−, Rag2−/− and Il2rg−/− and served as experimental model for HT1. FRG mice (in triplicate) were either continuously treated with 16 mg/l NTBC through their drinking water or deprived from NTBC therapy for seven consecutive days. Withdrawal samples were collected seven days after NTBC discontinuation.

first: Haaike

last: Colemonts-Vroninks

first: Jessie

last: Neuckermans

last: Claes

first: Steven

last: Branson

first: Geert

last: Martens

first: Tamara

last: Vanhaecke


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (ATAC-seq)

first: DAEUN

last: KIM

first: Chuna

last: Kim

first: Sanghyun

last: Sung

first: Yoonseok

last: Jung

first: Jenny

last: Seo

first: V


title: H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription

first: Andrew

last: Lippa

address: 300 Longwood Ave

department: Pediatrics, Division of Infectious Diseases

institute: Boston Children's Hospital

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

overall_design: Refer to individual Series


title: Transcriptome profiling of vascular fragments at the preclinical, progression and remission phase of EAE in imatinib and PBS treated mice

first: Manuel

last: Zeitelhofer

summary: Disruption of blood-brain barrier (BBB) integrity is a hallmark of several neurological disorders. Here we show that the BBB is dynamically and differentially affected during the preclinical, progression and remission phase of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). We isolated vascular fragments, representing the BBB, from spinal cords of imatinib and PBS treated mice at the preclinical, progression and remission phase of MOG-EAE as well as from non-immunized, naive mice.

overall_design: We analysed the transcriptome of vascular fragments of mice treated with imatinib or PBS at the preclinical, progression and remission phase of EAE (n=4 for all EAE time points and conditions), respectively, and of vascular fragments from healthy control mice (n=5, without EAE). We compared PBS versus imatinb and PBS versus naive for all time points.


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill


title: RNA sequencing of myoseptal and perivascular cells during spinal cord regeneration in larval zebrafish.

city: Erlangen

first: Daniel

last: Wehner

address: Staudtsraße 2

department: Division Biological Optomechanics

institute: Max Planck Institut for the Science of Light

summary: The goal of this study was to determine gene expression changes in pdgfrb-expressing (pdgfrb+) myoseptal and perivascular cells after spinal cord lesion in larval zebrafish.

overall_design: RNA profiles of GFP+ cells (also referred to as pdgfrb+ cells) isolated from unlesioned and spinal cord-lesioned BAC(pdgfrb:Gal4ff)ncv24;UAS:GFP trasgenic zebrafish larvae, were genared by RNA-seq, in quadruplicates, using Illumina Nextseq500


title: Development of gene signatures for doxorubicin resistance and cancer stem cell CD44+, CD24-/low ALD+ isolated from canine mammary adenocarcinoma cell line (microRNA)

city: Serdang

first: Gayathri

last: Selvarajah

address: University Putra Malaysia

department: Faculty of Veterinary Medicine

institute: University Putra Malaysia

summary: CMT-Stylo is a canine mammary gland adenocarcinoma cell line. From this cell line, a doxorubicin resistant subline called CMT-Star was developed by culturing the cells in the presence of doxorubicin from low concentration to 100 nM doxorubicin (to induce drug resistance). The CMT-Stylo cells were maintained in Dulbecco’s modified eagles medium (DMEM) supplemented with 10% Foetal bovine serum (FBS) and 1% Penicillin-Streptomycin (ThermoFisher Scientific, USA) in 5% CO2 at 370C. The CMT-Star cell line was maintained in additional 5 nM doxorubicin to maintain its resistant phenotype.

overall_design: We set out to identify differentially expressed messenger RNAs between the CMT-Stylo cells and CMT-Star cells using canine specific cDNA microarrays. Additionally, we isolated cancer stem cells from the cell line and its doxorubicin resistant subline using flow cytometry ( CD44+, CD24-/low and ALDH+ cells sorted using FACS sorter) and using microarray, we identified differentially expressed messenger RNAs between each cell line and its cancer stem cells. At a fold change of 2 and p-value of p < 0.05, a total of 26652 messenger RNA entities were identified as dysregulated between CMT-Stylo cells and CMT-Star cells. Similarly, we identified 28614 messenger RNA entities as differentially expressed between CMT-Stylo cells and their cancer stem cells, and 1808 messenger RNAs entities between CMT-Star cells and their cancer stem cells, using the same parameters.

first: Kabiru

last: Sahabi


title: Identification of SRSF6 splicing regulatory map and its impact on diabetes susceptibility genes regulation

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

summary: The downregulation of diabetes susceptibility gene GLIS3 contributes to pancreatic beta cell demise, at least in part, through downregulation of the  splicing factor SRSF6. Here, we used individual-nucleotide UV crosslinking and immunoprecipitation (iCLIP)  to map the RNA binding landscape of SRSF6 in pancreatic beta cells.

overall_design: Four independent iCLIP replicates for endogeneous SRSF6 from human pancreatic beta cells (EndoC-βH1 cell line)

first: Maria

last: Inês Alvelos

first: Mirko

last: Brüggemann

first: F

middle: X

last: Reymond Sutandy

first: Anke

last: Busch

first: Julian

last: König

first: Décio

last: Eizirik


title: Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest [sgRNA-seq]

status: Public on Dec 22 2020

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

institute: Agriculture Research Organization

summary: Different subsets of the tRNA pool in human are expressed in different cellular conditions. The “proliferation-tRNAs” are induced upon normal and cancerous cell division, while the “differentiation tRNAs” are active in non-dividing, differentiated cells. Here we examine the essentiality of the various tRNAs upon cellular growth and arrest. We established a CRISPR-based editing procedure with sgRNAs that each target a tRNA family. We measured tRNA essentiality for cellular growth and found that most proliferation tRNAs are essential compared to differentiation tRNAs in rapidly growing cell lines. Yet in more slowly dividing lines, the differentiation tRNAs were more essential. In addition, we measured the essentiality of each tRNA family upon response to cell cycle arresting signals. Here we detected a more complex behavior with both proliferation-tRNAs and differentiation-tRNAs showing various levels of essentiality. These results provide the so-far most comprehensive functional characterization of human tRNAs with intricate roles in various cellular states.

overall_design: sgRNA sequencing of induced HeLa, WI38 fast and WI38 slow iCas9 cells harboring sgRNAs that target 20 human tRNA families

first: Noa

last: Aharon-Hefetz

first: Idan

last: Frumkin

first: Yoav

last: Mayshar

first: Orna

last: Dahan

first: Yitzhak

last: Pilpel


title: Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest.


title: Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest [tRNA-seq]

overall_design: tRNA sequencing of induced HeLa iCas9 cells harboring sgRNAs that target 4 human tRNA families


title: Borrelia burgdorferi infection induces long-term memory-like responses in macrophages with tissue-wide consequences in the heart

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Lyme carditis is an extracutaneous manifestation of Lyme disease characterized by episodes of atrioventricular block of varying degrees and other less reported cardiomyopathies. The molecular changes associated with the response to Borrelia burgdorferi over the course of infection are poorly understood. Here, we identify broad transcriptomic and proteomic changes in the heart during infection that reveal a profound downregulation of mitochondrial components. We also characterize the long-term functional modulation of macrophages exposed to live bacteria, characterized by an augmented glycolytic output, increased spirochetal binding and internalization, and reduced IRF-4-dependent inflammatory responses. In vitro, glycolysis inhibition reduces the production of TNF by memory macrophages whereas in vivo, it produces the reversion of the Irf4-induced memory phenotype, the recovery of tissue mitochondrial components, and decreased inflammation and spirochetal burdens. These results show that B. burgdorferi induces long-term, memory-like responses in macrophages with tissue-wide consequences that are amenable to be manipulated in vivo.

overall_design: Genome-wide changes in gene expression in murine hearts from mice infected at different time points with Borrelia burgdorferi as well as those from mice infected and treated with a glycolysis inhibitor. Groups corresponding to times of infection 0, 7, 21 and 54 days as well as control-treated and 3-PO treated over the course of 5 weeks were generated by RNAseq.

first: Diego

last: Barriales

first: Itziar

last: Martín

last: Carreras-González

first: Marta

last: Montesinos-Robledo

first: Mikel

last: Azkargorta

first: Ibon

last: Iloro

first: Iraide

last: Escobés

first: Teresa

last: Martín-Mateos

first: Estibaliz

last: Atondo

first: Ainhoa

last: Palacios

first: Monika

last: Gonzalez

first: Diana

last: Cabrera

first: Ainize

last: Peña-Cearra

first: Sebastiaan

last: van Liempd

first: Juan

last: Falcón-Pérez

first: Miguel

last: Pascual-Itoiz

first: Leticia

last: Abecia

first: Aize

last: Pellon

last: Martínez-Chantar

first: Alberto

last: Pascual

first: Felix

last: Elortza

first: Edurne

last: Berra

first: José

last: Lavín

first: Héctor

last: Rodríguez

last: Anguita


title: Expression data of wild-type Salmonella enterica serovar Typhimurium strain 14028s treated with or without mitomycin C (3 μM)

city: Frederick

first: Sandra

middle: Lynn

last: Wolin

state: Maryland

address: Miller Drive

department: RNA Biology

institute: National Cancer Institute

summary: We showed that treatment with mitomycin C results in activation of an endonuclease that cleaves tRNAs in the anticodon loop. In an attempt to identify this nuclease, we performed RNA-seq on wild-type cells treated with and without mitomycin C.  Differential gene expression was performed to identify genes expressed upon mitomycin C treatment.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA profiles of S. Typhimurium with and without mitomycin C  3 μM  treatment for 2 hours.

first: Xinguo

last: Chen

first: Kevin

last: Hughes


title: Identification of 17-DMAG as a novel KDM4B inhibitor for combination therapy

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation

city: Cambridge

first: Charlie

middle: Y.

last: Shi

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Mus musculus

middle: Y

first: David

middle: P

last: Bartel


title: Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest [genomic_tRNAseq]

first: Roni

last: Rak

overall_design: genomic tRNA sequencing of induced HeLa and WI38 fast iCas9 cells harboring sgRNAs that target 4 human tRNA families

first: Noa

last: Aharon-Hefetz

first: Idan

last: Frumkin

first: Yoav

last: Mayshar

first: Orna

last: Dahan

first: Yitzhak

last: Pilpel


title: Identification of 17-DMAG as a novel KDM4B inhibitor for combination therapy [ChIP-seq]

summary: Histone demethylases such as KDM4B play critical roles in oncogenic pathophysiology and, therefore may be effective targets for anticancer therapy. Using a TR-FRET demethylation screen assay, in combination with multiple orthogonal validation approaches, we identified geldanamycin and its analog 17-DMAG as novel KDM4B inhibitors. In addition, we found that these Hsp90 inhibitors effect increased degradation of the alveolar rhabdomyosarcoma (aRMS) driver oncoprotein PAX3-FOXO1 and  induce the H3K9me3 and H3K36me3 at genomic loci of PAX3-FOXO1 targets. We found that as monotherapy 17-DMAG significantly inhibits expression of PAX3-FOXO1 target genes and multiple oncogenic pathways, induces a muscle differentiation signature, delays tumor growth and extends survival in aRMS xenograft mouse models. The combination of 17-DMAG with conventional chemotherapy significantly enhances therapeutic efficacy, indicating that targeting KDM4B in combination with chemotherapy may serve as a novel therapy to PAX3-FOXO1-positive aRMS.

overall_design: Examination of histone modification post geldanamycin treatment.

first: Jie

last: Fang

first: Jun

last: Yang


title: RNA sequencing of zebrafish embryos under simulated microgravity conditions

city: Changsha

first: Lvyun

last: Zhu

state: Hunan

address: 109 Deya Road, Kaifu District

department: College of Liberal Arts and Sciences

institute: National University of Defense Technology

summary: To reveal the potential mechanisms involved in the dysfunction of antiviral immune responses under simulated microgravity conditions, we investigated the transcriptional changes related to the status of innate immune responses by RNA-seq with poly I:C or mock PBS treatment under Normal gravity or simulated microgravity conditions. Our results indicate that the retinoic acid inducible gene (RIG)-I-like receptor (RLR) and Toll-like receptor (TLR) signal pathways, which are both involved in the type-I interferon induction, are significantly inhibited by simulated microgravity effects.

overall_design: Orthogonally examination of the zebrafish embryos stimulated with poly I:C or control buffer and cultured in the simulated microgravity condition generated by RCCS or the normal gravity condition in cell culture dish

first: Li

last: Nie


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets[Prdm1/Maf KO colonic CD4 T cells scRNA-seq]

status: Public on Dec 21 2020

city: Boston

first: Vijay

last: Kuchroo

address: 60 Fenwood Road

department: Neurology

institute: Brigham & Women's Hospital

summary: IL-27 is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, Atf3) and 2 negative (Irf9, Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators Prdm1 and Maf that cooperatively drive the expression of signature genes induced by IL-27 in Type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying the ll10 deficient mice. Our work provides insights for IL-27 driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.

overall_design: scRNA-seq of CD4 T cells from colonic lamina propria of control, CD4-Cre;Prdm1 f/f, CD4-Cre;Maf f/f and CD4-Cre; Prdm1 f/f; Maf f/f  mice at 3 weeks of age

first: Huiyuan

last: Zhang


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets[Tr1 deficient in TFs RNA-seq]

summary: IL-27 is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, Atf3) and 2 negative (Irf9, Irf8) Il10 regulators,  generating an experimentally refined regulatory network for Il10. We report two central regulators     Prdm1 and Maf     that cooperatively drive the expression of signature genes induced by IL-27 in Type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+regulatory T cells.  Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying the ll10 deficient mice. Our work provides insights for IL-27 driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.

overall_design: Bulk RNA-seq for in vitro derived Tr1 cells deficient in various transcription factors

first: Asaf

last: Madi

first: Norio

last: Chihara


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets [IL10+ vs IL10-T helper cell RNA-seq]

overall_design: RNA-seq of IL-10+ and IL-10- Th1, Th2, Th17 and Tr1 cells


title: NanoString PanCancer Immune Panel in Black and White Breast Cancer Patients in the Women's Circle of Health Study (WCHS)

status: Public on Dec 18 2020

city: Buffalo

first: Song

last: Yao

state: NY

address: Elm and Carlton Streets

department: Cancer Prevention and Control

institute: Roswell Park Comprehensive Cancer Center

summary: NanoString PanCancer Immune Panel with customized codesets from a total of 367 Black and White breast cancer patients in WCHS

overall_design: This is a case-series study of 367 Black and White women diagnosed with invasive breast cancer enrolled in the Women's Circle of Health Study (WCHS). Archieved FFPE tumor sections were used for RNA extraction and mRNA expression profiling of 750 genes.

first: Christine

last: Ambrosone


title: Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

status: Public on Dec 19 2020

city: Dubai

first: Ruchi

last: Jain

address: Al jaddaf

department: Genomics

country: United Arab Emirates

institute: Al jalila Children's Specialty Hospital

summary: We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity

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

first: Sathiskumar

last: Ramaswamy

first: Ahmad

middle: A

last: Tayoun


title: RNA-seq of SI adenoma tissue from ApcMin and ApcMin-PCdel Mice

status: Public on Dec 20 2020

city: Dallas

first: Ezra

last: Burstein

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Internal Medicine

institute: University of Texas Southwestern Medical Center

summary: Adenomas derived from PCdel mice exhibited reduced expression of paneth cell marker genes as well as Wnt3.

overall_design: RNA-seq profiles were created from adenoma samples harvested from adult ApcMin and ApcMin-PCdel Mice

first: Qing

last: Chen


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets[Prdm1/Maf KO Tr1 ATAC-seq]

overall_design: ATAC-seq for in vitro derived Tr1 cells that are deficient in Prdm1, Maf, or both


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets

overall_design: Refer to individual Series


title: The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies [ChIP-seq]

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

summary: Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and Polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose Polycomb Repressor Complex (PRC) 2 activity while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of Polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and confer vulnerability to USP7 loss, a core member of ncPRC1.1. SyS organoids thus provide a powerful model to define mechanisms of epigenetic dysregulation on which SyS cells are dependent.

overall_design:
ChIP-seq for the BAF complex subunit SMARCA2 and histone marks in synovial sarcoma and Ewing sarcoma spheroids, human pediatric mesenchymal stem cells (MSCs), MRC5 and MET5A cells.    ChIP-seq for the BAF complex subunit SMARCA2 and histone marks in mouse C3H10T1/2 cells. V5-tagged SYT-SSX was expressed in C3H10T1/2 cells using a lentiviral expression vector and ChIP-seq was performed using an anti-V5 antibody.    C3H10T1/2 cells expressing V5-SYT-SSX were further lentivirally induced with a control vector (pLKO) or a CRE recombinase (CRE) to knock-out the sequence encoding SYT-SSX.

Please note that the raw data from primary patient cells (GSM4477549-GSM4477588, GSM4477595-GSM4477600) cannot be released in GEO due to patient privacy concerns and will be submitted to dbGaP.

first: Gaylor

last: Boulay

first: Miguel

last: Rivera


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 1]

first: Charlie

last: Shi

summary: MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread post-transcriptional gene repression.  Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation.  Here we found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase.  This and other findings suggested and supported a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin–proteasome pathway exposes the miRNA for degradation.  Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs.  These results elucidate the mechanism of TDMD and expand the inferred role of TDMD in shaping miRNA levels in bilaterian animals.

overall_design: miRNA expression profiling by small-RNA sequencing of K562 cells expressing inducible KRAB-dCas9 and either a control guide RNA (gRNA), a gRNA targeting CYRANO, or one of two gRNAs targeting ZSWIM8.  This study consists of 12 libraries generated from three biological replicates per gRNA.

first: David

last: Bartel


title: Identification of 17-DMAG as a novel KDM4B inhibitor for combination therapy [RNA-seq]

first: Hongjian

last: Jin

summary: Histone lysine demethylases (KDMs) are emerging as therapeutic targets in cancer. Development of potent KDM inhibitors may provide additional options for epigenomics-oriented therapies. Using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) functional demethylation assay, in combination with a high-content immunofluorescence imaging phenotypic screen, Matrix-Assisted Laser Desorption/Ionization- Fourier Transform Ion Cyclotron Resonance mass spectrometry (MALDI-FTICR MS) and Amplified Luminescent Proximity Homogeneous Assay (ALPHA), we identified geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), as a novel inhibitor of JmjC-domain containing demethylases such as KDM4B. We further found that geldanamycin can destabilize the PAX3-FOXO1 fusion oncoprotein, an Hsp90 client, which is a driver of clinically unfavorable alveolar rhabdomyosarcoma (aRMS). We then hypothesized that dual inhibition of PAX3-FOXO1 and epigenetic modifiers of aRMS would have synergistic antitumor activity. We repurposed the geldanamycin analog 17-DMAG to target aRMS and found that 17-DMAG significantly delays tumor growth , extends survival in xenograft mouse models, and inhibits expression of PAX3-FOXO1 targets and multiple oncogenic pathways including MYC, E2F and NOTCH. In addition, the combination of 17-DMAG with conventional chemotherapy or the bromodomain inhibitor JQ1 significantly enhances therapeutic efficacy. In summary, we have identified geldanamycin and 17-DMAG as dual KDM/Hsp90 inhibitors and 17-DMAG is efficacious against PAX3-FOXO1-driven rhabdomyosarcoma.

overall_design: Rh30 cells were subcutaneously implanted in CB17 SCID mice. When tumor volume reached about 200 mm3, mice were treated with vehicle, 17-DMAG(25mg/kg), 17-AAG (50mg/kg), twice daily, via IP injection, on every Monday and Thursady. Total RNA was extracted from xenograft tissues by RNeasy Mini Kit (cat. # 74104) from QIAGEN. Paired-end sequencing was performed using the High-Seq platform with 100bp read length. Reads were aligned to the human GRCh37-lite using SJCRH’s Strongarm pipeline. Counts per gene were obtained using htseq-count version 0.6.1 with Gencode vM5 level 1and 2 gene annotations. Counts were normalized with VOOM and analyzed with LIMMA within the R statistical environment. Significance was defined as having a false discovery rate (FDR) <0.05.

first: Ahmed

last: Abu-Zaid

first: Jun

last: Yang


title: IL-27 driven transcriptional network identifies regulators of IL-10 expression across T helper cell subsets[Tr1 differentiation with IL-27 microarray]

first: Vijay

last: Kuchroo

overall_design: Affymetrix GeneChip Mouse Genome 430 2.0 Arrays

first: Asaf

last: Madi

first: Nir

last: Yosef

first: Caroline

last: Pot

first: Lionel

last: Apetoh


title: The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies.

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


title: The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies [RNA-seq]

overall_design:
Synovial sarcoma spheroids and pediatric mesenchymal stem cells (MSCs) were analyzed by RNA-seq. C3H10T1/2 cells were analyzed by RNA-seq. SYT-SSX was expressed in C3H10T1/2 with lentiviral expression vectors.     In a separate experiment, C3H10T1/2 pre-infected with SYT-SSX were also infected with a CRE recombinase to knock-out SYT-SSX.

Please note that the raw data from primary patient cells (GSM4477640-GSM4477646) cannot be released in GEO due to patient privacy concerns and will be submitted to dbGaP.


title: An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)

status: Public on Dec 15 2020

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

summary: Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. Here, we use a high-resolution quantitative approach to study alternative TSS and transcript end site (TES) usage during three different cell fate transitions in yeast: entry into gametogenesis, commitment to meiotic divisions and return to vegetative growth. We propose that an alternative transcriptome of mRNA isoforms and lncRNAs shapes local gene expression during cell fate transitions. Hence, changes in the types and proportions of different RNAs transcribed at a locus are important inputs for gene expression at distinct stages of development.

overall_design: Transcript Isoform sequencing (TIF) analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER).  For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Time points for each cell fate transition were pooled in equal proportions for library construction and sequencing. Two independent replicates were sequenced.. Details for library preparation are described below.

first: Minghao

last: Chia

first: Cai

last: Li

first: Sueli

last: Marques

first: Vicent

last: Pelechano


title: Impact of inflammation on hepatic subcellular energetics in anesthetized rats

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: Rats anesthetized with the two anesthetics i.e. isoflurane and propofol respond differently to inflammation initiated by cecal ligation and puncture.

overall_design: Single-end RNA sequencing

first: Robert

middle: H

last: Thiele

first: Hari

last: Osuru

first: Uma


title: Conserved Spermatogonial Gene Networks Couple to Glutathione and Pentose Phosphate Metabolism but not Cysteine Biosynthesis

status: Public on Dec 17 2020

first: F. Kent

last: Hamra

department: Obstetrics and Gynecology

institute: UT Southwestern Medical Center

summary: Here, gene profiles in rat spermatogonial stem cell lines are compared to publicly available mouse, monkey and human spermatogonial gene profiles. Interestingly, rat spermatogonia expressed metabolic control factors Foxa1, Foxa2 and Foxa3. Germline Foxa2 was enriched in Gfra1Hi and Gfra1Low undifferentiated A-single spermatogonia. Foxa2-bound loci in spermatogonial chromatin were over-represented by conserved stemness genes (Dusp6, Gfra1, Etv5, Rest, Nanos2, Foxp1) that intersect bioinformatically with conserved glutathione/pentose phosphate metabolism genes (Tkt, Gss, Gclc, Gclm, Gpx1, Gpx4, Fth), marking elevated spermatogonial GSH:GSSG. Cystine-uptake and intracellular conversion to cysteine typically couple glutathione biosynthesis to pentose phosphate metabolism. Rat spermatogonia, curiously, displayed poor germline stem cell viability in cystine-containing media, and, like primate spermatogonia, exhibited reduced transsulfuration pathway markers. Exogenous cysteine, cysteine-like mercaptans, somatic testis cells and ferroptosis inhibitors counteracted the cysteine starvation-induced spermatogonial death and stimulated spermatogonial growth factor activity in vitro.

overall_design: Gene expression in rat undifferentiated spermatogonia (USg) vs differentiating spermatogonia (DSg) and spermatocytes (Spc).  Foxa2 Chipseq in Rat Undifferentiated Spermatogonia

first: David

last: Proki

first: F

middle: K


title: Transcriptional trajectories highlight the transition from anterior-posterior to proximal-distal patterning in the early limb bud [scRNA-seq]

city: Montreal

first: Marie

last: Kmita

state: QC

address: 110 Pine Avenue

institute: IRCM (Institut de Recherches Cliniques de Montréal)

summary: Limb patterning relies in a large part on the function of the Hox family of developmental genes. While the differential expression of Hox genes shifts from the anterior-posterior (A-P) to the proximal-distal (P-D) axis around embryonic day 11 (E11), whether this shift coincides with a more global change of P-D versus A-P patterning program remains unclear. By performing and analyzing the transcriptome of the developing limb bud from E10.5 to E12.5, at single cell resolution, we have uncovered transcriptional trajectories which revealed a general switch from A-P to P-D genetic program between E10.5 and E11.5. Interestingly, the transcriptional trajectories at E10.5 all end with cells expressing either proximal or distal markers suggesting a progressive acquisition of P-D identity. Moreover, we observed that distally expressed Hox genes, namely Hoxa13 and Hoxd13, act as a key determinant for P-D patterning as their transcriptional control results in their distal restricted expression, which in turn restricts Hoxa11 in the proximal limb bud domain, in progenitor cells of the zeugopod. Finally, we identified three categories of genes expressed in the distal limb mesenchyme characterized by distinct temporal expression dynamics. As anticipated from previous results, HOX13 binding was observed within or in the neighborhood of several of these genes consistent with previous evidence suggesting that the transition from the early/proximal to the late/distal transcriptome of the limb mesenchyme largely relies on HOX13 function.

overall_design: Single-cell RNA-seq analysis of mouse forelimb bud at E10.5, E11.5 and E12.5

first: Ines

last: Desanlis

first: Rachel

last: Paul


title: An alternative transcriptome shapes cell fate transitions in yeast (MNase-seq)

overall_design:
MNase sequencing analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER). In addition, mutant strains include those with the following genotypes: set2, set3, set2 set3 and Spt16 with a C-terminal degron (SPT16-AID). 3 biological replicates of each condition were analysed for the sporulation and return to growth time courses. For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Degradation of Spt16-AID was induced at Spo 2h with 500 μM 3-indole-acetid acid (3-IAA, auxin). For the return to growth (RTG) time course, cells in meiotic prophase (Spo 6h) were washed and re-suspended in an equal volume of YPD. Details for library preparation are described below.
Please note that each .bw processed data was generated from both replicates and is linked to the corresponding replicate 1 sample records.


title: Denunded HUVEC/HUASMC spheroids vs. HUASMC spheroids

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Here, we investigated changes of the VSMC transcriptome by utilizing 3D human vascular organoids organized as a core of VSMCs enclosed by a monolayer of ECs. Unbiased microarray-based analyses indicated that interaction with ECs for 48 hours down-regulates the VSMC expression of genes controlling rate-limiting steps of the cholesterol biosynthesis such as HMGCR, HMGCS1, DHCR24 and DHCR7. Protein analyses revealed a decrease in the abundance of 24-dehydrocholesterol reductase and lower cholesterol levels in VSMCs co-cultured with ECs. On the functional level, the blockade of the DHCR24 activity impaired spreading, migration and proliferation of VSMCs.  Collectively, these findings indicate that ECs have the capacity to instruct VSMCs to shut down the expression of DHCR24 thereby limiting their capacity for cholesterol biosynthesis which may support their functional steady state.

overall_design: 3 samples of denunded HUVEC/HUASMC spheroids (80-90% of the HUVEC were removed) and 3 samples of HUASMCs spheroids were processed for RNA extraction

first: Thomas

last: Korff


title: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

first: Folkert


title: An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

overall_design: 5’ end RNA sequencing analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER). In addition, mutant strains include those with the following genotypes: set2, set3, set2 set3 and Spt16 with a C-terminal degron (SPT16-AID). 3 biological replicates of each condition were analysed for the sporulation and return to growth time courses. For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Degradation of Spt16-AID was induced at Spo 2h with 500 μM 3-indole-acetid acid (3-IAA, auxin). For the return to growth (RTG) time course, cells in meiotic prophase (Spo 6h) were washed and re-suspended in an equal volume of YPD. Details for library preparation are described below.

first: Minghao


title: Astrocyte-secreted IL-33 mediates homeostatic synaptic plasticity in the adult hippocampus

status: Public on Dec 14 2020

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: Hippocampal synaptic plasticity is important for learning and memory formation. Homeostatic synaptic plasticity is a specific form of synaptic plasticity that is induced upon prolonged changes in neuronal activity to maintain network homeostasis. While astrocytes are important regulators of synaptic transmission and plasticity, it is largely unclear how they interact with neurons to regulate synaptic plasticity at the circuit level. Here, we show that neuronal activity blockade selectively increases the expression and secretion of IL-33 (interleukin-33) by astrocytes in the hippocampal cornu ammonis 1 (CA1) subregion. This IL-33 stimulates an increase in excitatory synapses and neurotransmission through the activation of neuronal IL-33 receptor complex and synaptic recruitment of the scaffold protein PSD-95. We found that acute administration of tetrodotoxin in hippocampal slices or inhibition of hippocampal CA1 excitatory neurons by optogenetic manipulation increases IL-33 expression in CA1 astrocytes. Furthermore, IL-33 administration in vivo promotes the formation of functional excitatory synapses in hippocampal CA1 neurons, whereas conditional knockout of IL-33 in CA1 astrocytes decreases the number of excitatory synapses therein. Importantly, blockade of IL-33 and its receptor signaling in vivo by intracerebroventricular administration of its decoy receptor inhibits homeostatic synaptic plasticity in CA1 pyramidal neurons and impairs spatial memory formation in mice. These results collectively reveal an important role of astrocytic IL-33 in mediating the negative-feedback signaling mechanism in homeostatic synaptic plasticity, providing insights into how astrocytes maintain hippocampal network homeostasis.

overall_design: To identify astrocyte-secreted factors that potentially regulate homeostatic synaptic plasticity, we examined the differentially expressed genes in mixed neuron–glia hippocampal cultures following neuronal activity blockade with tetrodotoxin (TTX, 1 μM), a sodium channel blocker that inhibits action potentials.

first: Ye

last: Wang


title: Real-time quantitative PCR analysis of rainbow trout immune related gene expressed during exposure to Vibrio anguillarum

city: Frederiksberg

first: Asma

last: Karami

state: Denmark

address: Stigbojlen 7

institute: University of Copenhagen

summary:
Total RNA was extracted from V. angularium susceptible and resistant rainbow trout, tissues (liver, spleen, gill), in different time points using GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). After measuring quantity (NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark)) and quality (gel electrophoresis) of RNA, cDNA was synthetised in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Primers and probes for total of 28 genes including three housekeeping genes were synthesized at TAG Copenhagen AS, Denmark. qPCR reactions were run by Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark) for all samples. The fold changes analysed by the simplified 2-ΔΔCq method.
Fingerlings of rainbow trout (mean body weight of 12 g) were exposed (2 h bathing, 18°C) to the pathogen V. anguillarum serotype O1 in a solution of 1.5x107 cfu/ml and observed for 14 d. Disease signs appeared three days post exposure (dpe) whereafter morbidity progressed exponentially until 6 dpe reaching a total morbidity/mortality of 55% within 11 days.  we sampled fish for immune gene expression analysis when they first showed clinical signs, fish without clinical signs at the same time point and finally fish surviving the exposure to the pathogen. The different immune gene expression profiles in the different groups were addressed when discussing possible resistance mechanisms in rainbow trout.

overall_design: 15 rainbow trout with clinical signs (CS), 15 rainbow trout with no clinical signs (NCS) at the same time point (3 days post exposure), 15 rainbow trout surviving the challenge (11 days post exposure) were samples and for each time point and time point zero (before the challenge started) 15 rainbow trout were sampled from uninfected fish as control group for normalizing the data. Organs liver, spleen and gills were samples from all groups.

first: Per

last: Kania

first: Kurt

last: Buchmann


title: An alternative transcriptome shapes cell fate transitions in yeast (mRNA-seq)

last: van Werven

overall_design: mRNA sequencing analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER). In addition, mutant strains include those with the following genotypes: set2, set3, set2 set3 and Spt16 with a C-terminal degron (SPT16-AID). 3 biological replicates of each condition were analysed for the sporulation and return to growth time courses. For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Degradation of Spt16-AID was induced at Spo 2h with 500 μM 3-indole-acetid acid (3-IAA, auxin). For the return to growth (RTG) time course, cells in meiotic prophase (Spo 6h) were washed and re-suspended in an equal volume of YPD. Details for library preparation are described below.

last: Chia

first: Cai

last: Li


title: Impaired transcriptional profile in the hippocampus following loss of Kdm5a

first: Maria

last: Chahrour

address: 6000 Harry Hines Blvd

summary: KDM5A encodes a histone lysine demethylase that removes methyl groups from lysine 4 of histone H3, resulting in repression of target genes. In order to identify KDM5A targets, we profiled transcripts from hippocampi of WT and Kdm5a -/- mice. Loss of KDM5A resulted in dysregulation of 450 genes (FDR-corrected P ≤0.05 and log2 fold change ≥|0.3|), of which 191 genes were upregulated and 259 genes were downregulated.

overall_design: Hippocampal transcriptional profiles from 6-8-week old wild type (WT) and Kdm5a -/- (KO) mice were generated by sequencing of 5 biological replicates per genotype using Illumina NextSeq 500.

first: Lauretta

last: ElHayek