title: The impact of ageing on the transition of the euploid human GV oocytes to in vivo matured MII oocytes

city: Leeds

first: Panagiotis

last: Ntostis

address: Clarendon Way

department: Medicine and Health

institute: University of Leeds

summary:
Background: Early embryonic development is governed by maternal transcripts stored within the oocyte during oogenesis. Transcriptional activity of the oocyte ultimately dictates its developmental potential and may be influenced by maternal age, resulting in reduced competence of oocytes derived from women of advanced age, compared with the young. In the current study, RNA-Seq was used to perform transcriptome profiling of human GV and MII oocytes derived from young and advanced maternal age women.
Participants/Materials and Methods: Cumulus dissection from donated oocytes was performed. GV and MII oocytes underwent deep RNA sequencing using the SMART-Seq v4 Ultra Low Input RNA protocol (Takara-Clontech, USA) and Nextera XT DNA library preparation kit (Illumina, USA). Data processing, quality assessment and bioinformatics analysis were performed using source-software, including FastQC, HISAT2, StringTie, edgeR and DAVID.
Results: Following deep single-cell RNA-Seq on GV and MII oocytes, hundreds of transcripts were significantly differentially expressed between young maternal age (YMA) and advanced maternal age (AMA) groups, with the most significant biological processes relating to mitochondrial reserves. The GV to MII transition shares common biological processes between young and AMA groups, however, some genes involved in mitochondria function were altered during ageing. A decrease in mitochondrial-related transcripts was also observed during the GV to MII transition. However, there was a much greater reduction of mitochondrial-related transcripts in MII oocytes of AMA. This observation was confirmed when YMA MII oocytes were compared with the AMA MII group with mitochondrial-related transcripts being significantly higher expressed in the YMA group, including biological processes, such as mitochondrial electron transport and ATP biosynthetic process. These results indicate a higher energy potential in YMA MII oocytes that is decreased with age. Other significantly higher biological processes in the YMA MII group include transcripts involved in the regulation of ubiquitin-dependent degradation. Lack of these transcripts could lead to a non-appropriate removal of oogenesis remnants following fertilisation in the AMA MII group.
Discussion: Understanding reproductive ageing effects at the RNA level in human oocytes may reveal differences in the mechanisms regulating the GV to MII transition that impact on oocyte quality in YMA and AMA patients. Further investigations of the up-/down-regulated transcripts during ageing could guide and improved IVF outcomes for AMA patients.

overall_design: Fifteen patients treated for infertility in a single IVF unit agreed to participate in this study, where 5 GV and 5 MII oocytes derived from 8, 21-26 yo women (YMA group), and 5 GV and 6 MII oocytes from 7, 41-44yo women (AMA group). These oocytes were donated by women undergoing IVF treatment for research purposes. The samples were collected within a period of 3 months. RNA was isolated and deep sequenced at the single cell level.

last: Iles

first: Georgia

last: Kokkali

first: Terpsi

last: Vaxevanoglou

first: Emmanouel

last: Kanavakis

first: Agni

last: Pantou

last: Huntriss

first: Konstantinos

last: Pantos

first: Helen

last: Picton


title: Rat lung cancer model induced with smoky coal

status: Public on Jan 11 2022

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

country: China

institute: Yunnan university of Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: The Xuanwei area is a hot spot of lung adenocarcinoma in females in China, which is strongly associated with the consumption of local smoky coal. Comprehensive characterization of its genomic and immunological landscapes is crucial for cancer prevention and the development of precision therapy. Here, we report extensive genomic, transcriptomic, and immunological profiles of 117 Xuanwei female lung adenocarcinoma (XWFA), comprising 112 pairs of tumour-normal whole-exon sequencing (WES) profiles and 33 normal and 115 tumour mRNA-seq profiles.

overall_design: To investigate the molecular mechanism underlying lung cancer we established rat lung cancer model induced with smoky coal.


title: Expression data from parental and evolved Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration and lignocellulose-derived inhibitors

city: Madrid

first: Antonio

middle: David

last: Moreno

address: Avda. Complutense 40

department: Department of Energy

country: Spain

institute: CIEMAT

summary: Increasing yeast robustness against biomass-derived inhibitors and insoluble solids is essential for the realization of a bio-based economy. The xylose-fermenting Saccharomyces cereivisiae F12 strain was subjected to an adaptive laboratory evolution experiment in the presence of these stressors. The resulting evolved strain exhibit better fermentation performance in terms of xylose consumption and ethanol yields than the parental strain. The overexpression of genes related to cell wall integrity and the stress response, together with the downregulation of protein synthesis and iron transport and homeostasis were highlighted as the major biological processes responsible for the improved phenotype.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Parental and evolved S. cerevisiae F12 cells were collected during fermentation in presence of insoluble solids and lignocellulose-derived inhibitors for RNA extraction and hybridization on Affymetrix microarrays.

middle: D

first: Elia

last: Tomás-Pejó


title: Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

city: Bengbu

first: Zhaoyi

last: Lu

state: Anhui

address: 287 Changhuai Road

department: Department of Otolaryngology

institute: The First Affiliated Hospital of Bengbu Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer-RNA-Derived Small RNA (tsRNA) is  a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the fresh nasopharyngeal carcinoma tissue specimens (n = 4) and mucosal tissue specimens (n = 4) in patients’ primary nasopharyngeal carcinoma (P-NPC) and nasopharyngitis. Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of P-NPC.

overall_design: tiRNA and tRF profiles in the tissue specimens of primary nasopharyngeal carcinoma (P-NPC) and nasopharyngitis patients, in triplicate, using Illumina NextSeq 500 system.

first: Shiyin

last: Ma

first: Hui

last: Li


title: Effect of USP21 deficiency on transcriptomes in skeletal muscle of mice

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Skeletal muscle is the pivotal organ for energy homeostasis, but the regulatory mechanisms are largely unknown. Here, we report that ubiquitin specific protease 21 (USP21) is a regulator of skeletal muscle physiology. To elucidate features important for USP21, we performed RNA-sequencing analysis using the muscle tissue of muscle-specific USP21 knockout (USP21-MKO) mice or wild-type littermates with floxed genotype, screened and analyzed the differentially expressed genes. Transcriptomics assay enabled us to discover major signaling nodes persistently activated by USP21 ablation in close association with the genes linked to fuel oxidation. Consequently, USP21 ablation altered gross metabolic phenotypes.

overall_design: Examination of RNA expression in gastrocnemius muscles of WT or skeletal muscle-specific USP21 KO mice.

first: Ayoung

first: Sang

middle: G


title: Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy (ChIP-Seq 2)

city: Rochester

first: Zachary

middle: C

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

country: USA

institute: University of Rochester

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We suggest a novel paradigm for understanding the epigenetic mechanisms that govern terminal erythroid maturation, and underlie inherited and acquired erythroid disease.

overall_design: Two replicates of early or late erythroblasts for comparison of H3K36me3 and H3K27me3

first: Laurie

middle: A

last: Steiner


title: Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy (RNA-Seq)

overall_design: Two replicates of CD36 synchronization cultures at Day 7 and Day 10 are compared following RNA-seq


title: Silent Alcoholic Steatohepatitis vs Alcoholic Hepatitis: Clinical, Histological and Transcriptome Analysis

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: BACKGROUND: Alcohol-related liver disease ranges from silent alcoholic steatohepatitis (sASH), an asymptomatic and compensated phenotype, to life- threatening alcoholic hepatitis (AH). A systematic comparative study of the clinical, histological and molecular features of these subtypes is lacking. METHODS : Two large cohorts of patients were recruited in an international, observational multi-center study: a retrospective cohort of patients with sASH (n=110) and a prospective cohort of patients with AH (two subgroups with n=121 and 104). sASH and AH were compared by doing clinical, analytical, immunohistochemistry and hepatic RNA microarray analysis. FINDINGS: Age and mean alcohol intake were similar in patients with sASH vs AH. AH showed lower mean arterial pressure than sASH. AH patients had greater aspartate amino transferase/alanine amino transferase ratio and lower gamma- glutamyl transferase levels than AH. Individuals with AH demonstrated profound liver failure, lower blood pressure and increased mortality. Histologically, the grade of steatosis, ballooning and pericellular fibrosis were similar in both groups, while advanced fibrosis, Mallory-Denk bodies, bilirubinostasis, severe neutrophil infiltration and progenitor cell expansion were more frequent among AH patients. One-year mortality was 10% in sASH and 50% in AH. Transcriptome analysis revealed a profound gene dysregulation within both phenotypes when compare to controls. Globally, AH patients exhibited changes in 4,921 genes, while the number of dysregulated genes in sASH patients was less pronounced -1,327-. While sASH was characterized by deregulated expression of genes involved in matrisome and immune response, the development of AH resulted in a marked deregulation of genes involved in hepatocyte reprogramming and bile acid metabolism. INTERPRETATION: Despite comparable daily alcohol intake, AH patients presented with worse liver function and hemodynamic status compared to sASH. Bilirubinostasis, severe fibrosis and progenitor cell expansion were prominent features of AH. AH patients exhibited a more profound deregulation of gene expression compared to sASH.

overall_design: Hepatic gene expression profiling was assessed by DNA microarray in patients with sASH (n=8).

first: M

last: Ventura

first: J

middle: M

last: Argemi

middle: J

first: R

last: Bataller


title: Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy (ChIP-Seq 1)

overall_design: Two replicates of CD36 synchronization cultures at Day 7 and Day 10 are compared following ChIP-seq for RNA Pol II, or two replicates of early or late erythroblasts with appropriate controls


title: Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy

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

overall_design: Refer to individual Series


title: Skin expression data from psoriasis patients treated with the HSP90 inhibitor RGRN-305

status: Public on Jan 10 2022

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
HSP90 is a downstream regulator of TNFα and IL-17A signaling and may therefore serve as a novel target in the treatment of psoriasis.
We assessed global gene expression by microarray analysis to explore the molecular transformation in skin samples from psoriatic patients during treatment with the HSP90 inhibitor RGRN-305.

overall_design: Skin punch biopsies were taken from nonlesional (NL) and lesional (LS) psoriatic skin of 13 psoriatic patients before treatment and from lesional psoriatic skin at 4, 8, and 12 weeks during HSP90 inhibitor treatment. RNA was extracted from the skin biopsies and used for microarray analysis.

first: Claus

last: Johansen

first: Anne

last: Bregnehøj

last: Emmanuel

first: Lars

last: Iversen


title: SIRT5 loss promotes hepatocarcinogenesis via bile acid-induced immunosuppressive microenvironment

city: Shanghai

first: Renqiang

last: Sun

address: 131,Dong'an Road

institute: Fudan university

summary: Hepatocellular carcinoma (HCC) is a prototypical inflammation-associated cancer and the tumor microenvironment (TME) plays a pivotal role in HCC pathogenesis and response to therapy. The liver is a metabolically active organ, but how liver metabolism impacts TME during HCC development and response to immunotherapy are poorly understood. Here, we show that the metabolic regulator SIRT5 is downregulated in human primary HCC samples, and that Sirt5 deficiency in mice synergizes with oncogenes to increase bile acid (BA) production, which is due to hypersuccinylation and increased BA biosynthesis in the peroxisome. BA acts as a cell-signaling mediator to stimulate its nuclear receptor and promotes M2-like macrophage polarization, thereby creating an immunosuppressive microenvironment favorable for HCC initiating cells. Furthermore, high serum taurocholic acid, a major primary BA, correlates with low SIRT5 expression and increased M2-like tumor-associated macrophages (TAMs) in liver tissue samples from HCC patients. Importantly, administration of cholestyramine, a BA sequestrant and FDA-approved medication for hyperlipemia, reverses the effect of Sirt5 deficiency on promoting M2-like polarized TAMs and liver tumor growth. Our study thus uncovers a novel function of SIRT5 in orchestrating BA metabolism to prevent tumor immune evasion and suppress HCC. These results also suggest a potential strategy using clinically proven bile acid sequestrants for the treatment of HCC patients, especially those with decreased SIRT5 and abnormally high BAs.

overall_design: RNA-seq of 3 Sirt5+/+ and 3 Sirt5-/- livers at 20 days after YAP5SA hydrodynamic injection.

first: Ruoxuan

last: Bao


title: Increased expression of FOXM1 delays natural and progeroid aging phenotypes

city: Porto

first: Elsa

last: Logarinho

state: Porto

address: Rua Alfredo Allen, 208

country: Portugal

summary: The FOXM1 member of the forkhead family of transcription factors is known for its pleiotropic C-terminus transcriptional and N-terminus non-transcriptional functions in a wide set of biological processes critical for cellular homeostasis. We previously found that FOXM1 repression during cellular aging accounts for the accrual of senescence phenotypes, which were vastly restored by overexpressing transcriptionally active FOXM1. Here, we found cyclic induction of a N-terminus truncated FOXM1 transgene on progeroid and naturally aged mice, to offset an aging-associated repression of full-length endogenous FoxM1, thereby allowing reinstatement of both transcriptional and non-transcriptional functions. This translated into mitigation of molecular and histopathological progeroid features of progeroid mice, significantly extending its lifespan. Notably, FOXM1 transgene induction also delayed the progressive accumulation of aging phenotypes, while extending the lifespan of naturally aged mice.

overall_design: Targeted transcriptome sequencing of aorta and skeletal muscle of 1.7y-old Rosa26 and FoxM1-dNdK mice

first: Rui

last: Ribeiro

first: Anastasia

middle: V

last: Shindyapina


title: Developmental toxicity of Nafion byproduct 2 (NBP2) in the Sprague-Dawley rat

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: Nafion byproduct 2 (NBP2; CAS: 749836-20-2; Product #: 6164-3-3J; Lot: 512400; SynQuest Laboratories Alachua, FL, USA) is a polyfluoroalkyl ether sulfonic acid that was recently detected in surface water, drinking water, and human serum samples from monitoring studies in North Carolina, USA. We orally exposed pregnant Sprague-Dawley rats to NBP2 from gestation day (GD) 14–18 (0.1–30 mg/kg/d), GD17-21, and GD8 to postnatal day (PND) 2 (0.3–30 mg/kg/d) to characterize maternal, fetal, and postnatal effects. GD14-18 exposures were also conducted with perfluorooctane sulfonate (PFOS) for comparison to NBP2, as well as data previously published for hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX). NBP2 produced stillbirth (30 mg/kg), reduced pup survival shortly after birth (10 mg/kg), and reduced pup body weight (10 mg/kg). Histopathological evaluation identified reduced glycogen stores in newborn pup livers and hepatocyte hypertrophy in maternal livers at ≥ 10 mg/kg. Exposure to NBP2 from GD14-18 reduced maternal serum total T3 and cholesterol concentrations (30 mg/kg). Maternal, fetal, and neonatal liver gene expression was investigated using RT-qPCR pathway arrays, while maternal and fetal livers were also analyzed using TempO-Seq transcriptomic profiling. Overall, there was limited alteration of genes in maternal or F1 livers from NBP2 exposure with significant changes mostly occurring in the top dose group (30 mg/kg) associated with lipid and carbohydrate metabolism. Metabolomic profiling indicated elevated maternal bile acids for NBP2, but not HFPO-DA or PFOS, while all three reduced 3-indolepropionic acid. Maternal and fetal serum and liver NBP2 concentrations were similar to PFOS, but ∼10–30-fold greater than HFPO-DA concentrations at a given maternal oral dose. NBP2 is a developmental toxicant in the rat, producing neonatal mortality, reduced pup body weight, reduced pup liver glycogen, reduced maternal thyroid hormones, and altered maternal and offspring lipid and carbohydrate metabolism similar to other studied PFAS, with oral toxicity for pup loss that is slightly less potent than PFOS but more potent than HFPO-DA.

overall_design: Sprague-Dawley rats were exposed to NBP2 from gestation day (GD) 14–18 (0.1–30 mg/kg/d) and GD17-21. Maternal and fetal rat liver from 0, 0.1, 0.3, 1, 3, 10, and 30 mg/kg/d (n=4-6) exposure groups were harvested at GD 18. Maternal and fetal rat liver from 0, 1, 3, 10, and 30 mg/kg/d (n=3) expsoure groups were also harvested at GD 20. All tissues underwent targeted RNA-sequencing to characterize maternal and fetal transcriptional effects of NBP2.

first: Justin

last: Conley

first: Susan

last: Hester

first: Christy

last: Lambright

first: Nicola

last: Evans

first: Elizabeth

last: Medlock-Kakaley

first: Donna

last: Hill

first: L

middle: E

last: Gray Jr


title: Loss of Acta2 in cardiac fibroblasts does not prevent the myofibroblast differentiation or affect the cardiac repair after myocardial infarction

city: Norfolk

first: Sanjeeva

middle: Reddy

last: Dodlapati

state: VA

address: E&CS, odu

department: Computer Science

institute: old dominion university

summary: In response to myocardial infarction (MI), quiescent cardiac fibroblasts differentiate into myofibroblasts mediating tissue repair in the infarcted area. One of the most widely accepted markers of myofibroblast differentiation is the expression of Acta2 which encodes smooth muscle alpha-actin (SMαA) that is assembled into stress fibers. However, the requirement of Acta2/ SMαA in the myofibroblast differentiation of cardiac fibroblasts and its role in post-MI cardiac repair remained largely unknown. To answer these questions, we generated a tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line. Surprisingly, mice that lacked Acta2 in cardiac fibroblasts had a normal survival rate after MI. Moreover, Acta2 deletion did not affect the function or overall histology of infarcted hearts. No difference was detected in the proliferation, migration, or contractility between WT and Acta2-null cardiac myofibroblasts. It was identified that Acta2-null cardiac myofibroblasts had a normal total filamentous actin level and total actin level. Acta2 deletion caused a significant compensatory increase in the transcription level of non- Acta2 actin isoforms, especially Actg2 and Acta1, 2 other muscle actin isoforms. Moreover, in myofibroblasts the transcription levels of cytoplasmic actin isoforms were significantly higher than those of muscle actin isoforms. In addition, we found that myocardin-related transcription factor-A is critical for myofibroblast differentiation but is not required for the compensatory effects of non-Acta2 isoforms. In conclusion, the deletion of Acta2 does not prevent the myofibroblast differentiation of cardiac fibroblasts or affect the post-MI cardiac repair, and the increased expression and stress fiber formation of non-SMαA actin isoforms and the functional redundancy between actin isoforms are able to compensate for the loss of Acta2 in cardiac myofibroblasts.

overall_design: A tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line was generated. Data of varying modalities,including gene expression and chromatin accessibility profilig, for cardiac fibroblasts in both wild-type and knowout mice were collected and analyzed comparatively.

first: Xing

last: Fu

first: Jiangwen


title: Generation of tendon like tissues from human iPSC

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

country: Japan

institute: Tokyo Medical and Dental University

summary: We report the newly derived tendon like tissues from human iPSC. We depositted RNA sequencing data of human iPSC and derived MSC from human iPSC. We use these cells as materials to generae tenon-like tissues.

overall_design: Examination of transcriptome (RNA sequencing) of human iPSC and derived MSC.

first: Tsutsumi

last: Hiroki

first: Hiroshi

last: Asahara


title: Smilax glabra flavonoids treatment of 3T3-L1 adipocytes

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

summary: Smilax glabra Roxb, a traditional Chinese herb, has been widely used for folk medicine. Previous studies have found that it has various pharmacological activities, such as cytotoxic, anti-inflammation, anti-oxidant, hepatoprotective, and cardiovascular system protective activities. However, its roles in adipogenesis are poorly understood. We hypothesized that Smilax glabra Roxb and its main component may play important roles in regulating adipocyte diffrentiation and function. To test this hypothesis, we performed RNA-Seq on 3T3-L1 adipocytes treated with and without pure total flavonoids from Smilax glabra Roxb.

overall_design: mRNA profiles of 3T3-L1 adipocytes (8 days after differentiation) treated with and without Smilax glabra flavonoids were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Zhaowei

last: Cai


title: Non-cell Autonomous Mechanisms Control Mitochondrial Gene Dysregulation in Polycystic Ovary Syndrome

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

summary: The aim of this study was to gain further insight into the mechanisms leading to metabolic dysfunction in skeletal muscle in PCOS, and to determine whether primary myotubes retain the gene expression signature of PCOS in vivo. We investigated the transcriptomic profile of skeletal muscle tissue and primary myotube cultures from insulin resistant women with PCOS compared to healthy controls.

overall_design: We collected skeletal muscle biopsies (vastus lateralis) from 8 overweight insulin resistant PCOS women (PCOS) and 7 healthy lean control women (CTRL), all aged between 18-40 years old. Primary myotube cultures were established from skeletal muscle biopsies obtained from five of these women with PCOS and six control women. RNA-seq analysis was performed with both skeletal muscle and primary myotubes from both groups.

first: Alba

last: Moreno-Asso

last: Altıntaş

first: Luke

last: McIlvenna

first: Rhiannon

middle: K

last: Patten

first: Javier

last: Botella

first: Andrew

last: McAinch

first: Raymond

last: Rodgers

first: Romain

last: Barrès

first: Nigel

last: Stepto


title: Assessment of DNA methylation patterns related to ankylosing spondylitis

city: Guangzhou

first: Min

last: Xiao

state: Guangdong

address: 600 Tianhe Road

institute: Third Affiliated Hospital of Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary: The aim of this study was to seek more novel ankylosing spondylitis (AS)-associated DNA methylation. Genome wide DNA methylation profiling  was profiled in peripheral blood mononuclear cells (PBMCs) from 24 individuals (AS: health controls (HCs) = 12:12) with high-throughput array. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: DNA methylation was assessed in PBMCs from 12 health controls and 12 patients with AS. PBMC DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).

first: M

first: J

last: Gu


title: BET proteins regulate gene expression in early kidney development

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

country: Germany

institute: UKE Hamburg-Eppendorf

summary: In utero renal development is subject to maternal metabolic and environmental influences af-fecting long-term renal function and the risk to develop chronic kidney failure and cardiovascular disease. Epigenetic processes have been implicated in the orchestration of renal development and prenatal programming of nephron number. Bromodomain and extraterminal domain proteins act as histone acetylation reader molecules and promote gene transcription. BET family members Brd2, Brd3 and Brd4 are expressed in the nephrogenic zone during kidney development. Here, the effect of FDA-approved BET inhibitor JQ1 on renal development is evaluated. Inhibition of BET proteins via JQ1 leads to reduced growth of metanephric cultures, loss of the progenitor cell population, and premature and disturbed nephron differentiation.

overall_design: Bulk RNA sequencing of kidney cultures after 24 h treatment of DMSO or JQ1

first: Janina

last: Schreiber

first: Nastassia

last: Liaukouskaya

first: Tobias

middle: B

last: Huber


title: IL-27 production by splenic immune cells throughout persistent LCMV infection

city: San Diego

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

summary: The pleiotropic cytokine IL-27 is essential for the clearance of the persistent LCMV strain Clone 13, however the cellular sources of IL-27 during viral infection are incompletely mapped and their relative importance unknown. Here we utilised single-cell RNA-sequencing of splenocytes from IL27-p28-GFP mice infected with Clone 13 to quantify the temporal patterns of IL-27 p28 production. IL-27-p28-GFP+ and IL-27-p28-GFP- splenocytes were sorted at 4 timepoints during Clone 13 infection and analysed by 3' single-cell transcriptome sequencing. Dendritic cells were major producers of early IL-27 with macrophages and monocytes being the predominant IL-27 producers during acute and persistent phases of infection. Interestingly, we also identified activated B cells and plasma cells as a prominent subset of IL-27-producing splenocytes and through B-cell-specific deletion of IL-27-p28 demonstrated that B-cell derived IL-27 is essential for sustained function of CD4 T cells and eventual clearance of Clone 13.

overall_design: IL-27-p28-GFP+ and IL-27-p28-GFP- splenocytes from Tg(Il27-Gfp) reporter mice infected with LCMV Clone 13 were subjected to 3' single-cell transcriptome sequencing.

first: Jaroslav

last: Zak

first: Isaraphorn

last: Pratumchai


title: Single Cell RNA-Seq of iPSC-derived 3D Cardiac Organoids Reveals Cardiovascular Effects of Immunosuppressive Drugs

city: Pala Alto

first: Karim

last: Sallam

state: California

address: 300 Pasteur Dr, Rm S102C

institute: Stanford University

summary: We used scRNA-Seq to examine effects on Cardiac Organoids due to treatment.

overall_design: Control, Sirolimus and Tacrolimus treated cardiac Organoids were processed for scRNA-seq

first: Sadhana

last: Gaddam


title: iPSC-EC RNA-seq

city: Valencia

first: Imelda

last: Ontoria-Oviedo

address: Avda Fernando Abril Martorell 106

department: Regeneration and Heart transplantation Unit

institute: Instituto de Investigación Sanitaria La Fe

summary: The goal of this project was to analyze the genetic profile of endothelial cells derived from iPSCs of controls and TGA patients. Two control and two TGA iPSCs were analyzed

overall_design: Endothelial cells were differentiated from iPSC folllowing the protocol described by Prasain et al. 2014.

first: Pilar

last: Sepúlveda

first: Gabor

last: Földes

first: Joseph

last: Wu

first: Sian

last: Harding


title: Transcriptome profiling of left ventricles from systemic MIAT knockout mice

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

summary: Genome-wide transcriptomic analyses in left ventricles (LVs) from systemic MIAT knockout (KO) mice were performed to identify novel MIAT targets in the heart.

overall_design: The following 12 independent mouse LVs were used: three biological replicates for 4 groups (sham wild-type [WT], sham MIAT KO, myocardial infarction [MI] WT and MI MIAT KO). LVs were harvested after 4 weeks of sham or MI surgeries.

first: Tatsuya

last: Aonuma


title: Transcriptomic profiles revealed down regulation of low-density lipoprotein particle receptor activity pathway in survived from severe COVID-19-19.

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

summary: This submission contains a result of a study of transcriptiomic profiles of blood of COVID-19 patients.

overall_design: Examination of transcriptiomic profiles of the blood, derived from surviving and deceased COVID-19 patients.

first: Vlasov

last: Ivan

first: Panteleeva

last: Alexandra

first: Usenko

last: Tatiana

first: Nikolaev

last: Mikhael

first: Izumchenko

last: Artem

first: Gavrilova

last: Elena

first: Shlyk

last: Irina

first: Miroshnikova

last: Valentina

first: Shadrina

last: Maria

first: Polushin

last: Yurii

first: Pchelina

last: Sofya

first: Slonimski

last: Petr


title: Gene expression profiles of human mesangial cell line treated with and without ANGPT2

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

summary: Glomerular diseases are the leading cause of chronic kidney diseases with pathomechanisms largely unclear. It is known that ANGPT2 regulates endothelial cell homeostasis and function via TEK/TIE2 and its deregulation causes endothelial damage. We found that ANGPT2 is upregulated in glomerular diseases and wondered whether it has any effect on glomerular podocytes and mesangial cells given that they have no or low TEK expression. We treated podocytes and mesangial cells in culture with ANGPT2 and found no overt cellular changes. RNA-seq analysis showed that gene expression was altered in both podocytes and mesangial cells and that the regulated genes in the two cell types were fundamentally different. GO and KEGG analyses showed that the two groups of regulated genes were enriched in distinct processes and pathways. These results suggest that ANGPT2 exerts effects on both podocytes and mesangial cells and that increased ANGPT2 may be involved in glomerular injury by affecting podocytes and mesangial cells in addition to endothelial cells.

overall_design: Immortalized human mesangial cell line was purchased from the CELL SYSTEMS (WA, USA) were cultured with DMEM medium supplemented with 10% FBS at 37°C in 5% CO2 incubator for growth and then treated with 500 ng/ml recombinant ANGPT2 (MCE, HY-P7510) or left untreated with only vehicle for 24 hours. The cells were homogenized with Trizol (Invitrogen) and the total RNA was extracted following the manual instruction. The RNA was then subject to RNA-seq.

first: Shaolin

first: Lu

last: Ren

first: Jinsong


title: Single-cell RNA-seq data of human Tregs treated with TNFR2 agonist antibody

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

summary: Tumor necrosis factor receptor 2 (TNFR2), a membrane-bound tumor necrosis factor receptor expressed by regulatory T cells (Tregs), participates in Treg proliferation. Although a specific TNFR2 pathway has been reported, the signaling mechanism has not been completely elucidated. This study sought to clarify TNFR2 signaling in human Tregs using amplicon sequencing and single-cell RNA-sequencing to assess Tregs treated with a TNFR2 agonist antibody. Pathway enrichment analysis based on differentially expressed genes highlighted tumor necrosis factor α signaling via nuclear factor-kappa B, interleukin-2 signal transducer and activator of transcription 5 signaling, interferon-γ response, and cell proliferation-related pathways in Tregs after TNFR2 activation. TNFR2-high Treg-focused analysis found that these pathways were fully activated in cancer Tregs, showing high TNFR2 expression. Collectively, these findings suggest that TNFR2 orchestrates multiple pathways in cancer Tregs, which could help cancer cells escape immune surveillance, making TNFR2 signaling a potential anticancer therapy target.

overall_design: Examination of gene expression profile in Treg treated with TNFR2 agonist antibody.

first: Yo

last: Muraki

first: Shuji

last: Sato


title: Effect of ribociclib on breast cancer cells

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

summary: To study mechanisms underlying response to ribociclib.

overall_design: Examination of breast cancer cell transcriptome following treatment with ribociclib (600 nM).

first: Wilbert

last: Zwart


title: Expression data of human Tregs treated with TNFR2 agonist antibody


title: Gene expression profiles of human podocyte cell line treated with and without ANGPT2

overall_design: Immortalized human podocytes from Dr. Saleem M’s laboratory (University of Bristol, Bristol, UK) were cultured with RPMI1640 medium supplemented with 10% FBS, 1% Pen/Strep and 1% ITS at 33°C in 5% CO2 incubator for growth, followed by trypsinization, replating and culture at 37°C for 10 days to obtain differentiated cells. Then the differentiated podocytes were either treated with 500 ng/ml recombinant ANGPT2 (MCE, HY-P7510) or left untreated with only vehicle for 24 hours. The cells were homogenized with Trizol (Invitrogen) and the total RNA was extracted following the manual instruction. The RNA was then subject to RNA-seq.


title: LSD1-directed therapy affects glioblastoma tumorigenicity by deregulating the protective ATF4-dependent integrated stress response

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

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

overall_design: Refer to individual Series


title: LSD1-directed therapy affects glioblastoma tumorigenicity by deregulating the protective ATF4-dependent integrated stress response [RNA-seq]

summary: Tumor-initiating cells (TICs) play a critical role in glioblastoma (GBM) maintenance being responsible for its heterogeneity and resistance to standard therapy. A step toward clinical translation includes GBM TIC targeting. Among the molecules tested for GBM treatment, are those targeting epigenetic modifiers. By using patient-derived TICs and xenograft orthotopic models, we identified Lysine-specific histone demethylase 1A (LSD1) as a potentially druggable target in GBM. LSD1-directed therapy by means of the selective, orally bioavailable and brain penetrant inhibitor DDP_38003 effectively impairs growth, stem-like features and tumorigenic potential of GBM TICs. Our findings point to LSD1 as a positive regulator of Activating Transcription Factor 4 (ATF4)-dependent response in all stress conditions arising during tumor growth and therapy. Thus, through the downregulation of either ATF4 and its adaptive genes, LSD1 targeting is likely a promising strategy to hit GBM TICs by counteracting the ATF4-mediated adaptation to stress.

overall_design: Examination of gene expression profile of 1) LSD1-silenced GBM TICs versus control. 2)GBM TIC treated  with LSD1 inhibitor or DMSO (vehicle).

first: Stefania

last: Faletti

first: Elena

last: Ceccacci

first: Giuliana

last: Pelicci


title: LSD1-directed therapy affects glioblastoma tumorigenicity by deregulating the protective ATF4-dependent integrated stress response [ChIP-seq]

overall_design: Genome binding/occupancy profiling by high throughput sequencing


title: LSD1-directed therapy affects glioblastoma tumorigenicity by deregulating the protective ATF4-dependent integrated stress response [ATAC-seq]

overall_design: Examination of chromatin accessibility of GBM TIC treated  with LSD1 inhibitor or DMSO (vehicle).


title: Expression data for effect of LY294002 on White Matter

city: Padova

first: Andrea

middle: Domenico

last: Rivera

address: Via Gabelli 67

department: Neuroscience

institute: University of Padova

summary:
Characterisation of the effect of the PI3K/AKT modulator LY294002 in the murine optic nerve.
Microarray analysis was performed using the Affymetrix Genechip Mouse 430 2.0 on murine optic nerves to identify bipartite effect of LY294002 on glia

overall_design: P 35-45 C57BL/6 Optic nerves were maintained in organotypic culture for 3 days in vitro (DIV) with 0,5 uM, 50uM LY294002 or control conditions. Total RNA was extracted and processed for analysis

first: Arthur

last: Butt


title: High-fat high-sugar diet-induced changes in the lipid metabolism are associated with mildly increased COVID-19 severity and delayed recovery in the Syrian hamster

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Pre-existing comorbidities such as obesity or metabolic diseases can adversely affect the clinical outcome of COVID-19. Chronic metabolic disorders are globally on the rise and often a consequence of an unhealthy diet, referred to as a Western Diet. For the first time in the Syrian hamster model, we demonstrate the detrimental impact of a continuous high-fat high-sugar diet on COVID-19 outcome. We observed increased weight loss and lung pathology, such as exudate, vasculitis, hemorrhage, fibrin, and edema, delayed viral clearance and functional lung recovery, and prolonged viral shedding. This was accompanied by and increased trend of systemic IL-10 and IL-6, as well as a dysregulated serum lipid response dominated by polyunsaturated fatty acid-containing phosphatidylethanolamine, recapitulating cytokine and lipid responses associated with severe human COVID-19.  Our data support the hamster model for testing restrictive or targeted diets and immunomodulatory therapies to mediate the adverse effects of metabolic disease on COVID-19.

overall_design: High-fat high-sugar diet vs. Regular diet

first: Julia

last: Port

first: Danielle

last: Adney

first: Benjamin

last: Schwarz

first: Jonathan

last: Schulz

first: Daniel

first: Brian

last: Smith

first: Victoria

last: Avanzato

first: Myndi

last: Holbrook

first: Jyothi

middle: N

last: Purushotham

first: Kaitlin

last: Stromberg

first: Ian

last: Leighton

first: Catharine

last: Bosio

first: Carl

last: Shaia

first: Vincent

last: Munster


title: Low dose chronic angiotensin II induces selective senescence of kidney endothelial cells

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

summary: Here we evaluated the contribution of cellular senescence to the effect of chronic exposure to low dose angiotensin II in a mouse model that mimics the initiation of hypertension. We utilized the INK-ATTAC (p16ink4a - Apoptosis Through Targeted Activation of Caspase 8) mouse model that allows for conditional elimination of p16ink4a -dependent senescent cells by administration of AP20187. INK-ATTAC mice received continuous low doses of angiotensin II over 3 weeks and AP20187 vs vehicle. In the kidneys increased expression of ATM, p15 and p21 matched with angiotensin II induction of senescence-associated secretory phenotype genes MMP3, FGF2, IGFBP2, and tPA. AP20187-mediated elimination of p16-dependent senescent cells prevented physiologic, cellular and molecular responses to angiotensin II. We conclude that angiotensin II induces a relatively selective senescence transformation of renal endothelial cells that could provide a novel therapeutic target for senolytic drugs as alternative treatment options for hypertension and resulting tissue damage.

overall_design: Kidney mRNA profiles of ATTAC c57 mice treated with ANGII and/or AP20187

first: Irfan

middle: S

last: Khan

first: Anton

last: Wellstein


title: The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

summary: The epigenetic landscape of a cell frequently changes in response to fluctuations in nutrient levels, but the mechanistic link is not well understood. In fission yeast, the JmjC domain protein Epe1 is critical for maintaining the heterochromatin landscape. Loss of Epe1 results in heterochromatin expansion and overexpression of Epe1 leads to defective heterochromatin. Through a genetic screen, we found that mutations in genes of the cAMP signaling pathway suppress the heterochromatin defects associated with Epe1 overexpression. We further demonstrated that the activation of Pka1, the downstream effector of cAMP signaling, is required for the efficient translation of epe1+ mRNA to maintain Epe1 overexpression. Moreover, inactivating the cAMP-signaling pathway, either through genetic mutations or glucose deprivation, leads to the reduction of endogenous Epe1 and corresponding heterochromatin changes. These results reveal the mechanism by which the cAMP signaling pathway regulates heterochromatin landscape in fission yeast.

overall_design: ChIP-seq of H3K9me2 in WT cell grown in YEA or YEA low glucose media (0.1% glucose, 3% glycerol) for 6 hours.

first: Kehan

last: Bao

first: Chun-Min

last: Shan

first: Xiao

last: Chen

first: Gulzhan

last: Raiymbek

first: Jeremy

last: Munroe

first: Yimeng

last: Fang

first: Takenori

last: Toda

first: Kristin

last: Koutmou

first: Kaushik

last: Ragunathan

first: Chao

last: Lu

first: Luke

last: Berchowitz


title: RNA sequencing of Hoxb8 yolk sac- and bone marrow-derived

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Progenitor cells of yolk sac and bone marrow origin were transduced with an estrogen receptor Hoxb8 fusion protein to generate stable cell lines. Macrophages were differentiated with M-CSF in the absence of estrogen, and then stimulated with IL-4 or LPS. Hoxb8 progenitor cells and differentiated macrophages were analyzed by RNA sequencing.

overall_design: RNA profile of YS vs. BM Hoxb8 cell lines (progenitors and differentiated macrophages - unstimulated/ IL4-/ LPS-treated for 5 hours

first: C

last: Schulz

first: S

last: Elhag

last: Stremmel

first: M

last: Bonin


title: Inhibition of CDK9 activity compromises global splicing in prostate cancer cells

city: Helsinki

first: Harri

last: Itkonen

address: Room B125b / B129b

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki

summary: Cyclin-dependent kinase 9 (CDK9) phosphorylates RNA polymerase II to promote productive transcription elongation and the phosphorylation also regulates recruitment of the splicing machinery. Here we show that acute CDK9 inhibition affects splicing of thousands of mRNAs. CDK9 inhibition impairs global splicing and there is no evidence for a coordinated response between alternative splicing and the overall transcriptome. Alternative splicing is feature of aggressive prostate cancer (CRPC) and enables generation of an anti-androgen resistant version of a ligand-independent androgen receptor, AR-v7. We show that CDK9 inhibition compromises splicing of the androgen receptor (AR) mRNA due to the faulty utilization of alternative 3’splice site and introduction of premature stop codon. Consequently, this defective splicing results in the loss of AR and AR-v7 expression in models of CRPC. We show that CDK9 expression increases as PC cells develop CRPC-phenotype both in vitro and also in patient samples.

overall_design: mRNA profiles of LNCaP cells after knockdown of OGT for 48 hours and treated with either DMSO or CDK inhibitor (0.5μM AT7519) for 4 hours prior to harvesting.

first: Qiang

last: Hu

first: Ninu

last: Poulose

first: R

last: Steele

first: Song

last: Liu

first: Dean

last: Tang

first: Ian

last: Mills


title: Phosphodiesterase 10A (PDE10A) as a novel target to suppress β-catenin and RAS signaling in ovarian cancer

city: Mobile

first: Lucian

last: Madeira da Silva

state: AL

address: 1660 Springhill Ave

department: Mitchell Cancer Institute

institute: University of South Alabama

summary: The goal of this study was to investigate molecular pathways associated with PDE10A in ovarian cancer. We used CRISPR/Cas9 to knockout PDE10A in SKOV3 cells. We used the Illumina NextSeq500  to generate between 30-35 million paired end 75bp sequencing reads per sample for transcript level abundance.

overall_design: Comparison of SKOV3 parental and Empty Vector clone 1B9 (EV 1B9) vs. SKOV3 PDE10A KO clones 5H5 and 2F4 (two biological replicates per cell line)

first: Luciana

last: da Silva

first: Rebecca

last: Borneman


title: TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

summary: Our aim was to investigate the contribution of TWIST1 on Neuroblastoma (NB) tumor formation and dissemination using TWIST1 knock-out (KO) in the SK-N-Be2C cell line.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: TWIST1 knock-out (KO) was performed in the SK-N-Be2C cell line by CRISPR/Cas9 technology. SK-N-Be2c-TWIST1-Control and -TWIST1-KO cells (50'000) were injected orthotopically in the adrenal glands of athymic Swiss nude mice. Transcriptomic analyses of the cells in vitro and their derived tumors   were carried out by RNA-seq (Illumina Hiseq4000).

first: Maria Vittoria

last: Sepporta

first: Viviane

last: Praz

first: Katia

last: Balmas Bourloud

first: Hervé

last: Sartelet

first: Audrey

last: Petit

first: Jean Yves

last: Scoazec

first: Jean Marc

last: Joseph

first: Nicolas

last: Jauquier

first: Raffaele

last: Renella

first: Annick

last: Mühlethaler-Mottet


title: RNA sequencing analysis for mouse ovarian cancer cells and tumors response to B7-H3 (Cd276) depletion

city: Kyoto

first: Taito

last: Miyamoto

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University

summary: Analysis of mouse ovarian cancer cell lines HM-1 and ID8, and HM-1 tumors inoculated to B6C3F1 mice with B7-H3 (Cd276) knockout (KO) by CRISPR-Cas9. We identified B7-H3 expression is upregulated in IFN-γ–low, PD-L1–low non-immunoreactive tumors of high grade serous ovarian cancer. We explored the influence of B7-H3 on immune evasion outside of its direct regulatory function on target cells by generating B7-H3 knockout cell lines and tumors in syngeneic mouse models.

overall_design: Total RNA from HM-1-B7-H3 KO cells, ID8-B7-H3 KO cells or their control cells, or intradermal tumors of HM-1-B7-H3 KO cells or their control cells at day 10 of tumor growth were extracted and used for RNA sequencing. Differential expression analysis was performed using DESeq2 (RRID: SCR_015687) between control (n = 3) and B7-H3 KO (n = 3) groups of the ID8 and HM-1 cell lines, and HM-1 intradermal tumors.

first: Ryusuke

last: Murakami

first: Shiro

last: Takamatsu


title: Licochalcone A activate glycolysis by via PI3K / AKT pathway to play an anti-aging effect on adipose stem cells and aging mice [hippocampus]

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hippocampus of 12M mice; These mice with the treatment of Licochalcone A for 30 days.


title: Licochalcone A activate glycolysis by via PI3K / AKT pathway to play an anti-aging effect on adipose stem cells and aging mice


title: Bulk segregant RNA seq samples from young leaf tissue of sesame seedlings with either SiCD-A or SiCD-B allele

city: Rehovot

first: Naama

last: Teboul

address: Hankin 18

department: Plant sciences and genetics

country: Israel

institute: Hebrew University

summary: Transcriptome analysis was performed on young leaves from 17-day old sesame seedling. The experiment aimed to shed light on the polar regulatory gene network in sesame under KANADI1 loss of function and identify candidate genes underlie the hyponastic leaf phenotype. We compaired between homozygous lines for either SiCD-A allele contains KAN1 (WT) or SiCD-B allele contains kan1 (mutant) on S.indicum LG8.

overall_design: Bulk segregant RNA sequencing (BSR-seq) experimental approach. We used two groups of Recombinant Inbred Lines each consisted of 19 plants, homozygous for either SiCD-A allele (consists KAN1 (WT)) or SiCD-B allele (consists kan1 (mutant)) on S.indicum LG8.Three bulked equimolar pools consisted RNA from nine randomly selected plants were assembled from each of the two allelic groups, each represented a biological replicate.

first: Zvi

last: Peleg


title: Time course transcriptome capturing a directed extraembryonic endoderm (XEN) differentiation protocol of wild type and Ago2_KO mESCs

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

summary: Purpose:  The goals of this study was to identify novel regulators of XEN differentiation and the role of AGO2 and miRNAs therein

overall_design:
mRNA profiles of E14 mESCs were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.

Please note that some of the previous samples in GSE78971, GSE80210 studies are included in the current study. The sample records are duplicated for the convenient retrieval of the complete raw data from SRA (i.e. [re-used] samples) as indicated in the corresponding sample description field.


title: Differential gene expression during encystation in Giardia intestinalis

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: In this study we analyzed how gene expression is regulated through the process of encystation in Giardia

overall_design: Examination of differential gene expression during the encystation process of Giardia intestinalis

first: Laura

last: Rojas

first: Elin

last: Einarsson

first: Ulf

last: Ribacke

first: Sascha

last: Krakovka

first: Staffan

last: Svard


title: Transcriptomic profile of MYC wild type and knockdown NUGC3 cells

first: Yumin

last: Han

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: The goal of this study is to profile the transcriptomic profile of MYC deficient cells.

overall_design: mRNA profiles of WT, MYC knockdown NUGC3 cells. Duplicate for each WT or knockdown group.

first: Jingyu

last: Lang


title: Expression data from Saccharomyces cerevisiae

status: Public on Jan 09 2022

city: Chengdu

first: Ranran

last: Su

address: Chuanda Road

institute: SiChuan University

summary:
Saccharomyces cerevisiae is an excellent microorganism for industrial succinic acid production, but high succinic acid concentration will inhibit the growth of Saccharomyces cerevisiae then reduce the production of succinic acid.
Through analysis the transcriptomic data of Saccharomyces cerevisiae with different genetic backgrounds under different succinic acid stress, we hope to find the response mechanism of Saccharomyces cerevisiae to succinic acid.

overall_design: In order to comprehensively analyze the response mechanism of Saccharomyces cerevisiae to succinic acid stress, we selected three yeast strains (KF7, NBRC1958, NBRC2018), each of them was exprement with three different concentrations of succinic acid (0 g/L, 20 g/L, 60 g/L)


title: Single-cell RNA sequencing of tobacco Bright Yellow-2 cell line reveals heterogeneity in cell cycle phase

city: 杭州市

first: Yao

last: Jie

state: 浙江

address: 浙江大学紫金港校区农学院A

institute: ZheJiang University

summary: Cell proliferation and division are fundamental processes of plant development and homeostasis. With the feature of high homogeneity, tobacco Bright Yellow-2 (BY-2) cells, a so-called “HeLa” cell line in plants, provide a useful system for study the cell cycle of plants, particularly when in combination with the latest high-throughput single-cell RNA sequencing (scRNA-seq) technology. Here, we generated both scRNA-seq and bulk RNA-seq data from the BY-2 cells and found that the enzymatic hydrolysis during protoplasting was the major factor contributing to cell clustering noise. We introduced the ppScoring concept to filter out confounding cells due to protoplasting and clustered the remaining cells into clusters corresponding to G0-G1, S, and G2-M phases as well as clusters with phase transition arrested or cell cycle exit cells. The clustering results were supported by cell cycle phase specific marker genes and reconstruction of the continuous full cell cycle phases, i.e., from G0-G1 to S to G2-M, based on pseudotime trajectory analysis. The clustering results also identified a set of 896 cell cycle marker genes. This work demonstrated cell cycle-dependent transcriptional heterogeneity of the BY-2 cell population,  provided marker genes for study of the cell cycle of plants and new insights into the progression of cell division.

overall_design: Single cell RNA sequencing for more than 12000 cells (total) from tobacco BY-2 cell line with two replicates. Bulk RNA sequencing for pre- or post-protoplasted BY-2 cells with three replicates in each treatment.

first: Jie

last: Yao

first: Hongyu

last: Chen

first: Qian-Hao

last: Zhu

first: Longjiang

last: Fan

first: Qinjie

last: Chu


title: RNA sequencing of splenic reticular cells in healthy and LCMV-infected mice

city: Melbourne

first: Luke

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

country: Australia

institute: WEHI

summary: We report the transcriptome of subsets of mouse splenic mesenchymal reticular cells and lymph node reticular cells obtained from healthy Ccl19-cre x R26R-EYFP mice on a C57BL/6 background. We also examine splenic reticular cells from these mice infected with lymphocytic choriomeningitis virus (LCMV) strain Armstrong (acute infection) or strain Clone 13 (chronic infection). Subsets of CD45- CD31- Ter119- reticular cells were analyzed including PDPN+ T zone reticular cells (TRC) and MAdCAM-1+ marginal reticular cells (MRC) from spleen and lymph nodes. Additionally from the spleen we analyzed PDPN+ CD140a- cells, PDPN+ EYFP- cells, and EYFP+ red pulp reticular cells (RPRC) in healthy mice. We analyzed TRC, MRC, PDPN+ EYFP- cells, and EYFP+ RPRC  from mice infected with LCMV Armstrong or LCMV Clone-13 on day 8 or on day 30 after infection. Our study represents the first detailed analysis of splenic reticular cell transcriptomes in healthy and LCMV-infected mice, with biologic replicates, generated by RNA-sequencing. We find substantial differential gene expression across subsets of splenic and lymph node reticular cells. We reveal significant changes in gene expression induced after virus infection that differ markedly with disease.

overall_design: mRNA profiles of 5 splenic and 2 lymph node reticular cell subsets in healthy mice and mice with acute or chronic virus infection

first: Scott

last: Mueller


title: Transcripts associated with chronic lung allograft dysfunction in transbronchial biopsies of lung transplants

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: Transplanted lungs suffer worse outcomes than other organ transplants with many developing chronic lung allograft dysfunction (CLAD), diagnosed by physiologic changes. Histology of transbronchial biopsies (TBB) yields little insight, and the molecular basis of CLAD is not defined. We hypothesized that gene expression in TBBs would reveal the nature of CLAD and distinguish CLAD from changes due simply to time posttransplant. Time was associated with increased expression of inflammation genes e.g. CD1E and immunoglobulins. After correcting for time, CLAD manifested not as inflammation but as parenchymal response-to-wounding, with increased expression of genes such as HIF1A, SERPINE2, and IGF1 that are increased in many injury and disease states and cancers, associated with development, angiogenesis, and epithelial response-to-wounding in pathway analysis. Fibrillar collagen genes were increased in CLAD, indicating matrix changes, and normal transcripts were decreased – dedifferentiation. Gene-based classifiers predicted CLAD with AUC 0.70 (no time-correction) and 0.87 (time-corrected). CLAD-related gene sets and classifiers were strongly prognostic for graft failure and correlated with CLAD stage. Thus, in TBBs molecular changes indicate that CLAD primarily reflects severe parenchymal injury-induced changes and dedifferentiation.

overall_design: Whole-genome mRNA profiling was performed with microarrays in 949 prospectively collected TBBs from the INTERLUNG study, 90 diagnosed as CLAD.


title: Histone arginine demethylation by RDMe1

first: Charilie

middle: Degui

address: No. 320 YueYang Road

country: China

institute: SIBCB

summary: Histone methylation mainly occurs on lysine and arginine residues. While lysine methylation can be removed by LSD1 and JmjC domain-containing demethylases, the existence of histone arginine demethylases is highly controversial. Here, we performed a high-content cell-based screening of a cDNA library containing 2,500 nuclear proteins and identified RDMe1 as a histone arginine demethylase. Overexpression of RDMe1 in HEK293T cells reduces H3R2me1/2a and H4R3me1/2a levels. In vitro, RDMe1 specifically demethylates H3R2me1/2a and H4R3me1/2a, and generates formaldehyde and succinate. The enzymatic activity requires Fe(II) and α-ketoglutarate as cofactors. RDMe1 is mainly located in the nucleolar and regulates rRNA transcription by demethylating H3R2me2a. ChIP-seq reveals that RDMe1 demethylates H4R3me2a in the promoter in a genome-wide scale. NMR reveals that RDMe1 binds iron and substrate peptides with N and C termini, respectively. Mutation of the iron binding residues abolished the binding and the demethylase activity. Thus, we identify a histone arginine demethylase and reveal the reversibility of arginine methylation.

overall_design: Examination of RDMe1 binding and histone H4R3me2a modification in control and RDMe1 knockdown cells.

first: Charli

middle: D

first: Xiongwen

last: Cao


title: The Replication Kinase Cdc7 Marks Histones to Regulate Biosynthesis Genes

city: Charlottesville

first: Stephen

middle: Aurelien

last: Hoang

state: Virginia

address: 501 Locust Ave, Suite 301

institute: HemoShear Therapeutics

summary: We demonstrate that the Cdc7/Dbf4-dependent histone modification, H3 threonine 45 phosphorylation (H3T45p), is specifically enriched at origins of replication, and highly transcribed genes involved in protein synthesis and glycolysis. Furthermore, we show that H3T45p also mediates polymerase recruitment and expression of these genes.

overall_design: Histone H3 threonine 45 phosphorylation mapped in S. cerevisiae using ChIP-seq

first: Erdem

last: Sendinc

first: Xiaojiang

last: Xu

first: Musinu

last: Zakari

first: Jennifer

middle: L

last: Gerton

first: Stefan

last: Bekiranov

first: Patrick

last: Grant


title: Identification of new microRNA-22-5p and -199a-5p/MMP1 functional interactions in stress-induced senescent human dermal fibroblasts

city: Saint-Viance

first: Pauline

last: Rouaud-Tinguely

address: ZI de la Nau

department: R&D

country: France

institute: SILAB

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: Identification of new microRNA-22-5p and -199a-5p/MMP1 functional interactions in stress-induced senescent human dermal fibroblasts [miRNA]

summary: To study and correlate modulations of miRNome with modifications of transcriptome in human stress-induced senescent fibroblasts, Agilent microarrays data were compared by bioinformatics analysis with a focus on ECM components. We identified two unreported direct interactions since we highlighted a reduction in the expression of both miR-22-5p and -199a-5p in senescent fibroblasts, correlated to an increase of MMP1 expression.

overall_design:
MicroRNAs expression in stress-induced senescent (SIS) fibroblasts was measured after 4 days of irradiation.  Four independent experiments were performed for each condition (normal human fibroblasts [NHF] and SIS-fibroblasts) using different donors for each experiment.
Contributor: R&D department, SILAB, France


title: Transcriptional analysis of transposon mutants disrupted in glutathione biosynthesis in Acinetobacter baumannii

status: Public on Jan 08 2022

city: Fresno

first: Mamta

last: Rawat

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

summary: In this study we compare logrithmically grown Acinetobacter baumannii wildtype to a transposon mutant that is disrupted in gshA, the first step in glutathione biosynthesis using RNASeq to identify novel pathways where glutathione may be involved.

overall_design: RNASeq analysis of wildtype cells and gshA:Tn grown logarithmically at 37C while shaken.

first: Rawat

last: Mamta

first: Thomas

last: Jason


title: CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice

city: beijing

first: pengyu

last: li

address: beijing

institute: Beijing Union Medical College


title: CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice [RNA-Seq]

summary: Male spermatogenesis is sustained by homeostatic balance between the self-renewal and differentiation of spermatogonial stem cells (SSCs), which is dependent on the strict regulation of transcriptional factor and chromatin modulator gene expression. Chromodomain helicase DNA-binding protein 4 (CHD4) is highly expressed in SSCs but roles in mouse spermatogenesis are unexplored. Here, we report that the germ-cell-specific deletion of Chd4 resulted in complete infertility in male mice, with rapid loss of SSCs and excessive germ cell apoptosis. Chd4-knockdown in cultured SSCs also promoted the expression of apoptosis-related genes and thereby activated the tumor necrosis factor signaling pathway. Mechanistically, CHD4 occupies the genomic regulatory region of key apoptosis-related genes including Jun and Nfkb1. Together, our findings reveal the determinant role of CHD4 in SSCs survival in vivo, which will offer insight into the pathogenesis of male sterility and potential novel therapeutic targets.

overall_design: We sequenced the SSCs mRNA from both control  and Chd4-KD  and three biological replicates were generated per condition.

first: Pengyu

last: Li

first: Wei

last: Song


title: CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice [CUT&TAG]

overall_design: We sequenced the binding sites of CHD4  in WT mouse and Two biological replicates were generated per condition.


title: Quantitative Assessment of transcriptomic changes induced by aberrant BCL10/MALT1 signaling in primary keratinocytes [CDL]

city: Munich

first: Zsuzsanna

last: Kurgyis

address: Ismaningerstr. 22

institute: Technical University of Munich

summary:
Purpose: The goal of this study is to assess the transcriptomic changes induced by aberrant BCL10/MALT1 signaling downstream of a constitutively active Card11 construct (Rosa26Card11dLinker-lox-STOP-lox x K14Cre) in keratinocytes.
Methods: Keratinocytes were isolated from newborn mice, cultured for 5 days and harvested for RNA isolation. mRNA profiles were generated by RNA sequencing using Illumina NextSeq 550.
Results: Differential expression analysis identified 293 genes (plus the transgene Card11) to be significantly upregulated (log2 fold change > 1.5, FDR < 0.05) in Card11dLinker expressing keratinocytes compared to those isolated from only KRT14Cre-expressing littermate controls.

overall_design: mRNA profiles of in vitro cultured keratinocytes from Card11ΔLinker-K14Cre mice and K14Cre littermate controls

first: Jürgen

last: Ruland


title: Identification of new microRNA-22-5p and -199a-5p/MMP1 functional interactions in stress-induced senescent human dermal fibroblasts [mRNA]

overall_design:
Gene expression in stress-induced senescent (SIS) fibroblasts was measured after 4 days of irradiation.  Four independent experiments were performed for each condition (normal human fibroblasts [NHF] and SIS-fibroblasts) using different donors for each experiment.
Contributor:  R&D department, SILAB, France


title: Quantitative Assessment of transcriptomic changes induced by the loss of BCL10/MALT1 signaling in primary keratinocytes and its effects on IL-17A stimulation [Bcl10ko]

summary:
Purpose: The goal of this study is to assess the transcriptomic changes induced by the loss BCL10/MALT1 signaling in keratinocytes and ist effect on IL-17A stimulation
Methods: Keratinocytes were isolated from newborn Bcl10+/− and Bcl10−/− mice, cultured for 5 days, stimulated with IL-17A for 5 hours and harvested for RNA isolation. mRNA profiles were generated by deep sequencing, using Illumina NextSeq 550.
Results: as shown by Gene Set Enrichment Analysis, IL-17A stimulation induced significant enrichment of an IL17 signature defined by Chiricozzi et al (JID 2011) in both Bcl10+/− and Bcl10−/− murine keratinocytes. However, direct comparison of Bcl10+/− and Bcl10−/− keratinocytes demonstrated a stronger enrichment of this signature in Bcl10 competent keratinocytes than in Bcl10 deficient cells.

overall_design: mRNA profiles of in vitro cultured keratinocytes from Bcl10−/− mice and Bcl10+/− littermate controls


title: RNA-seq of Paneth cells

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

summary: The impact of removal of Mll1 in intestinal Paneth cells expressing an constitutively active form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted Paneth cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) mice at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (52-93%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- Paneth cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 in Paneth cells shifted their identity towards a mixed Paneth-goblet cell fate.

overall_design: mRNA profiles of beta-cateninGOF; Mll1+/- (control) and beta-cateninGOF; Mll1-/- (knockout) Paneth cells were generated by deep sequencing in quadruplicates.

first: Johanna

last: Grinat

first: Frauke

last: Kosel

first: Neha

last: Goveas

first: Andrea

last: Kranz

first: Michael

last: Sigal

first: Klaus

last: Rajewsky

first: Walter

last: Birchmeier

first: Julian

last: Heuberger

first: Dimitra

last: Alexopoulou


title: DNA methylation features of LUSC in promoter and enhancer region [methylation]

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: The purpose of this study is to compare methylation profiles of LUSC between tumor tissue and normal tissue

overall_design: (1) Genomic DNA quantitation: DNA samples were checked for their quality using NanoDrop® ND-2000 UV-Vis Spectrophotometer. The samples were electrophoresed on agarose gels and those with intact genomic DNA, showing no smear upon agarose gel electrophoresis, were selected for subsequent experiment. Intact genomic DNA was diluted to 50 ng/㎕ based on Quant-iT PicoGreen (Invitrogen) quantitation. Concentrations were adjusted according to these results. All prepared samples were bisulfite-converted according to the EZ DNA methylation kit (Zymo Research) protocols. (2) Bisulfite conversion (Zymo EZ DNA methylation kit): For the bisulfite conversion, 600 ng of input gDNA was required. Conversion reagent was added, followed by subsequent incubation in a thermocycler to denature. CT-converted DNA was washed and de-sulfonated with de-sulfonation buffer, after which, the DNA was washed again and eluted with 12-ml elution buffer. (3) Sample amplification and hybridization for BeadChips: The whole-genome amplification process required 250 ng of input bisulfite-converted DNA, MA1, and created a sufficient quantity of DNA (1000× amplification) to be used on a single BeadChip in the Infinium methylation assay (Illumina RPM and MSM). After amplification, the product was fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and re-suspended in formamide-containing hybridization buffer (RA1). The DNA samples were denatured at 95 °C for 20 min, and placed in a humidified container for a minimum of 16 h at 48 °C, allowing CpG loci to hybridize with the 50-mer capture probes. (4) Allele-specific single-base extension and staining on BeadChips: Following hybridization, the BeadChip/Te-Flow chamber assembly was placed on a temperature-controlled Tecan flow-through chamber rack, and subsequent washing, extension, and staining were performed by the addition of reagents to the Te-Flow chamber. For the allele-specific single-base extension assay, primers were extended with a polymerase and labeled nucleotide mix (TEM), and stained with repeated application of STM (staining reagent) and ATM (anti-staining reagent). After completion of staining, the slides were washed with low-salt wash buffer (PB1), immediately coated with XC4, and then imaged in the iScan System. (5) Imaging the BeadChip and data analysis: The iScan System has a two-color (532 nm/658 nm) confocal fluorescent scanner with 0.54-μm pixel resolution. The scanner excited the fluorophores generated during signal amplification/ staining of the allele-specific (one color) extension products on the BeadChips. The image intensities were extracted using Illumina’s GenomeStudio Software.

first: Jae-Won

last: Cho

first: Hyo Sup

last: Shim

first: Chang Young

last: Lee

first: Seong Yong

last: Park

first: Min Hee

last: Hong

first: Insuk

first: Hye

last: Kim


title: DNA methylation features of LUSC in promoter and enhancer region


title: RNA seq analysis of calcium channel blocker, nifedipine in combination with metformin, MCC950 and anakinra treated Tet2-/- + Boy/J (1:1 ratio, mixed BM cells) transplanted Ob/Ob recipient mice

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Characterized by the accumulation of somatic mutations in blood cell lineages, clonal hematopoiesis (CH) of indeterminate potential (CHIP) involves expansion of mutated hematopoietic stem and progenitor cells (HSC/Ps) that leads to an increased risk of hematologic malignancy and cardiovascular disease (CVD). However, risk factors that contribute to CHIP-associated CH are poorly understood. A common, pro-inflammatory comorbidity responsible for enhancing the risk for developing type 2 diabetes mellitus (T2DM), CVD and cancer, obesity may exacerbate CHIP-associated diseases. We analyzed exome sequencing and clinical data from 47,466 individuals with valid CHIP in the UK Biobank. CHIP was present in 5.8% of the study population, and was associated with a significant increase in waist-to-hip ratio (WHR). The cancer genome atlas (TCGA) interrogation revealed that the mutation rate of CHIP is higher in patients with high BMI (>30 kg/m2) compared to those with low BMI (≤25 kg/m2) in six different cancer types. Utilizing mouse models of obesity bearing CHIP mutations, we show that both the compound mutant mice (Tet2-/-;Ob/Ob, Dnmt3a+/-;Ob/Ob) and CHIP mutant bone marrow (BM; Tet2-/-, Dnmt3a+/-, Asxl1+/- and Jak2+/-) transplanted into Ob/Ob mice develop rapid CH, leading to severe MPN/AML as well as CVD, which among other things, is associated with upregulation of intracellular calcium (Ca2+) levels and pro-inflammatory cytokines. Remarkably, calcium channel blocker nifedipine, in combination with metformin, MCC950 and anakinra, suppressed the growth of mutant CHIP cells, cardiovascular disease and restored normal hematopoiesis as well as serum Ca2+ and inflammatory cytokines. Thus, obesity is highly associated with the presence of CHIP and targeting CHIP mutant cells with a combination of metformin/nifedipine/MCC950/anakinra is a safe and inexpensive approach to treat CH and its associated abnormalities in obese individuals.

overall_design: To explain the mechanism of action of calcium channel blocker, nifedipine in combination with metformin, MCC950, anakinra treatment on Tet2-/- + Boy/J (1;1 ratio, mixed BM cells) transplanted into Ob/Ob mice, total RNA was isolated form the BM cells of 7 different drug treatment groups (Group 1: Vehicle, Group 2: Metformin, Group 3: Pioglitazone, Group 4: Nifedipine, Group 5: metformin+pioglitazone+MCC950+anakinra, Group 6: metformin+nifedipine+MCC950+anakinra and Group 7: Tet2-/-+Boy/J to WT (Un-treated) mice). RNA-sequencing (RNA-seq) was performed on samples from 3 independent mice from each group. treatment groups (Group 1: Vehicle, Group 2: Metformin, Group 3: Pioglitazone, Group 4: Nifedipine, Group 5: metformin+pioglitazone+MCC950+anakinra, Group 6: metformin+nifedipine+MCC950+anakinra and Group 7: Tet2-/-+Boy/J to WT (Un-treated) mice). RNA-sequencing (RNA-seq) was performed on samples from 3 independent mice from each group.

first: Chi

last: Zhang

first: Santhosh

last: Pasupuleti

first: Reuben

last: Kapur


title: Recruitment of highly cytotoxic CD8+ T cell receptors in mild SARS-CoV-2 infection

status: Public on Jan 07 2022

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

institute: TU Munich

summary: T cell immunity is crucial for the control of SARS-CoV-2 infections and has been widely studied on a quantitative level. However, quality of responses, in particular of CD8+ T cells, has only been marginally investigated so far. Here, we isolated T cell receptor (TCR) repertoires specific for immunodominant SARS-CoV-2 epitopes restricted to common Human Leucocyte Antigen (HLA) class I molecules in convalescent individuals. SARS-CoV-2-specific CD8+ T cells were detected up to twelve months from infection. TCR repertoires were diverse, with heterogeneous functional avidity and cytotoxicity towards virus-infected cells, as demonstrated for TCR-engineered T cells. High TCR functionality correlated with gene signatures that, remarkably, could be retrieved for each epitope:HLA combination analyzed. Overall, our data demonstrate that polyclonal and highly functional CD8+ TCRs – classical features of protective immunity - are recruited upon mild SARS-CoV-2 infection, providing tools to assess the quality and to potentially restore functional CD8+ T cell immunity.

overall_design: scRNA sequencing data for single SARS-CoV-2 peptide-stimulated CD8 T cell samples from convalescent donors

first: Karolin

middle: I

last: Wagner

first: Laura

middle: M

last: Mateyka

first: Vincent

last: Grass

first: Simone

last: Weber

first: Kilian

last: Schober

first: Monika

last: Hammel

first: Teresa

last: Burrell

first: Behnam

last: Kalali

first: Holger

last: Poppert

first: Henriette

last: Beyer

first: Sophia

last: Schambeck

first: Stefan

last: Holdenrieder

first: Andrea

last: Strötges-Achatz

first: Verena

last: Haselmann

first: Michael

last: Neumaier

first: Johanna

last: Erber

first: Alina

last: Priller

first: Sarah

last: Yazici

first: Hedwig

last: Roggendorf

first: Marcus

last: Odendahl

first: Torsten

last: Tonn

last: Dick

last: Witter

first: Hrvoje

last: Mijočević

first: Ulrike

last: Protzer

first: Percy

middle: A

last: Knolle

first: Andreas

last: Pichlmair

first: Claudia

last: Crowell

first: Markus

last: Gerhard

first: Elvira

last: D’Ippolito

first: Dirk

middle: H

last: Busch


title: Whole transcriptome analysis of mouse maturation ameloblasts with or without WDR72

city: San Francisco

first: Yan

last: Zhang

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

summary: We report the bulk RNA-seq analysis on maturation ameloblasts collected from P12 wild type and Wdr72 knock out mouse first molars.

overall_design: Examine the overall gene expression profile of wild type and Wdr72 gene ablation mouse molar maturation ameloblasts.

first: Pamela

last: DenBesten


title: Type I and II PRMTs Inversely Regulate Post-Transcriptional Intron Detention through

city: New York

first: Omar

last: Abdel-Wahab

address: 1275 York Ave

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Protein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I PRMT enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed Splicing Kinetics and Transcript Elongation Rates by Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhibition resulted in altered splicing rates. Surprisingly, co-transcriptional splicing kinetics did not correlate with final changes in splicing of polyadenylated RNA. This was particularly true for retained introns (RI). By using actinomycin D to inhibit ongoing transcription, we determined that PRMTs post-transcriptionally regulate RI. Subsequent proteomic analysis of both PRMT-inhibited chromatin and chromatin-associated polyadenylated RNA identified altered binding of many proteins, including the Type I substrate, CHTOP, and the Type II substrate, SmB. Targeted mutagenesis of all methylarginine sites in SmD3, SmB, and SmD1 recapitulated splicing changes seen with Type II PRMT inhibition, without disrupting snRNP assembly. Similarly, mutagenesis of all methylarginine sites in CHTOP recapitulated the splicing changes seen with Type I PRMT inhibition. Examination of subcellular fractions further revealed that RI were enriched in the nucleoplasm and chromatin. Together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns.

overall_design:
Splicing Kinetics and Transcriptional Elongation Rates by Sequencing (SKaTER-seq) was performed two days following treatment with either 0.01% DMSO, 1 ÂµM GSK591, or 1 ÂµM MS023 in A549 cells. Poly(A)-RNA sequencing was completed at two-, four-, and seven-days following treatment with either 0.01% DMSO, 1 ÂµM GSK591, or 1 ÂµM MS023 in A549 cells.

Actinomycin D poly(A) RNA sequencing was performed two days following treatment with either 0.01% DMSO, 1 µM GSK591, or 1 µM MS023 in A549 cells. Following two days of PRMT inhibition, 5 µg/mL of Actinomycin D was added and cells were incubated for an additional 60 minutes prior to poly(A) RNA isolation and sequencing.

first: Maxim

last: Maron

first: Alyssa

last: Casill

first: Varun

last: Gupta

first: Jacob

last: Roth

first: Simone

last: Sidoli

first: Charles

middle: C

last: Query

first: Matthew

middle: J

last: Gamble

first: David

last: Shechter


title: Endothelial RNF20 regulates the self-renewal and differentiation of neural precursor cells during embryonic development

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To further explore how endothelial RNF20 regulates embryonic neurogenesis, RNA isolated from the endothelial cells of RNF20fl/fl and RNF20cKO-Tie2  brain cortex at E13 was analyzed by RNA-seq to determine the genome-wide changes.
Methods:  mRNA from E13 isolated endothelial cells of RNF20fl/fl and RNF20cKO-Tie2 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics
Results: Approximately  one thousand transcripts showed differential expression between the RNF20fl/fl and RNF20cKO-Tie2 mice brain cortex, with a fold change ≥2 and p value <0.05.  Gene ontology analysis of downregulated genes showed the genes were enriched in terms related to neuron differentiation, cell communication and secretion by cells.Concomitantly, upregulated genes were enriched in terms related to negative regulation of cytokine production and cell development.The results showed that endothelial RNF20 is critical for neurogenesis.
Conclusions:  Endothelial RNF20 RNA-seq would provide a overall understanding how endothelial RNF20 regulates the self-renewal and differentiation of neural precursor cells during embryonic development

overall_design: mRNA profiles of E13  RNF20fl/fl and RNF20cKO-Tie2 mice  were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

first: Mengtian


title: Analysis of fluphenazine for castration-resistant prostate cancer

city: Shinjuku-ku

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi

department: Urology

institute: Keio University School of Medicine

summary: To investigate mode of funcsion of fluphenazine for prostate cancer, we examined the changes in global gene expression before and after treatment of fluphenazine.

overall_design: PC3 cells after treatment of DMSO (control) or 10uM fluphenazine were used for microarray.

first: Takeo

last: Kosaka


title: DNA methylation features of LUSC in promoter and enhancer region [RNA-seq]

first: JAE WON

last: CHO

summary: The purpose of this study is to compare transcriptional profiles of LUSC between tumor tissue and normal tissue

overall_design: 37 tumor biopsies and 37 adjacent normal samples from 37 LUSC patients were obtained. Each sample was subsequently prepared by TruSeq RNA Access Library Prep Guide Part # 15049525 Rev. B with TruSeq RNA Access Library Prep Kit. RNA-sequencing was performed by HiSeq 2500 with HiSeq 2500 System User Guide Document # 15035786 v01 HCS 2.2.70.

first: Jae-Won

last: Cho

first: Hyo Sup

last: Shim

first: Chang Young

last: Lee

first: Seong Yong

last: Park

first: Min Hee

last: Hong

first: Insuk

first: Hye

last: Kim


title: Identification of the Similarities and Differences of Molecular Networks Associated With Fear Memory Formation, Extinction, and Updating in the Amygdala [miRNA-seq]

city: jinan

first: Qi

middle: shuai

last: Zhuang

address: Shandong First Medical University, Qingdao Road, Huaiyin District

institute: Shandong First Medical University

summary: In this study, we systematically observed the expression of mRNAs, microRNAs (miRNA), long non-coding RNAs (lncRNAs), and circRNAs in the basolateral amygdala of mice after fear memory formation, extinction, and updating by whole-transcriptional sequencing, then a variety of inter-group comparison and bioinformatics analysis were used to find the differential expressed RNAs, enrich the function of them, and construct the molecular interaction networks. Moreover, competing endogenous RNA (ceRNA) molecular networks and transcriptional regulatory networks for the candidate circRNAs were constructed. Through these analyses, we found that about 10% of molecules were both involved in the fear memory extinction and formation, but the molecules and their signaling pathways were almost completely different between fear memory extinction and updating. This study describes a relatively detailed molecular network for fear memory updating, which might provide some novel directions for further mechanism research, and help to develop a specific physical method for fear memory intervention, based on the regulation of these key molecules.

overall_design: Retinal mRNA profiles of control, memory formation (F) group, fear memory extinction group (E), and fear memory retrieval-extinction group (RE)


title: Identification of the Similarities and Differences of Molecular Networks Associated With Fear Memory Formation, Extinction, and Updating in the Amygdala

summary:
 In this study, we systematically observed the expression
of mRNAs, microRNAs (miRNA), long non-coding RNAs (lncRNAs), and circRNAs in
the basolateral amygdala of mice after fear memory formation, extinction, and updating
by whole-transcriptional sequencing, then a variety of inter-group comparison and
bioinformatics analysis were used to find the differential expressed RNAs, enrich the
function of them, and construct the molecular interaction networks. Moreover, competing
endogenous RNA (ceRNA) molecular networks and transcriptional regulatory networks
for the candidate circRNAs were constructed. Through these analyses, we found that
about 10% of molecules were both involved in the fear memory extinction and formation,
but the molecules and their signaling pathways were almost completely different between
fear memory extinction and updating. This study describes a relatively detailed molecular
network for fear memory updating, which might provide some novel directions for further
mechanism research, and help to develop a specific physical method for fear memory
intervention, based on the regulation of these key molecules.

overall_design: Refer to individual Series


title: Identification of the Similarities and Differences of Molecular Networks Associated With Fear Memory Formation, Extinction, and Updating in the Amygdala [circRNA-seq]

summary: circRNA sequencing for 6 samples. In this study, we systematically observed the expression of mRNAs, microRNAs (miRNA), long non-coding RNAs (lncRNAs), and circRNAs in the basolateral amygdala of mice after fear memory formation, extinction, and updating by whole-transcriptional sequencing, then a variety of inter-group comparison and bioinformatics analysis were used to find the differential expressed RNAs, enrich the function of them, and construct the molecular interaction networks. Moreover, competing endogenous RNA (ceRNA) molecular networks and transcriptional regulatory networks for the candidate circRNAs were constructed. Through these analyses, we found that about 10% of molecules were both involved in the fear memory extinction and formation, but the molecules and their signaling pathways were almost completely different between fear memory extinction and updating. This study describes a relatively detailed molecular network for fear memory updating, which might provide some novel directions for further mechanism research, and help to develop a specific physical method for fear memory intervention, based on the regulation of these key molecules.

overall_design: Examing 2 conditions, each with 3 replicates


title: Phenotypic switching and filamentation in Candida haemulonii, an emerging opportunistic pathogen of humans

city: Shanghai

first: LI

last: TAO

state: Shanghai

address: Yangpu district Songhu Road

institute: Fudan University

summary: In this study, we report the identification of three distinct phenotypes in C. haemulonii

overall_design: total RNA profiles of C. haemulonii white and pink cells

first: Li

last: Tao


title: m6A-Epitranscriptomic Microarray analysis of CD11b+Mac-Spleen from HFD-Mettl3-LysM-Cre mice

city: New Haven

first: Xinshou

last: Ouyang

state: CT

address: 1 Gilbert street

department: Internal Medicine

institute: Yale University

summary: We processed m6A-Epitranscriptomic Microarray analysis on splenic CD11b+ macrophages isolated from 10-week old Mettl3f/f-LysM-Cre KO and  littermate WT mice.

overall_design: Examine m6A targed gene profile of  spleen CD11b+ macropahges  in Mettl3-Lysm-Cre KO and littermate controls  of C57/BL6 mice


title: RNA-seq and sRNA-seq analysis of maize W22 lines containing B chromosomes

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: The maize B chromosome is a non-essential chromosome and is not detrimental to plant development at low copy numbers. Nondisjunction of the maize B chromosome occurs at the second pollen mitosis. Maize lines containing B chromosomes are widely used in a variety of studies, such as gene dosage effect, centromere function and engineering of artificial chromosomes etc. An understanding of how the B chromosome affect gene expression is required for utilizing the B chromosome as tools for genetic studies and engineering. Therefore, we performed RNA-seq and small-RNA seq experiments on maize lines containing one through seven copies of B chromosomes to examine how gene expression responds to change of B copy numbers.

overall_design: Maize lines W22 with B chromosomes were screened by Fluorescence in situ hybridization at their seedling stage for identification of B chromosomes. W22 lines with one through seven copies of B chromosomes were used as the experimental group whereas W22 lines without B chromosome were used as the control group for RNA-seq and small-RNA seq experiments. 2-4 biological replicates were used for each experimental or control conditions.

first: James

last: Birchler


title: Pleiotropic loci associated with foot disorders and common periparturient diseases in Holstein cattle

city: Davis

first: Anita

last: Oberbauer

state: CA

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

summary: Lameness is an animal welfare issue that incurs substantial financial and environmental costs. This condition is commonly caused by digital dermatitis (DD), sole ulcers (SU), and white line disease (WLD). Susceptibility to these three foot disorders is due in part to genetics, indicating that genomic selection against these foot lesions can be used to reduce lameness prevalence. It is unclear whether selection against foot lesions will lead to increased susceptibility to other common diseases such as mastitis and metritis. Thus, the aim of this study was to determine the genetic correlation between causes of lameness and other common health disorders to identify loci contributing to the correlation. Genetic correlation estimates between SU and DD and between SU and WLD were significantly different from zero (P  < 0.05), whereas estimates between DD and mastitis, DD and milk fever, and SU and metritis were suggestive (P  < 0.1). All five of these genetic correlation estimates were positive. Two-trait genome-wide association studies (GWAS) for each of these five pairs of traits revealed common regions of association on BTA1 and BTA8 for pairs that included DD or SU as one of the traits, respectively. Other regions of association were unique to the pair of traits and not observed in GWAS for other pairs of traits. The positive genetic correlation estimates between foot disorders and other health disorders imply that selection against foot disorders may also decrease susceptibility to other health disorders. Linkage disequilibrium blocks defined around significant and suggestive SNPs from the two-trait GWAS included genes and QTL that were functionally relevant, supporting that these regions included pleiotropic loci.

overall_design: Whole blood was collected from 417 cows  from the coccygeal vein in the tail. Blood samples were centrifuged, and genomic DNA was extracted from the resulting buffy coat layer using the QIAGEN QIAamp DNA Blood Mini Kit . DNA samples were genotyped on the Illumina BovineHD BeadChip, and Illumina’s GenCall algorithm was used to call genotypes. Of the 417 samples, eight were removed during quality filtering, leaving 409 cows for analysis.

first: Ellen

last: Lai

first: Alexa

last: Danner

first: Thomas

middle: R

last: Famula


title: RNA -Seq analysis of CD11b+Mac-Spleen from HFD-Mettl3-LysM-Cre mice

summary: We processed RNA-sequencing on splenic CD11b+ macrophages isolated from 10-week old Mettl3f/f-LysM-Cre KO and  littermate WT mice.  NO_4-1, NO_4-2 are Mettl3f/f-LysM-Cre KO. NO_5-2, NO_5-3 are WT littermate controls.

overall_design: Examine the mRNA profile of  spleen CD11b+ macropahges  in Mettl3-Lysm-Cre KO and littermate controls  of C57/BL6 mice


title: Genomic profiles of oxidative stress-induced renal cell carcinomas developed in A/J mice

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

type: Genome variation profiling by genome tiling array

summary: Intraperitoneal administration of ferric nitrilotriacetate initiates Fenton reaction in the renal proximal tubules in rodents. Its repeated administration ultimately leads to the development of renal cell carcinoma (RCC). We performed high-resolution microarray comparative genomic hybridization to identify characteristics in the genomic profiles of oxidative stress-induced RCCs in the mice of A/J strain.

overall_design: The carcinogenesis protocol was started with 58 male A/J mice. Eighteen of the mice developed a renal cell carcinoma in total. Genomes of 4 samples from the RCCs were profiled on Agilent 180K mouse genome CGH microarrays.

first: Cheng

last: Zhen

first: Akatsuka

last: Shinya

first: Toyokuni


title: AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation [Hs]

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: We identified enrichment of a disease-enhancing, proinflammatory subpopulation of microglia in human AD patient brains with the R47H-TREM2 mutation, and uncovered that enhanced Akt signaling in microglia underlies the proinflammatory cytokine state and synaptic toxicity in our R47H-TREM2 tauopathy mouse model.

overall_design: Droplet-based single nuclear RNA sequencing of frontal cortical tissues from AD patient with and without the TREM2-R47H mutation and their age, pathology, and sex-matched, controls

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