title: Expression data from murine gut and spleen tissues

city: Stanford

first: Panagiota

last: Iliopoulou

address: 269 Campus Dr.

institute: Stanford University

summary:
TIM-1 is a gene that regulates immune responses including transplantation tolerence, allergy and asthma, autoimmunity, viral infections as well as cancer, however its role in transplantation has not been evaluated. Here we use a murine model of graft versus host disease (GVHD) to evaluate the therapeutic potential of blocking TIM-1 using an antibody.
We used microarray data to look for difference in gene expession in the gut which is one of the main organs that are afffected by GVHD as well as the spleen an organ when the immune response is generated. This will give us evidence as to whether the blocking TIM-1 mAb may modulate the immune response and protects against GVHD and promoted a less proinflammatory immune response

overall_design: Gut and spleen tissue was collected on day 9 post transplantation for RNA extraction and hybridization on Affymetrix microarray. The mice received anti-TIM-1 mAb (3D10)  a day prior to bone marrow transplantation (BMT) and then on day 3, 7, 11,17 post BMT

first: Yujun

last: Yang


title: RNA-seq analysis using glomeruli isolated from control and podocyte-specific bPIX deficient mice

status: Public on Oct 12 2019

city: Montreal

first: Tomoko

last: Takano

state: Quebec

address: 1001 Decarie Boulevard

department: Department of Medicine

country: Canada

institute: McGill University Health Centre (MUHC)

type: Expression profiling by high throughput sequencing

summary: We found that podocyte-specific bPIX deficient (KO) mice developed progressive proteinuria starting at ~8 weeks of age, and glomerulosclerosis and podocyte loss by 13 weeks of age. To investigate the mechanism of podocyte loss induced by bPIX deficiency, we analyzed mRNA expression by RNA-sequence using isolated glomeruli from control (CTRL) and KO mice.

overall_design: mRNA profiles of glomeruli isolated from 3 CTRL and 3 podocyte-specific bPIX KO mice were generated.

first: Jun

last: Matsuda


title: Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and farnesol-treated P. aeruginosa PAO1 Transcriptomes

status: Public on Oct 11 2019

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

country: China

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of farnesol-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis.
Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.
Results: Our RNA-seq results showed that less than 100 genes of P. aeruginosa PAO1 were differentially expressed following farnesol treatment. We found that about 1.7% of all detected genes (96 of 5554 genes) were more than two-fold differentially expressed following farnesol treatment.
Conclusions:

overall_design: The mRNA profiles of P. aeruginosa PAO1 (ck) and farnesol-treated P. aeruginosa PAO1 (sample1) were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000.

first: Wen-Ru

first: Hai-Ling


title: miRNAs regulate lung development and surfactant homeostasis via directly targeting SFTPC and TTF-1 in reprogramming-derived bovine model of NRDS

city: Beijing

first: Yifan

last: Rao

address: yuanmingyuanxi street

institute: Chinese academy of agricultural sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, We proposed a reprogramming-derived bovine model of NRDS based on typical phenotypes of neonatal respiratory distress syndrome (NRDS) and high reproducibility and replication rates as well as a steerable background of neonatal cloned cows suffering from NRDS. With the aid of miRNA sequencing, construction of the miRNA–gene network and functional enrichment of target genes, the effects of specific miRNAs on lung development and surfactant homeostasis were determined in this model. We identified 12 miRNAs targeting SFTPB, SFTPC and NKX2-1 genes, demonstrated repression effects of three miRNAs on NKX2-1 and SFTPC expression in vivo and through which miRNAs disturbed lung development and surfactant homeostasis in the NRDS bovine model.

overall_design: Two equal pools of total RNA (500 ng per sample), each from four cows, were produced from lung tissues of neonatal cloned and normal cows

first: Huabin

last: Zhu

first: Xiuzhu

last: Sun

first: Xiaojing

last: Jiang

first: Linhua

last: Huang

first: Xiaogai

last: Guo

first: Qiuling

first: Weihua

last: Du

first: Haisheng

last: Hao

first: Xueming

last: Zhao

first: Dong

last: Wang

first: Yunwei

last: Pang

first: Yan

last: Liu


title: Transcriptome analysis of synthetic miR-155 oligo-treated mouse CD4+ T-cells

city: Jingzhou

first: Min

last: Yao

address: Jingmi Road #266

institute: Yangtze University

summary: High-density gene expression profile of 20,000+ genes for synthetic miR-155 oligo-treated mouse CD4+ T-cells using RNA deep sequencing technology.

overall_design: Mouse CD4+ T-cells were purified with a CD4+ T-cell isolation kit (Miltenyi Biotec, Shanghai, China) and by magnetic bead separation. Cell purity was confirmed by flow cytometry. A total of 3 × 104 cells were transferred by synthetic miR-155 oligo. At 8 h post transfection, cells were collected and total RNA was isolated. Sequencing libraries were prepared with an Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Single-read sequencing (read length: 50 bp) was conducted on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA).

first: Tinghua


title: ChIPseq mapping of chromatin proteins Cren7 and Sso7D in the Sulfolobus solfataricus genome

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

country: USA

institute: University of Nebraska-Lincoln

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: To identify the genome binding sites of Cren7 and Sso7D, and to determine whether binding patterns differ between wild type and an epigenetically evolved strain in which they are heritably hypomethylated. Because methylated residues were solvent facing, it was predicted that binding patterns would not change between the strains.
Methods: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina Hiseq.
Results: Cren7 and Sso7D had distinct binding patterns. ChIPseq peak patterns had slight variation between wild type and the evolved strain, but not at genes whose expression was thought to be epigentically dependent.
Conclusions: As predicted, neither binding location or binding affinity correlated with epigenetic expression patterns in the evolved strain.

overall_design: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina HiSeq3000

first: Sophie

last: Payne


title: Influences of CDK9 on gene expressions

city: Nanjing

first: Lang

last: Lei

state: Jiangsu

address: Zhongyang Road 30, Xuanwu District

institute: Nanjing Stomatological Hospital, Medical School of Nanjing University

summary: To understand better the contribution of CDK9 in P. gingivalis-stimulated gene expression, gene chips were performed. Lentiviral vectors carrying CDK9 shRNA or not were transfected into cells for 96 hours, with the assist of Envirus. NC group was transfected with non-targeting scramble and stimulated with PBS. NC and Pg group was transfected with non-targeting scramble and stimulated with P. gingivalis. CDK9 shRNA group was transfected with CDK9 shRNA and stimulated with PBS. CDK9 shRNA and Pg group was transfected with CDK9 shRNA and stimulated with P. gingivalis.

overall_design: Gene expressions were measured at 2 hours after the stimulation of P. gingivalis, and three independent experiments were performed in each groups.

first: Jiao

first: Jiahong

last: Shi


title: Comparison of chromatin accessibility between human and non-human primates

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

institute: Duke University

summary: Evolution of transcriptional regulation is thought to be a major cause of the evolution of phenotypic traits. We compared DNase I Hypersensitive sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and macaque). We identified approximately 90,000 DHS sites, of which 59% are not significantly different between species, 27% are differential and likely due to a single evolutionary change, and 14% are differential and likely due to multiple changes. We found that including additional closely related species allows us to better distinguish between accessibility changes that are specific to a single species and those that have experienced changes in chromatin accessibility across multiple species during evolution.

sample_organism:
Macaca mulatta
Gorilla gorilla
Pan troglodytes
Pongo pygmaeus
Homo sapiens

overall_design:
DNase-seq of 3 biological replicates from each of 5 species: human, chimpanzee, gorilla, orangutan, and macaque.

Grant ID: HOMINID 0827552
Funding source: NSF
Grant title: Genetic Bases for the Evolution of Human Diet
Grantee name: Gregory Wray

first: Greg

last: Wray


title: RNA-Seq analysis of MIN6 cells following control KD or Paupar KD

status: Public on Oct 10 2019

city: New York

first: Ruth

middle: A

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

summary: Aim:Transcriptional analysis of the MIN6 beta cell line following control or Paupar lncRNA KD to identify genes regulated by Paupar  Methods:MIN6 cells subjected to either control or Paupar KD were transfected for 48 hours before extraction of total RNA using the Qiagen Mini kit. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 30 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq2.  Results: We did not observe any signficant changes in genes important for beta cell function   Conclusion: Paupar does not have a signficant regulatory function in beta cells

overall_design: mRNA profiles of MIN6 cells following either control KD or Paupar KD were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Lori

last: Sussel


title: Silencing Dicer-like genes reduces sRNA generation and virulence in Penicillium italicum

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

summary: Nine sRNA libraries were prepared and sequenced using Illumina sequencing

overall_design: we sequenced 9 sRNAs libraries prepared from the transformants of DCL1RNAi, DCL2RNAi and wide type.

first: Liang

last: Gong

first: Chunxiao

last: Yin


title: Regulation of Lifespan by Neural Excitation and REST [Day 10]

city: Boston

first: Derek

last: Drake

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Explore the effects of spr-4 and spr-3 on daf-2 function and lifespan.

overall_design: Comparison of spr-4;spr-3;daf-2, daf-2, spr-4;spr-3, and N2 C. elegans at day 10 with 3 biological replicates per group.

first: Joseph

last: Zullo

first: Bruce

last: Yankner


title: Regulation of Lifespan by Neural Excitation and REST

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

overall_design: Refer to individual Series


title: The long noncoding RNA Paupar modulates PAX6 regulatory activities to promote alpha cell development and function


title: The effects of Zoledronate on human peripheral blood mononuclear cells

city: Shinagawa

first: Reiko

last: Takimoto

state: Tokyo

department: Department of Biochemistry

country: Japan

institute: Showa University, School of Dentistry

summary: Zoledronate is well known to act on osteoclasts to inhibit bone resorption.Zoledronate is administrated intravenously in clinical use, however,  actions of zoledronate on cells in blood circulation are not fully understood. To understand its actions of human peripheral blood mononuclear cells (h-PBMC), we performed gene expression profiling in zoledronate-treated h-PBMC.

overall_design: h-PBMC were incuvated for 8 hours with 5 mM of Zoledronate (Zol. (+)) or without (Zol. (-)).

first: Atsushi

last: Yamada

first: Yoichi

last: Miyamoto

first: Tetsuo

last: Suzawa

first: Kentaro

last: Yoshimura

first: Kiyohito

last: Sasa

first: Tatsuo

last: Shirota

first: Ryutaro

last: Kamijo


title: RNA-Seq analysis of the pancreatic islets from 6-week-old Paupar WT and KO mice

summary: Transcriptional analysis of the pancreatic islets of adult Paupar KO mice versus Paupar WT mice. Total RNA from Paupar WT and Paupar KO mice was converted into cDNA libraries (TruSeq RNA sample preparation kit, Illumina) according to manufacturer’s instructions. Sequencing was performed to a depth of 30 million, single-end reads in three biological replicates per genotype. Reads were aligned to the mouse genome (mm9) using HISAT2 v2.1.0 (Kim et al., 2013). Aligned reads were assigned to genes using annotations from Ensembl (Mus_musculus.GRCm38.73.gtf) and HTseq-count v0.10.0 (Anders et al., 2015). Differential expression across cohorts was assessed using DESeq2 v1.18 (Love, Huber, and Anders, 2014). Among the downregulated genes with a p-value < 0.05 genes important for alpha cell identity and function.

overall_design: mRNA profiles of the pancreatic islets of 6 week old Paupar WT and KO mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.


title: Regulation of Lifespan by Neural Excitation and REST [Day 2]

overall_design: Comparison of spr-4;spr-3;daf-2, daf-2, spr-4;spr-3, and N2 C. elegans at day 2 with 3 biological replicates per group.


title: Circulating Uromodulin inhibits systemic oxidative stress by inactivating the TRPM2 channel

city: INDIANAPOLIS

first: TAREK M. (ASHKAR)(M.D.)

last: EL-ACHKAR

state: IN

address: 950 w walnut- r2 202

institute: INDIANA UNIVERSITY, DIVISION OF NEPHROLOGY

summary: High serum concentrations of kidney-derived protein uromodulin (Tamm-Horsfall protein or THP) have recently been shown to be independently associated with low mortality   in both older adults and cardiac patients, but the underlying mechanism remains unclear. Here, we show that THP inhibits the generation of reactive oxygen species (ROS) both in the kidney and systemically. Consistent with this experimental data, the concentration of circulating THP in patients with surgery-induced acute kidney injury (AKI) correlated with systemic oxidative damage. THP in the serum dropped after AKI, and was associated with an increase in systemic ROS. The increase in oxidant injury correlated with post-surgical mortality and need for dialysis. Mechanistically, THP inhibited the activation of the TRPM2 channel. Furthermore, inhibition of TRPM2 in vivo in a mouse model, mitigated the systemic increase in ROS during AKI and THP deficiency. Our results suggest that THP is a key regulator of systemic oxidative stress by suppressing TRPM2 activity and our findings might help to explain how circulating THP deficiency is linked with poor outcomes and increased mortality.

overall_design: Compare kidney S3 proximal tubules from THP+/+ and THP -/- Mice

first: Kaice

last: LaFavers

first: Tarek

middle: M

last: El-Achkar

first: Shehnaz

last: Khan

first: Radmila

last: Micanovic


title: Genome-wide profiling of YCC16 gastric cancer cell line upon silencing of OCT4 or RXRalpha

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

country: India

institute: Madurai Kamaraj University

summary: Dysregulation of OCT4 and RXRalpha has been reported in many cancers. Towards understanding the role of OCT4 and RXRalpha mediated transcriptional programs in gastric cancer, OCT4 and RXRalpha were silenced in YCC16 cells using lentiviral knockdown method. The OCT4 and RXRalpha shRNA encoding lenti-viral infected and non-targeting control (NTC) infected YCC16 cells were selected with puromycin. The stable cells were profiled using Human Transcriptome Array 2.0.

overall_design: Total RNA was isolated from YCC16 gastric cancer cell line, transduced with shL-OCT4, shL-RXRalpha and shL-NTC as a control and profiled using GeneChip® Human Transcriptome Array 2.0 (HTA-2_0).

first: Jaishree

last: Pandian

first: Karthikeyan

last: Selvarasu


title: The Comparative Analysis of Phenotypic and Whole Transcriptome Gene Expression Data of Ascites Susceptible Versus Ascites Resistant Chickens

city: Tabriz

first: Karim

last: Hasanpur

state: East Azarbayjan

address: Jam-Jam street

department: Animal Science

country: Iran

institute: University of tabriz

summary: Ascites syndrome (AS) is a metabolic disorder that mainly occurs at later ages of meat-type chickens. Despite many research, there is no consensus about the origin of this syndrome. Our main purpose were to investigate the syndrome using both phenotypic and RNA-Seq data to elucidate the most causative factors predisposing the birds to AS. Phenotypic data analysis showed that AS indicator traits (AITs) were moderate to high heritable. Inexistence of consistent direct genetic correlation between AITs and growth related traits (GRTs), indicated that neither faster growth rate nor heavier body weight is the most causative factor affecting the susceptibility of broilers to AS. However, respiratory capacity was revealed to be the most probable factor predisposing the birds to AS, as both lung weight and lung percentage were negatively correlated with AITs. Transcriptomic data analysis revealed 125 differentially expressed genes (DEGs) between the ascitic and healthy groups. Up-regulated genes in ascitic group enriched mainly in gas transport biological process, while down-regulated genes involved in defense response to bacteria, biological adhesion, cell adhesion, killing of cells of another organism and cell division. Genetic association of the DEGs with human cardiovascular diseases suggested an excessive heart problems of the ascitic chicks. Heart is, probably, the first tissue suffering from the incompetence of small respiratory system of the AS-susceptible chickens. In other word, tissue hypoxia, that cause free radicals to concentrate in heart cells, may be the commencement of events that finally result to heart failure, suffocation and death of chicks due to the AS.

overall_design: Right heart ventricule mRNA profiles of 39-day old ascitic and healthy chickens were generated by deep sequencing, in duplicate using Illumina Hiseq 2000

first: Mohammadreza

last: Nassiri

first: Ghasem

middle: H

last: Salekdeh


title: ChIP-seq analysis of Pax6 binding in alphaTC1 cells following control or Paupar KD

first: Ruth

last: Singer

summary: We determined that Paupar KD in alphaTC-1 cells causes genome-wide changes in Pax6 transcription factor binding

overall_design: Examination of Pax6 binding sites in alphaTC1 cells following control KD or Paupar KD in duplicate biological samples

first: Lori

last: Sussel


title: Single-cell RNA-seq analysis of Drosophila neuroblast tumors

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

summary:
Inactivation of prospero in Drosophila neuroblasts during larval stages induces unlimited neuroblast amplification leading to tumors that persist growing in adults. Tumors present in the ventral nerve cord of adult flies were dissected, dissociated and GFP-labelled tumor neuroblasts were isolated by FACS. 10000 neuroblasts were then processed for single-cell RNA-seq analysis.  Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.

eLife 2019;8:e50375 DOI: 10.7554/eLife.50375

overall_design: FACS sorted tumor neuroblasts were processed using the Chromium Single Cell Controller  (10X  genomics, Pleasanton).  Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions.  Analysis using molecular indexing information provides an absolute digital measurement of gene expression levels.  Sequencing was performed using a NextSeq 500 Illumina device (1sample) containing transcript lengh of 57 bp.Droplet Based

first: Cassandra

last: Gaultier

first: Fabrice

last: Daian

first: Cédric

last: Maurange


title: mRNA expression profiles of Neural Tube Defects (NTDs) in the 2nd trimester of human fetus

city: Columbus

first: Zhaojun

last: Qiu

state: Ohio

address: 460 West 12th Ave

institute: The Ohio State University

summary: Neural Tube Defects (NTDs) are serious health problems of infants, accounting for large proportion of live birth defects in infants and miscarriage in women worldwide. Although some epidemiologic studies suggest both genetic and environmental factors were involved in the progression of the diseases, the etiologies of NTDs are not well understood at present. The objective of our study was to generate and to compare mRNA profiles of NTDs with those of normal controls in the 2nd trimesters of pregnancy. Illumina microarray chips (beadarrays) were utilized to identify the altered mRNA transcripts in the organ samples recruited from Luliang Prefecture in Shanxi Province, China, which has the highest occurrence of NTDs in world. The beadarrays identified 101 un-regulated and 194 down-regulated mRNA transcripts in the NTDs compared with the controls in the spinal cord. A number of genes in the cholesterol biosynthesis pathway were down-regulated. In particular, SIRT2, a key regulator of cholesterol biosynthesis, was significantly down-regulated in NTD samples. Our findings provide evidences that, the decrease of cholesterol biosynthesis in the spinal cord of NTD may affect the neural tube closure in the affected fetuses.

overall_design: mRNA profiles from NTD affected fetal samples were compared to those of the normal controls in the same period of fetal development.

first: Runlin

middle: Z

last: Ma

first: Wei

last: Zhang


title: Analysis of gene expression in hindgut cells of EdnrB mutant embryonic day 14 mice

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Neural Crest Cells (NCC) migrate through the gut during mouse development and are involved in mesenchymal patterning. However, in a Tcof hetrozygous mutant, NCC cells stop their migration at E14.5. Mutation of the EdnrB receptor also inhibits cell migration, but farther back. A FLEX conditional knockout of EdnrB only in NCC cells, also halts migration, however is still permissible for transplantated wt NCC cells. In order to better understand mechanisms of cell migration, the transcriptional environment of the gut was characterized by array analysis of Ednrb mutants.

overall_design: EdnrB mutant, EdnrB-FLEX(NCC-/-) mutant, and WT mouse cells of the hind gut at 14.5 days are compared using Affymetrix MOE430 version 2 for a total of 9 arrays.

first: Paul

last: Trainor

first: Amanda

last: Barlow


title: RNA-Seq analysis identifies pancreatic lncRNAs

summary: Aim: Identification of long noncoding RNAs using transcriptional analysis of e15.5 mouse embryonic pancreas and adult mouse islets Methods: rRNA-depleted total RNA from e15.5 embryonic mouse pancreata and 12-week-old mouse islets was prepared using the Ribo-Zero rRNA removal kit. Biological replicates indicate that each RNA-seq data set was generated from individual mice (islets) or 3-4 pooled e15.5 embryonic pancreata. Libraries were prepared with Illumina TruSeq RNA sample preparation kit and then sequenced with 60 million, 2 x 100 paired reads on an Illumina HiSeq 2000 V3 instrument. To reconstruct the transcriptomes, we first mapped all reads of total RNAs to the mouse reference genome (mm10) with TopHat v1.3.2 (Trapnell et al., 2012). Cufflinks (v1.2.1) was subsequently applied to assemble the whole transcriptome and to identify all possible transcripts. Significantly differentially expressed genes were calculated using DEseq2.

overall_design: LncRNA and mRNA profiles of the e15.5 mouse pancreas and 12-week-old adult mouse islets were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.


title: Cytoskeletal TAGLN2 is involved in gender-dependent adipose tissue expandability

status: Public on Oct 09 2019

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

summary: The preadipocytes’ shape changes dramatically during differentiation, in parallel with lipid accumulation and cytoskeletal reorganization. Failure to do so may impact the flexibility of adipose tissue (AT) to shift between lipid storage and mobilization, leading to impaired metabolism and insulin resistance. Transgelin 2 (TAGLN2) was identified as a cytoskeletal protein expressed in AT and associated with obesity and inflammation both in mice and humans, being normalized upon weight loss. Tagln2 knockdown in preadipocytes revealed a key functional role, being required for proliferation and biosynthetic and oxidation pathways. The phenotype of gain of function in vivo (aP2-Tagln2 mice) disclosed important gender-related differences, in whom transgenic female mice over-expressing Tagln2 in AT exhibited “healthy” obesity, characterized by increased fat mass, hypertrophic adipocytes, and preserved insulin sensitivity. Conversely, transgenic males exhibited enhanced activation of T helper cells, mitochondrial dysfunction, and impaired fatty acid metabolism in AT, together with decreased insulin sensitivity and the prevalence of small adipocytes, suggestive of defective AT expandability. The metabolic relevance of TAGLN2 in humans was supported by the existence of single nucleotide polymorphisms that can modulate TAGLN2 gene expression in AT and are associated with obesity and protection from ischemic heart disease in GWAS public databases. Collectively, current findings highlight the contribution of cytoskeletal TAGLN2 to AT expansion and protection from cardiometabolic disease in a gender-dependent manner.

overall_design: 24 samples were analyzed: aP2_TAS (n=6);  aP2_TAV (n=6); WT_TAS  (n=6); WT_TAV (n=6);

first: Francisco

middle: J

last: Ortega

first: José

last: Fernández-Real


title: Dysregulated microRNAs in calcific aortic valve disease

city: Qingdao

first: Rongjian

last: Xu

address: No.38 Dengzhou Road

institute: The Affiliated Hospital of Qingdao University

summary: Calcific aortic valve disease (CAVD) is a common heart valve disease, yet its underlying mechanism remains pooly understood. We aimed to explore the microRNAs funtion in CAVD and to develop novel miRNA therapy for CAVD.

overall_design: noncalcified aortic valves 3 vs. calcified aortic valves 2

first: Yun

last: Yang


title: Differential 5-methylcytosine and 5-hydroxymethylcytosine in Parkinson’s and Alzheimer’s Disease.

city: Grand Rapids

first: Alison

middle: I

last: Bernstein

state: MI

address: 400 Monroe Ave NW

department: Translational Neuroscience

institute: Michigan State University

summary: Background: 5-methylcytosine (5-mC) and its oxidized form, 5-hydroxymethylcytosine (5-hmC), are distinct epigenetic marks that help regulate gene expression in the mammalian brain. Existing studies have identified associations between 5-mC and neurodegenerative disease, but little work has examined the potential role of 5-hmC in Parkinson’s disease (PD) or Alzheimer’s disease (AD). Here, we utilized PD postmortem brain tissue and a public dataset from postmortem AD brains to analyze the effect of neurodegenerative disease on paired 5-mC and 5-hmC levels.   Results: In PD samples, we measured genome-wide 5-mC and 5-hmC from control (n=3) and PD (n=6) brains using the Illumina EPIC array combined with bisulfite and oxidative bisulfite treatments (BS/oxBS-EPIC). In publicly sourced data, genome-wide 5-mC and 5-hmC were measured from control (n=25) and AD (n=62) human entorhinal cortex tissue using the Illumina 450K array combined with bisulfite and oxidative bisulfite treatment (BS/oxBS-450K). Paired 5-mC and 5-hmC beta values were generated using a custom pipeline of bioinformatics tools, and we modeled the effect of disease on paired 5-mC and 5-hmC data using a mixed effects beta regression model with a random effect for ID and an interaction term between disease category and DNA modification category (“5-mC” or “5-hmC”). We identified a number of CpG probes (AD: n=699, PD: total n = 80) that showed a significant interaction between disease status and DNA modification category (p-value < 2.4x10-7).  Conclusions: While our PD data requires additional validation, our analyses suggest that there are widespread shifts in the balance between 5-mC and 5-hmC in Parkinson’s and Alzheimer’s disease.

overall_design: Control (n=3) and PD (n=6) postmortem brain tissue samples from two tissues -- parietal and cingulate cortex. Total n=18 (n=9 per tissue type). Samples were both bisulfite treated and oxidative bisulfite treated to generate paired 5-mC and 5-hmC. Total number of data files = 36 (n=18 per method).

first: Joseph

last: Kochmanski

first: Sarah

middle: E

last: VanOeveren

first: Marie

last: Adams

first: Marla

last: Gearing


title: RNA-seq of 10dpp wild type and Dazl SKO mouse testes

city: Shanghai

first: Haixin

last: Li

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

institute: Tongji University

summary: The autosomal gene Dazl is a member of highly conservative DAZ family, all of which contains a RNA binding domain and expresses in germ cells. In mice, Dazl plays an essential role in germ cell development, germ cell lost in Dazl knockout mouse on pure C57BL/6 strain background. Here we generated conditional DAZL knockout mice which allowed us to examine the roles of DAZL in postnatal spermatogenesis without affecting its early function in PGC. RNA was extracted from 10dpp wild type and Stra8-cre KO mouse testes to perform RNA-seq, StringTie software was used to assess the expression level by formula log2(FPKM+1).

first: Eugene

middle: Y


title: Genome-wide transcriptome profiling of wild-type and Kmt2d-deficient ATDC5 differentiated chondrocytes and undifferentiated mesenchymal cells

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

summary: We performed genome-wide transcriptome profiling in stable Kmt2d-/- (bi-allelic deletion of the catalytic SET domain) and Kmt2d+/+ ATDC5 chondrocyte cell lines 7 days after induction of differentiation and in stable Kmt2d-/- and Kmt2d+/+ undifferentiated ATDC5 cells.

overall_design: RNA-seq was performed on two (Kmt2d-/-) and three (Kmt2d+/+) biological replicates for each differentiation state (chondrocytes vs undifferentiated cells); each biological replicate is a distinct clonal cell line. Two technical replicates were performed for each cell line. Technical replicates were the same libraries run on different flow cells.

first: Jill

last: Fahrner

first: Kasper

middle: D

last: Hansen

first: Hans

middle: T

last: Bjornsson

first: WanYing

last: Lin


title: Transcriptomic analysis reveals new hippocampal gene networks induced by prolactin

city: Ciudad de Mexico

first: Erika Alejandra

last: Cabrera-Reyes

state: Cd. de Mexico

address: AV. Universidad 300

country: Mexico

institute: UNAM

summary: Prolactin (Prl) is a pleiotropic hormone with multiple functions in several tissues and organs, including the brain. In the hippocampus, Prl has been implicated in several functions, including neuroprotection against excitotoxicity in lactating rats and in Prl-treated ovariectomized animals. However, the molecular mechanisms involved in Prl actions in the hippocampus have not been completely elucidated. The aim of this study was to analyse the hippocampal transcriptome of female Prl-treated ovariectomized rats. Transcriptomic analysis by RNASeq revealed 162 differentially expressed genes throughout 24 h of Prl treatment. Gene Ontology analysis of those genes showed that 37.65% were involved in brain processes that are regulated by the hippocampus, such as learning, memory and behaviour, as well as new processes that we did not foresee, such as glial differentiation, axogenesis, synaptic transmission, postsynaptic potential, and neuronal and glial migration. Immunodetection analysis demonstrated that Prl significantly modified microglial morphology, reduced the expression of Cd11b/c protein, and altered the content and location of the neuronal proteins Tau, Map2 and Syp, which are involved in axogenic and synaptic functions. This novel delineation of Prl activity in the hippocampus highlights its importance as a neuroactive hormone, opens a new avenue for understanding its actions and supports its participation in neuronal plasticity of this brain area.

overall_design: We performed time course experiments during a period of 24 h of PRL treatment in adult ovariectomized rats (Rattus norvegicus) to obtain total hippocampus. The experimental groups were divided into Control (Solution salina 0.9%), and PRL (500µg/kg) treated during 3, 6 and 24 hours. Total RNA isolated from the hippocampus of each animal was sequenced by using the Hi-seq500 Illumina Platform in three biological replicates of each experimental group. A total of 365,050,464 reads, with an average of 30.4 million reads (paired end 2x72 bp long), were obtained for each of the four of the treated groups. Up to 93.5% of the reads were successfully mapped to transcripts in the NCBI, Rnor 6.0 as genome reference

first: Erika

first: América

last: Vanoye–Carlo

first: Mauricio

last: Rodríguez-Dorantes

first: Edgar

middle: R

last: Vázquez-Martínez

first: Nadia

last: Rivero-Segura

first: Omar

last: Collazo-Navarrete

first: Marco

last: Cerbón


title: Prolyl Hydroxylase Substrate Adenylosuccinate Lyase Is An Oncogenic Driver In Triple Negative Breast Cancer

city: Chapel Hill

first: Travis

last: Ptacek

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

summary: Protein hydroxylation extensively regulates cellular signaling by affecting protein stability, activity, and interactome, therefore contributing to the pathogenesis of various diseases including cancers. However, because of the transient nature of the hydroxylase-substrate interaction, identifying new prolyl hydroxylation substrates remains a daunting challenge. Here, by developing a novel enzyme-substrate trapping strategy coupled with TAP-TAG or orthogonal GST- purification followed by mass spectrometry, we identify Adenylosuccinate lyase (ADSL) as a bona fide EglN2 prolyl hydroxylase substrate in triple negative breast cancer (TNBC). ADSL expression is significantly higher in TNBC than other breast cancer subtypes or normal breast tissues. Functionally, ADSL knockout greatly impairs TNBC 2-D and 3-D cell proliferation and invasiveness in vitro, as well as TNBC tumorigenesis and lung colonization in xenograft models. Mechanistically, an integrated transcriptomics and metabolomics analysis revealed that ADSL promotes the activation of the oncogenic cMYC pathway by regulating cMYC protein level via a mechanism requiring ADSL hydroxylation on proline 24. Specifically, hydroxylation-proficient ADSL, by affecting adenosine levels, represses the expression of the long non-coding RNA MIR22HG, thus upregulating the oncogene cMYC protein level and its target gene expression. Our findings identify the critical role of ADSL hydroxylation in controlling cMYC and TNBC tumorigenesis.

overall_design: Transcriptional profiling of MDA-MB-231 cells treated with sgRNA targeting ADSL or control sgRNA

first: Qing

last: Zhang

first: Giada

last: Zurlo

first: Jeremy

last: Simon


title: Gene Expression Alterations in Bronchial Epithelium of Electronic Cigarette Users

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

institute: Boston University School of Medicine

summary: Background:  While electronic cigarette (ECIG) use is rapidly rising, their safety profile remains uncertain. The effects of tobacco cigarette (TCIG) smoke on bronchial airway epithelial gene-expression have provided insights into tobacco-related disease pathogenesis.  Understanding the impact of electronic cigarettes (ECIGs) on airway gene-expression could provide insights into their potential long-term health effects.  Objectives: We sought to compare the bronchial airway gene-expression profiles of former TCIG smokers now using ECIGs with the profiles of former and current TCIG smokers.  Methods: We performed gene-expression profiling of bronchial epithelial cells collected from TCIG smokers not using ECIGs (n=21), former smokers using ECIGs (n=15), and current TCIG smokers not using ECIGs (n=9). We then compared our findings with previous studies of the effects of TCIG use on bronchial epithelium, as well an in vitro model of ECIG exposure.  Results:  Amongst 3,165 genes whose expression varied between the three study groups (q < 0.05), we identified 468 genes significantly altered in ECIG users relative to former smokers (p < 0.05). 79 of these genes were up or down-regulated concordantly between ECIG and TCIG. We did not detect ECIG-associated gene expression changes in known pathways associated with TCIG usage. Genes downregulated in ECIG users are enriched among the genes most downregulated by exposure of airway epithelium to ECIG vapor in vitro.  Conclusions: TCIG exposure was associated with a larger number of airway gene-expression changes than with ECIG exposures. ECIGs induce both distinct and shared patterns of gene expression relative to TCIGs in the bronchial airway epithelium.

overall_design: Bronchial epithelial cells were collected from former TCIG smokers not using ECIGs (n=21), former smokers using ECIGs (n=15), and current TCIG smokers not using ECIGs (n=9).

first: Sean

last: Corbett

first: Avrum

last: Spira

first: Marc

last: Lenburg


title: MITF-low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease

city: Edinburgh

first: Jana

last: Travnickova

address: Crewe Road South

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: MRC Human Genetics Unit & Cancer Research UK EC

summary: The MITF-low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa (MITF-low) to study this biological subtype. We performed whole bulk RNA-seq to classify zebrafish MITF-low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients’ MITF-low subgroups. Furthermore, using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single-cell and low input RNA-seq we characterise these MITF independent cells and show that they pre-exist in the primary tumour.

overall_design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.

first: Ava

last: Khamseh

first: Philippe

last: Gautier

first: E

last: Patton


title: Role of NF-kappaB2-p100 in regulatory T cell homeostasis and activation

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

institute: National Institute of Immunology

summary: RNAseq analysis of Ex vivo Treg cells were isolated from wild type or Nfkb2-/- mice.

overall_design: WT and Nfkb2-/- Tregs were isolated as described above from spleens of bi-parental bone marrow chimeras. Sorted cells were rested in complete RPMI at 37°C for 2 h before being re-suspended in 1ml TRIzol reagent (Thermofisher Scientific, CA) and stored at -80°C. Three such biological repeats of WT and Nfkb2-/- Tregs were collected. RNA was isolated by treatment with chloroform, isoporopanol and ethanol according to the RNA isolation protocol using TRIzol reagent as recommended. The RNA extracted was quantified using NanoDrop1000 (Thermofisher Scientific, CA). Unstranded RNAseq libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Ilumina, San Diego) according to the kit protocol. Barcoded libraries were sequenced in Illumina HiSeq 2500.

first: G


title: Dazl HITS-CLIP on 25dpp C57BL/6 mouse testes

first: Haixin

last: Li

summary: The autosomal gene Dazl is a member of highly conservative DAZ family, all of which contains a RNA binding domain and expresses in germ cells. In mice, Dazl plays an essential role in germ cell development, germ cell lost in Dazl knockout mouse on pure C57BL/6 strain background. Here we use HITS-CLIP to globally characterize the genome-wide target RNA of Dazl in mouse testes.  Sequencing data provides large quantities of clues to help us to get close to the truth of Dazl function. We find over 1700 RNAs are bind by Dazl mainly at 3’UTR and the genes associated with transcription, RNA splicing and reproductive cellular process are enriched significantly.

overall_design: We performed 2  biological duplicate, every duplicate used 4 testes from 4 wild type C57BL/6 25dpp mouse. We successfully identified Dazl-RNA complex at 33kDa and radiolabel RNA was detective at 33kDa and about 40kDa smear shift. We constructed two independent cDNA libraries from two 33kDa samples, which is sample 1 and sample 2, and mixed two 40kDa samples together to be one, sample 3. At the same time, we also performed RNA-seq of total 25dpp mouse testes as input background.

first: Eugene

last: Xu


title: Gene network analysis reveals a role for striatal glutamatergic receptors in dysregulated risk-assessment behavior of autism mouse models

status: Public on Oct 08 2019

city: Safed

first: Evan

last: Elliott

state: Galilee

address: Henrietta Szold Street, 8

department: Neurobiology

country: Israel

institute: Bar Ilan University

summary: Autism Spectrum Disorder (ASD) presents a wide, and often varied, behavioral phenotype. Impulsivity and improper assessment of risks has been widely reported among individuals diagnosed with ASD. However, there is little knowledge of the molecular underpinnings of the impaired risk-assessment phenotype. In this study, we have identified impaired risk-assessment activity in multiple male ASD mouse models.  By performing network-based analysis of striatal whole transcriptome data from each of these ASD models, we have identified a cluster of glutamate receptor–associated genes that correlate with the risk-assessment phenotype. Furthermore, pharmacological inhibition of striatal glutamatergic receptors was able to mimic the dysregulation in risk-assessment.  Therefore, this study has identified a molecular mechanism that may underlie impulsivity and risk-assessment dysregulation in ASD.

overall_design: Examination of whole transcriptome in dorsal striatum of four ASD mouse models and controls

first: Oron

last: Oded

first: Elliott

last: Evan


title: Expression profiling of CLL derived T Cells treated with pevonedistat

city: Portland

first: Alexey

last: Danilov

state: Oregon

address: 3681 SW Sam Jackson Rd

department: Knight Cancer Institute

institute: Oregon Health and Science University

summary: Novel targeted agents used in therapy of lymphoid malignancies, such as inhibitors of B-cell receptor-associated kinases, are recognized to have complex immune-mediated effects. NEDD8-activating enzyme (NAE) has been identified as a tractable target in chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma. We and others have shown that pevonedistat (TAK-924), a small molecule inhibitor of NAE, abrogates NF-κB signaling in malignant B cells. However, NF-κB pathway activity is indispensable in immune response, and T-cell function is altered in patients with CLL. Using T cells derived from patients with CLL, we demonstrate that while targeting NAE results in markedly differential expression of NF-κB-regulated genes and downregulation of IL-2 signaling during T-cell activation, T cells evade apoptosis. Meanwhile, NAE inhibition favorably modulates polarization of T cells in vitro, with decreased Treg differentiation and a shift towards TH1 phenotype, accompanied by increased interferon-γ production. These findings were recapitulated in vivo in immunocompetent mouse models. T cells exposed to pevonedistat in washout experiments, informed by its human pharmacokinetic profile, recover NAE activity and maintain their response to T-cell receptor stimulation and cytotoxic potential. Our data shed light on the potential immune implications of targeting neddylation in CLL and lymphoid malignancies.

overall_design: Isolated primary T cells were stimulated and treated with either pevonedistat or vehicle (DMSO) at 3hrs and 24 hrs with 4 replicates.

middle: V

first: Nur

last: Bruss


title: Expression data from HEK293T cells transfected with pNTAP-2×flag-VRTN or empty vectors

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

summary: To further investigate whether VRTN is a transcription factor, we examined global transcriptomic changes in human HEK293T cells after treating them with VRTN using whole-genome microarrays containing 28,869 oligonucleotide probes.

overall_design: The total RNA was extracted from HEK293T transfected with pNTAP-2×flag-VRTN (3 replicates) or empty vectors (3 replicates)  and hybridized on Affymetrix microarrays.

last: Duan

first: Hui

last: Zhang

first: Zhen

first: Jun

last: Gao

first: Jie

last: Yang

first: Zhongping

last: Wu

first: Yin

last: Fan

first: Yuyun

last: Xing

first: Lin

first: Shijun

last: Xiao

last: Ren

first: Lusheng

last: Huang


title: VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development [ChIP-seq]

summary: The number of vertebrae is precisely defined in almost all vertebrate species, but varies considerably in pigs, making this animal an excellent model for studying the mechanisms that control vertebral number. Vertnin (VRTN) variants have been associated with thoracic vertebral number (TVN) in pigs. However, the causal relation between VRTN and TVN remains to be established, and the role of VRTN in modulating TVN is not yet known. Here, we demonstrate that VRTN is one of the genes responsible for determining TVN. We show that VRTN is a DNA-binding transcription factor, which is essential for the formation of thoracic vertebrae during early embryogenesis as VRTN-null mice showed embryonic lethality at the later thoracic somite stages and had fewer somites than their wild-type and heterozygous littermates. We also show that VRTN causative variants increase Notch signaling in pig embryos, suggesting that VRTN controls segment number by altering the pace of somatic segmentation. These findings advance our understanding of the role of VRTN in the formation of thoracic vertebrae and reveal new aspects of somite developmental biology.

overall_design: Examination of VRTN binding sites in HEK293T cells transfected with pNTAP-2×flag-VRTN vector.

last: Li


title: Transcriptomic analysis to identify the putative genes under the regulation of two component system BtrK/BtrR in C. acetobutylicum

city: shanghai

first: Yunpeng

address: 300， Fenglin Road

institute: Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences

summary: To identify the putative genes under the regulation of two component system BtrK/BtrR, we performed a comparative transcriptomic analysis of the BtrK/BtrR overexpressing strain and the contron strain.  Finally, we found that BtrK/BtrR was a global regulator and exerted pleiotropic regulatory role in C. acetobutylicum

overall_design: Samples for RNA extraction and microarray analysis were collected after 24 and 48 h of fermentation. From this analysis, 691 and 424 genes exhibited significantly altered transcription (fold change ≥ 2.0) after the overexpression of btrK/btrR at 24 and 48 h, respectively. Among these genes, 153 genes showed significantly different expression at both 24 and 48 h.


title: Transcriptome analysis among senescent cells induced by various stimuli

city: Minato-ku

first: Yoshikazu

last: Johmura

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

summary: We carried out the analysis using human skin fibrobllast HCA2 (MJ90) cells. Cells were indcued to be senescent cells by treatment with doxorubicin for 24 hrs, tert-butyl-hydroperoxide for 24 hrs, or serial passages as well as nultin3a + RO3306. As a result, we found simailar transcriptome signatures among senescent cells induced by various stimuli

overall_design: Examination of young and 4 types of senescent HCA2 cells induced by different stimuli.

first: Makoto

last: Nakanishi


title: VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development

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

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: Refer to individual Series


title: Chromatine immunoprecipation of atonal binding sites in Drosophila L3 eye imaginal discs

city: Paris

first: Radoslaw

middle: Kamil

last: Ejsmont

address: 8-10 rue Charles V

institute: CRI

summary: Atonal is a proneural transcription factor expressed in the Drosophila eye imaginal discs. To characterize the putative targes of Atonal in the eye discs we have used an endogenously GFP-tagged version of atonal to immunoprecipate disc samples with anti-GFP antibodies

overall_design: L3 larvae of the Ato::GFP genotype where dissected to collect the discs. The fixed sample was homogenized by sonication. A 10% of the sonicated volume was processed as input controls while the rest was Immunoprecipitated with antiGFP antibodies, purified and sequenced.

first: Natalia

last: Mora

first: Mark

last: Fiers

middle: K

first: Bassem

last: Hassan


title: MITF-low melanoma subtype models in zebrafish reveal transcriptional sub-clusters and MITF-independent residual disease

first: Jana

last: Travnickova

summary: The MITF-low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa (MITF-low) to study this biological subtype. Using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression.  We performed single cell RNA-seq (Smart-seq2) to characterise cells at the site of residual disease, and put in relation with primary tumours and recurring disease.

overall_design: We performed single cell RNAseq experiment (Smart-seq2) of zebrafish primary superficial and nodular melanomas, corresponding residual diseases and beginning of recurrence (nodular melanoma only).

first: Ava

last: Khamseh

first: E

last: Patton


title: FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University


title: Elimination of the four extracellular matrix molecules tenascin-C, tenascin-R, brevican and neurocan modifies the expression of key molecules of synapse formation and transmission

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

summary: The extracellular matrix (ECM) molecules tenascin-C (Tnc), tenascin-R (Tnr), brevican (Bcan) and neurocan (Ncan) are completely knocked out in the quadruple knockout mouse. This removal of these central ECM molecules lead to an altered gene expression in the hippocampus of postnatal day (P) 21 old quadruple knockout mice. Among others, the expression of genes involved in the process of synapse formation associated with synaptic transmission were significantly changed in the quadruple knockout hippocampus compared to the wildtype hippocampus. We found e.g. an upregulated expression of Gamma-aminobutyric acid receptor subunit theta (Gabrq), Glutamate decarboxylase (Gad2) and semaphorin 4c (Sema4c), which are known contributors at synapses. Interestingly, some extracellular molecules e.g. like glypican 3 (Gpc3), calreticulin (Calr) and three different types of collagens (Col1a2, Col4a3 and Col27a1) showed also a modified expression. These data indicate the importance of the four ECM molecules for an intact gene expression in the murine hippocampus.

overall_design: In total 6 samples were analyzed: 3 wild-type & 3 quadruple knockout (Tnc, Tnr, Bcan, Ncan)

first: A

last: Faissner

first: C

last: Gottschling

first: B


title: VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development [RNA-seq]

first: Yanyu

last: Dean

overall_design: The whole embryo mRNA profiles of  homozygous for the two QTNs (QQ) and wild type pig at 17.5-18.0 dpc were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 sequencer.

last: Duan

first: Hui

last: Zhang

first: Zhen

first: Jun

last: Gao

first: Jie

last: Yang

first: Zhongping

last: Wu

first: Yin

last: Fan

first: Yuyun

last: Xing

first: Lin

first: Shijun

last: Xiao


title: Calcitonin gene related peptide negatively regulates alarmin-driven type 2 innate lymphoid cell responses

city: Cambridge

first: Samantha

last: Riesenfeld

address: 415 Main St

institute: Broad Institute

summary: Neuroimmune interactions have emerged as critical modulators of allergic inflammation, and type 2 innate lymphoid cells (ILC2s) are an important cell type for mediating these interactions. Here, we show that ILC2s expressed both the neuropeptide CGRP (Calcitonin Gene-Related Peptide) and its receptor. CGRP potently inhibited alarmin-driven type 2 cytokine production and proliferation by lung ILC2s both in vitro and in vivo. CGRP induced marked changes in ILC2 expression programs in vivo and in vitro, attenuating alarmin-driven proliferative and effector responses. A distinct subset of ILCs scored highly for a CGRP-specific gene signature after in vivo alarmin stimulation, suggesting CGRP regulated this response. Finally, we observed increased ILC2 proliferation and type 2 cytokine production and exaggerated responses to alarmins in mice lacking the CGRP receptor. Together, these data indicate that endogenous CGRP is a critical negative regulator of ILC2 responses in vivo.

overall_design: For in vitro bulk RNA-seq experiments, there are 32 samples total, representing 2 biological replicates, each split into 2 technical replicates, of 4 conditions at 2 time points. For in vivo scRNA-seq experiments, there are 8 samples total, representing 2 biological replicates of 4 conditions at 1 time point. For in vitro ATAC-seq experiments, there are 6 samples total, representing 3 replicates of 2 conditions at 1 time point.

first: Antonia

last: Wallrapp

first: Patrick

last: Burkett

first: Se-Jin

last: Kim

first: Elena

last: Christian

first: Raja-Elie

last: Abdulnour

first: Pratiksha

last: Thakore

first: Alexandra

last: Schnell

first: Conner

last: Lambden

first: Rebecca

last: Herbst

first: Pavana

last: Khan

first: Kazutake

last: Tsujikawa

first: Isaac

last: Chiu

first: Bruce

last: Levy

first: Aviv

last: Regev

first: Vijay

last: Kuchroo


title: FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis [RNA-seq]

first: Chenjiang

last: You

summary: Plant  microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5’-3’ exonuclease genes XRN2 and XRN3, we found that a large number of 21-nt risiRNAs were generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlated with pre-rRNA processing defects in these mutants. We also show that these risiRNAs were loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.

overall_design: RNA-seq in WT, fry1-6, fry1-6 rdr6-11, and fry1-6 rdr1-1, each with 2 biological replicates


title: Expression data from human perivascular stem cell-derived extracellular vesicles (PSC-EVs) and PSCs

first: Aaron

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

summary: The vascular wall from diverse human organs is a source of mesenchymal progenitor cells that are able to induce skeletal repair, primarily by paracrine mechanisms.  To investigate these paracrine mechanisms, FACS purified human perivascular stem cells (PSC) were observed to induce mitogenic, pro-migratory, and pro-osteogenic effects on osteoprogenitor cells while in non-contact co-culture, and did so via elaboration of extracellular vesicles (EVs).  PSC-derived EVs shared mitogenic, pro-migratory, and pro-osteogenic properties of their parent cell. EVs represent a mixture of protein, lipid, and RNA that may affect cellular processes of the recipient cell. To begin to examine this, the RNA content of PSC-EVs was examined in comparison to the parent cell using total RNA sequencing.

overall_design: 6 Total samples were analyzed: 3 x PSC total RNA and 3 x Extracellular Vesicle RNA biologic replicates

first: Jiajia

last: Xu


title: Single cell transcriptome in aneuploidies reveals mechanisms of gene dosage imbalance

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

summary: Aneuploidy is a major source of gene dosage imbalance due to copy number alterations (CNA) and viable human trisomies are model disorders of altered gene expression. We studied gene and allele specific expression (ASE) of 9668 single-cell fibroblasts from T21 discordant twins and from mosaic T21, T18, T13 and T8. We examined 928 single cells with deep scRNAseq. Expected and observed overexpression of trisomic genes in trisomic vs. diploid bulk RNAseq was not detectable in trisomic vs. diploid single cells. Instead, for trisomic genes with low-to-average expression, their altered gene dosage was mainly due to the higher fraction of trisomic cells simultaneously expressing these genes, in agreement with a stochastic 2-state burst-like model of transcription. These results, confirmed in a further analysis of 8740 single fibroblasts, suggest that the specific transcriptional profile of each gene contributes to the phenotypic variability of trisomies.  We propose an improved model to understand the effects of CNA and, more generally, of gene regulation on gene dosage imbalance.

overall_design:
Single-cell RNA seq study on 9668 human fibroblasts in different Trisomies, in order to investigate gene dosage imbalance mechanisms.
This study make use of some data already published in GSE123028 (mosT18, mosT8 and most of twins) and newly produced data (mos13, mos21). the processed.data file contains the processing of all trisomies in the context of the new manuscript.  See README.txt below.

first: Geogios

last: Stamoulis

first: Marco

last: Garieri

first: Periklis

last: Makrythanassis

first: Audrey

last: Letourneau

first: Michel

last: Guipponi

first: Nikolaos

last: Panousis

first: Frédérique

last: Sloan-Béna

first: Emilie

last: Falconnet

first: Pascale

last: Ribaux

first: Christelle

last: Borel

first: Stylianos

last: Antonarakis


title: Single cell RNA-seq resolves lineage-specific activation dynamics of human blood and tissue T cells

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Human T cells coordinate adaptive immunity and persist as heterogeneous subsets in tissues and circulation, yet the impact of localization on T cell function remains unclear. Here, we profile activation of T cells from human lungs, lymph nodes (LN), bone marrow (BM) and blood following TCR/CD3 stimulation by single cell RNA-seq. Analysis of >50,000 individual resting and activated T cells using new factorization methods reveals conserved lineage-specific gene expression signatures and activation trajectories across sites. CD4 T cells exhibit a transient intermediate activation state while CD8 T cells show an “all-off/all-on” activation pattern. Lung and LN T cells exhibit tissue-specific profiles, while blood T cells closely resemble those in BM. Our results define the lineage-specific activation dynamics of human T cells from different anatomical sites.

last: Szabo

first: Hanna

last: Mendes Levitin

first: Donna

middle: L

last: Farber


title: RNASeq of Drosophila intestinal progenitor cells upon Notch knockdown or microbiome alterations

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116st and 85ave

department: MMI

institute: University of Alberta

summary: We sequenced the transcriptome of the proliferative progenitor cells of the intestine to determine how the microbiome was affecting growth in wild-type intestines and those with Notch-deficient tumors

overall_design: A total of 6 conditions and 17 samples were analyzed. For each condition, we used 3 biological replicates, except for the Gfesgts where an n=2 was used due to the loss of one sample upon RNA extraction.

first: Meghan

last: Ferguson

first: Kristina

last: Petkau

first: Minjeong

last: Shin

first: Anthony

last: Galenza

first: David

last: Fast


title: Changes in the biologica function of necroptotic, peripheral blood mononuclear cells under irradiation in vitro

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: The secretome of y-irradiated peripheral blood mononuclear cells (PBMC) is well known for its pleiotropic effects on tissue protection and regeneration. Irradiation of PBMC lead to necroptosis of a certain amount of PBMC in a cell-sorter analysis. The aim of this study was to investiage the trancriptomic changes of PBMC and PBMC subsets (CD4, CD8, CD19, CD56, CD14) in response to y-irradiation

overall_design: In total 72 samples obtained from four healthy donors were analysed (0h= cells immediately after purification, 24h_0Gy = cells cultivated for 24 hours without prior radiation; 24h_60Gy = cell cultivated for 24 hours after irradiation with 60Gy). At each time point six different cell populations were analysed (unseparated PBMC, and separated PBMC subsets: CD4, CD8, CD14; CD19; CD56).

first: Elisabeth

last: Simader

first: Lucian

last: Beer

first: Hendrik

last: Ankersmit

first: Michael

last: Mildner


title: A cluster of miRNAs regulate MYB repressors to promote anthocyanin accumulation in grapes [Degradome]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

institute: National Center for Biological Sciences

summary: MicroRNAs  are a class of endogeneously expressed non-coding small, ~21nt RNAs involved in the negative regulation of gene expression. In plants, miRNAs are known to play a critical role in developmental and metabolic pathways, as they predominantly target transcription factors. Studies in Arabidopsis and apple have shown that few microRNAs and small interfering (si) RNAs target MYB transcription factors, which are key regulators of phenylpropanoid pathway. However, it is not well-understood how miRNAs mediate regulation of MYBs to produce secondary metabolites such as anthocyanins and flavonoids. Here we show that, a cluster of abundant miRNAs target MYB transcription factors in anthocyanin rich fruits such as grapes. Using RNA-sequencing we establish that grape varieties with high anthocyanin content express abundant MYB-targeting miRNAs resulting in differential expression of MYB proteins among grape varieties, thereby regulating the phenylpropanoid pathway.

overall_design: Degradome sequencing of two cultivars of grapes with varying levels of anthocyanin.

first: Padubidri

last: Shivaprasad

first: Swetha

last: Chenna

first: Varsha

last: Tirumalai


title: Non-oncogene addiction to SIRT3 plays a critical role in lymphomagenesis

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: Diffuse large B-cell lymphomas (DLBCLs) are genetically heterogeneous and highly proliferative neoplasms derived from germinal center (GC) B-cells. Herein, we show that DLBCLs are dependent on mitochondrial lysine deacetylase SIRT3 for proliferation, survival, self-renewal, and tumor growth in vivo regardless of disease subtype and genetics. SIRT3 knockout attenuated B-cell lymphomagenesis in VavP-Bcl2 mice without affecting normal GC formation. Mechanistically, SIRT3 depletion impaired glutamine flux to the TCA cycle via glutamate dehydrogenase and reduction in acetyl-CoA pools, which in turn induce autophagy and cell death. We developed a mitochondrial-targeted Class I sirtuin inhibitor, YC8-02, that phenocopied the effects of SIRT3 depletion and killed DLBCL cells. SIRT3 is thus a metabolic non-oncogene addiction and therapeutic target for DLBCLs.

overall_design: RNAseq results of SIRT3 expression in DLBCL

first: Meng

last: Li

first: Ari

last: Melnick


title: Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage

first: Kenneth

last: Birnbaum

address: 12 Waverly Place

department: Biology Department

institute: New York Univerisity


title: Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [ChIP-Seq]

summary: Plants and plant cells exhibit extraordinary regenerative capacity, yet plant cells stably maintain their identities once acquired. Although this capacity was recognized more than 100 years ago, our mechanistic understanding of the establishment, maintenance, and erasure of cellular identities in plants remains limited. Here we develop a cell-type specific reprogramming system than can be probed at the genome-wide scale for alterations in gene expression and histone modifications before and during reprogramming. We show that the relationship between H3K27me3 and H3K4me3 and gene expression in a single cell type mirrors trends from more complex tissue, and that H3K27me3 dynamics is a critical regulator of guard cell identity. Further, guard cells can sense and resist inappropriate reprogramming, in part via regulation of the wounding response through H3K27me3. The matched single cell-type ChIP-seq and RNA-seq datasets created for this analysis also serve as a resource enabling inquiries into the dynamic and global-scale distribution of histone modifications.

overall_design: Examination of 2 different histone modifications in fully differentiated Arabidopsis guard cells and genetically reprogrammed guard cells.

first: Laura

last: Lee

first: Dominque

last: Bergmann


title: FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis [miRNA-seq]

city: Shanghai

first: Chenjiang

last: You

overall_design:
Total sRNA: WT as control, fry1-6 and fry1-8 are two alleles of FRY1 gene, and fry1-6 rdr6-11 is a paritally rescue line of fry1-6, each with 2 biological replicates.
AGO1-IP: AGO1-IP in WT, fry1-6 and fry1-6 rdr6-11, with 3, 3, and 2 biological replicates respectively. Controls are corresponding samples from total sRNA.
AGO2-IP: AGO2-IP in WT, fry1-6, fry1-6 rdr6-11, each with 2 biological replicates. Controls are corresponding samples from total sRNA.

first: Xuemei

last: Chen

first: Chenjian


title: Differential Nucleosome Spacing in Neurons and Glia [RNA-seq]

status: Public on Oct 07 2019

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: Eukaryotic chromosomes are composed of chromatin, in which regularly spaced nucleosomes containing ~147 bp of DNA are separated by linker DNA. Most eukaryotic cells have a characteristic average nucleosome spacing of ~190 bp, corresponding to a ~45 bp linker. However, cortical neurons have a shorter average spacing of ~165 bp. The significance of this atypical global chromatin organization is unclear. We have compared the chromatin structures of purified mouse dorsal root ganglia (DRG) neurons, cortical oligodendrocyte precursor cells (OPCs) and cortical astrocytes. DRG neurons have short average spacing (~165 bp), whereas OPCs (~182 bp) and astrocytes (~183 bp) have longer spacing. We measured nucleosome positions by MNase-seq and gene expression by RNA-seq. Most genes in all three cell types have a promoter chromatin organization typical of active genes: a nucleosome-depleted region at the promoter flanked by regularly spaced nucleosomes phased relative to the transcription start site. In DRG neurons, the spacing of phased nucleosomes downstream of promoters (~178 bp) is longer than expected from the genomic average, whereas phased nucleosome spacing in OPCs and astrocytes is similar to the global average (~183 bp). Thus, the atypical nucleosome spacing of neuronal chromatin does not extend to promoter-proximal regions.

overall_design: Three different mouse cell types (purified primary cultures): dorsal root ganglia (DRG) neurons, oligodendrocyte progenitor cells (OPCs) and astrocytes. Three biological replicate experiments for each.

first: Sean

last: Clark

first: Philip

first: R

last: Fields

first: David


title: RNA sequencing of blood-brain barrier cells exposed to interleukin-6

city: Oullins

first: Florian

last: SIMON

address: 165 Chemin du Grand Revoyet

institute: University Lyon 1

summary: To study the impact of inflammation on the blood-brarrier permeability we choose to expose hCMEC/D3 cells, a blood-brain barrier cell line, to interleukin-6 as an inflammatory marker.

overall_design: Examination of transcriptomic modifications after 72h interleukin-6 exposure on hCMEC/D3 cells, a blood-brain barrier model. The study was carried out in triplicate.

last: Simon


title: An RNAi Screen for Skin Morphogenesis Unravels The Complexities of Rho GTPase Networks

first: Nicholas

last: Gomez

state: New York

address: 1230 York Ave

department: Laboratory of Mammalian Cell Biology and Development

institute: Rockefeller Univeristy

summary: During embryogenesis, antagonism and synergy between developmental signaling pathways dictate cell fate decisions. How these circuits orchestrate the complex cellular remodeling needed for tissue morphogenesis remains poorly understood. As effectors of cytoskeletal dynamics, Rho GTPases and their regulators are likely to be involved. However, their daunting complexity has hindered progress in dissecting their functions. Here we overcome this hurdle by developing an unbiased, high throughput RNAi-mediated screening approach to identify physiological regulators of morphogenesis. Exploiting in utero lentiviral delivery methods to transduce embryonic mouse skin progenitors, we screened for Rho GTPases and GTPase regulators that differentially function in epidermal versus hair follicle development. Our screen unveiled hitherto unrecognized roles for specific family members in cytoskeletal remodeling events that impact these diverse morphogenetic processes, including epidermal differentiation, follicle downgrowth and planar cell polarity. Our findings underscore the power of our screening strategy for unravel the physiological significance of complex gene families.

overall_design:
Embryonic day 14.5 epidermal cell mRNA profiles from shScramble (control) and shRhou-505 transduced animals were generated by deep sequencing, in triplicate, using Illumina.
Embryonic day 17.5 epidermal cell mRNA profiles from WNT intermediate epidermal, WNT high hair follicle and WNT low hair follicle cells were generated by deep sequencing, in duplicate, using Illumina. Differential expression was determined using a matrix of all samples (WNT Hi, Wnt Low, Epidermal).

first: Melanie

last: Laurin

first: Elaine

last: Fuchs


title: Expression data from human bone marrow mesenchymal stem cells - treated with perivascular stem cell-derived extracellular vesicles control (in osteogenic medium)

city: Baltimore

first: Aaron

last: James

summary: The vascular wall from diverse human organs is a source of mesenchymal progenitor cells.  FACS purified human perivascular stem cells (PSC), identified by expression of CD146 or CD34, were observed to induce mitogenic, pro-migratory, and pro-osteogenic effects on osteoprogenitor cells via elaboration of extracellular vesicles (EV).  These EV mediated effects were dependent on surface-associated tetraspanin expression, including CD9 and CD81.  PSC derived EV stimulate bone defect repair, and do so via stimulation of skeletal progenitor cell proliferation, migration, and osteodifferentiation.  In sum, PSC-EV represent an ‘off the shelf’ alternative for bone tissue engineering and regenerative medicine.

overall_design: In this dataset, we include the expression data obtained from human BMSC treated with osteogenic medium and PBS (Control) or perivascular stem cell-derived extracellular vesicles (2.5 μg/mL) after 48 hours. There were 4 biologic replicates each, n=8 samples in total.

first: Jiajia

last: Xu


title: Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity (RNA-Seq)

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

summary: Tissue environment plays a powerful role in establishing and maintaining the distinct phenotypes of resident macrophages, but the underlying molecular mechanisms remain poorly understood.  Here, we characterized transcriptomic and epigenetic changes in repopulating liver macrophages following acute Kupffer cell depletion as a means to infer signaling pathways and transcription factors that promote Kupffer cell differentiation.  We obtain evidence that combinatorial interactions of the Notch ligand DLL4 and transforming growth factor-b (TGF-?) family ligands produced by sinusoidal endothelial cells and endogenous LXR ligands were required for the induction and maintenance of Kupffer cell identity.  DLL4 regulation of the Notch transcriptional effector RBPJ activated poised enhancers to rapidly induce LXR? and other Kupffer cell lineage-determining factors.  These factors in turn reprogrammed the repopulating liver macrophage enhancer landscape to converge on that of the original resident Kupffer cells.  Collectively, these findings provide a framework for understanding how macrophage progenitor cells acquire tissue-specific phenotypes.

overall_design:
RNA-seq for Blood Ly6C high monocytes from C57BL/6J mice; RLMs (repopulating liver macrophages) from Clec4f-Cre/DTR mice; Kupffer cells from Clec4f-Cre/DTR mice, Nr1h3 flox/flox mice, Nr1h3 flox/flox Clec4f-cre+/– mice, Smad4 flox/flox mice, or Smad4 flox/flox Clec4f-Cre+/– mice; BMDMs (bone marow-derived macrophages) from C57BL/6J mice, Smad4 flox/flox mice, or Smad4 flox/flox LysM-cre+/– mice stimulated with or without DLL4, TGF-β, DAPT, and/or DMHCA.
RNA-seq for RLMs (repopulating liver macrophages) from Clec4f-Cre/DTR mice treated with or without LY411575 or antibodies for DLL1 and DLL4; bone marrow monocytes stimulated with or without DLL4, TGF-beta, and/or desmosterol.

first: Mashito

last: Sakai

first: Ty

last: Troutman

first: Jason

middle: S

last: Seidman

first: Zhengyu

last: Ouyang

first: Nathanael

last: Spann

first: Yohei

last: Abe

first: Kaori

middle: M

last: Ego

first: Cassi

last: Bruni

first: Zihou

last: Deng

first: Johannes

last: Schlachetzki

first: Alexi

last: Nott

first: Hunter

last: Bennett

first: Jonathan

last: Chang

first: BaoChau

last: Vu

first: Martina

middle: P

last: Pasillas

first: Verena

last: Link

first: Lorane

last: Texari

first: Sven

last: Heinz

first: Bonne

last: Thompson

first: Jeffrey

middle: G

last: McDonald

first: Frederic

last: Geissmann


title: Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity (ATAC-Seq)

first: Christopher

last: Glass

summary: Tissue environment plays a powerful role in establishing and maintaining the distinct phenotypes of resident macrophages, but the underlying molecular mechanisms remain poorly understood.  Here, we characterized transcriptomic and epigenetic changes in repopulating liver macrophages following acute Kupffer cell depletion as a means to infer signaling pathways and transcription factors that promote Kupffer cell differentiation.  We obtain evidence that combinatorial interactions of the Notch ligand DLL4 and transforming growth factor-b (TGF-β) family ligands produced by sinusoidal endothelial cells and endogenous LXR ligands were required for the induction and maintenance of Kupffer cell identity.  DLL4 regulation of the Notch transcriptional effector RBPJ activated poised enhancers to rapidly induce LXRα and other Kupffer cell lineage-determining factors.  These factors in turn reprogrammed the repopulating liver macrophage enhancer landscape to converge on that of the original resident Kupffer cells.  Collectively, these findings provide a framework for understanding how macrophage progenitor cells acquire tissue-specific phenotypes.

overall_design: ATAC-seq for Blood Ly6C high monocytes from C57BL/6J mice; RLMs (repopulating liver macrophages) and Kupffer cells from Clec4f-Cre/DTR mice; Kupffer cells from Nr1h3 flox/flox mice, Nr1h3 flox/flox Clec4f-cre+/– mice, Smad4 flox/flox mice, or Smad4 flox/flox Clec4f-Cre+/– mice; BMDMs (bone marow-derived macrophages) from C57BL/6J mice stimulated with or without DLL4.

first: Mashito

last: Sakai

first: Ty

last: Troutman

first: Jason

last: Seidman

first: Zhengyu

last: Ouyang

first: Nathanael

middle: J

last: Spann


title: Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain Kupffer cell identity (ChIP-Seq)

overall_design: H3K27ac ChIP-seq for Blood Ly6C high monocytes from C57BL/6J mice; RLMs (repopulating liver macrophages) and Kupffer cells from Clec4f-Cre/DTR mice; BMDMs (bone marow-derived macrophages) from C57BL/6J mice stimulated with or without DLL4. SMAD4 ChIP-seq for Kupffer cell nuclei from Clec4f-cre mice or BMDMs from C57BL/6J mice. RBPJ ChIP-seq for Kupffer cell nuclei from Clec4f-cre mice or BMDMs from C57BL/6J mice.

first: Yohei

last: Abe

first: Kaori

last: Ego

first: Cassi

last: Bruni

first: Johannes

last: Schlachetzki

first: Alexi

last: Nott


title: Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [RNA-Seq]

first: Kenneth

last: Birnbaum

overall_design: Gene expression profiles of fully differentiated and reprogrammed Arabidopsis guard cells from 12 dpg plants.

first: Laura

last: Lee

first: Dominque

last: Bergmann


title: Common transcriptomic coding gene signature in the brain and the blood after focal brain ischemia in monkey as a tool to study neuroprotection

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

overall_design: Two monkeys (S1 and S2) were operated and sacrificed about 5:30 hours after onset of occlusion. The brain was removed after craniotomy and placed into a mold specifically designed for coronal brain slicing (cut 2 named C2 and cut 3 named C3). Blood samples were obtained at T0 before surgery but after general anesthesia, and at T1:2 H00, T2:3H30 and T3: 4H30 after MCA occlusion.

first: Estelle

last: Rousselet

first: Cyrille

last: Orset

first: Serge

last: Timsit


title: Circular RNAs,mRNAs and lncRNAs in backfat associated with porcine castration-related fat deposition

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

summary: We firstly compared the expression file of circRNAs, mRNAs and lncRNAs in backfat between the castrated and intact Huainan male pigs to identify the key circRNAs, mRNAs and lncRNAs involved in the genetic basis of castration associated fat deposition.

overall_design: The backfat from three Huainan intact pigs and three Huainan castrated pigs.

first: Liushuai

last: Hua


title: Blood transcriptional profiles discriminates cerebral and mild malaria patient living in Senegal

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary:
PBMCs were obtain from mild malaria and cerebral malaria patient at the onset of P. falciparum infection. Patient recruitment took place in two hospital centers in Senegal
Total RNAs from PBMCs of mild and cerebral malaria patients were profiled after hybridization with Agilent SurePrint G3 Human GE 8x60K Microarray to identify blood biomarkers for cerebral malaria phenotype
Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis leading to the severe form of the disease are not fully understood. Blood transcriptional profiles were investigated in patient with cerebral malaria, noncerebral malaria , and mild malaria by using the microarray technology. We identified a set of 447 genes that was differentially expressed between the three patient groups after a false discovery rate of 10%. Since the cerebral patients displayed a particular transcriptional pattern, we focused our analysis on the differences between cerebral malaria patients and mild malaria patients. We further found 849 genes differentially expressed after a false discovery rate of 10%. We validated our results by using the qPCR method for 5 genes. The enrichment analysis of their functional annotation indicates that genes involved in A, B, C pathways play a role in the occurrence of cerebral malaria. These results provide new insight into the potential effect of the dysregulation of gene expression and specific pathways. Host genetic variation may partly explain such alteration of gene expression. Further studies are required to investigate this in African populations.

overall_design: Total RNAs was extracted from PBMCs of 16 patients including 6 mild malaria and 6 cerebral malaria

first: Alassane

last: Thiam

first: Michel

last: Sanka

first: Magalie

last: Magali

first: Genevieve

last: Victorero

first: Babacar

last: Mbengue

first: Alioune

last: Dieye

first: Beatrice

last: Loriod

first: Nicolas

last: Fernandez

first: Pascal

last: Rihet

first: Gora

last: Diop

first: Rokhaya

middle: N

last: Diallo


title: Determining effects of microbial metabolite, Urolithin A on colon epithelial cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Numerous studies signify that diets rich in phytochemicals reduce the risk of inflammatory bowel diseases (IBDs). However, their effects are often not uniform among individuals, possibly due to inter-individual variation in gut microbiota. The host indigenous gut microbiota and their metabolites have emerged as factors that greatly influence the efficacy of dietary interventions. The biological activities, mechanisms of actions and the specific targets of several microbial metabolites are unknown. Urolithin A (UroA) is one such natural microbial metabolite, which showed (including our recent study) anti-carcinogenic, anti-oxidative and anti-inflammatory activities. The goal of the experiment to determine if Urolithin A blocks the genes induced by lipopolysaccharide (mimicking bacterial effects on colon) as well as determine effects of Urolithin A alone.

overall_design: Examination of the effects of Urolithin A on lipopolysaccharide (mimicking bacterial effects on colon) as well as effects of Urolithin A alone using five conditions (vehicle; Urolithin A, 25um; Urolithin A, 50uM; lipopolysaccharide; Urolithin A, 50uM + lipopolysaccharide) with three replicates per condition.

first: Venkatakrisha

last: Jala

first: Julia

last: Chariker

first: Sabine

last: Waigel


title: Transcriptional responses of human insulinoma cells to acute cytokine exposure

first: Dax

last: Fu

address: 733 N Broadway st

institute: JHU

summary:
Purpose: The goal of this study is to characterize the effects of acute cytokine stimulations on human insulinoma cells, EndoC-betaH1, at the transcriptome level.
Methods: mRNA profiles of EndoC-betaH1 cells with or without cytokine exposure were generated by deep sequencing, using Illumina Illumina HiSeq 2500.
Results: Using an optimized data analysis workflow, we mapped about 100 million (2x100bp) paired reads per sample to the human genome (build hg38) and identified about 44,000 transcripts per sample with Star/Class workflow.  Approximately 600 known genes showed differential expression between the Control and Cytokines, with a log fold change ≥1.5, at least one of the FPKM >=2 and p-value <0.05.
Conclusions: Cytokine exposure did not alter the overall transcriptome profile. All three branches of the unfold protein response (UPR) were engaged in cytokine stress with upregulations of ER chaperones, protein disulfide isomerase and key transcription factors involved in adaptive UPR signaling. Key components of the apoptotic program were largely unchanged or modestly upregulated. In contrast, genes in the ER-associated protein degradation (ERAD) pathway were sharply activated. These findings provide a framework for comparative investigations of cytokine-induced differential protein expression by quantitative proteomics.

overall_design: mRNA profiles of EndoC-betaH1 cells were generated by deep sequencing, using Illumina Illumina HiSeq 2500.

first: Chengfeng

last: Merriman


title: Expression of HPGD in regulatory T cells prevents adipose tissue inflammation and metabolic dysfunction (data set 1)

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Regulatory T cells (Treg cells) are important for the prevention of autoimmunity and lately, their role in maintaining tissue homeostasis has been demonstrated. They exert their function via different suppressive mechanisms including soluble factors. Here, we show that Treg-cell specific expression of hydroxyprostaglandin dehydrogenase (HPGD), which catabolizes prostaglandin E2 (PGE2) into 15-keto PGE2, enforces a new suppressive mode of action through accumulation of the PPAR-γ ligand 15-keto PGE2. PPAR-γ-dependent HPGD expression acts as the critical molecular link between prostaglandin metabolism, adipose tissue (AT)-associated Treg-cell function, and maintenance of AT homeostasis. In mice, loss of HPGD results in increased numbers of functionally impaired Treg cells accumulating in visceral adipose tissue resulting in increased local inflammation and systemic insulin resistance. This observation is recapitulated in humans with type 2 diabetes. These data support HPGD as a novel tissue- and context-dependent suppressor mechanism by Treg cells to maintain adipose tissue homeostasis.

overall_design: Isolation of WT (n=4) and Hpgd-deficient (n=3) Treg cells from mLN of Rag-/- mice 8 weeks after injection with WT naive T cells, WT Treg cells and either YFP+ WT or YFP+ Hpgd-deficient Treg cells

first: Lisa

last: Schmidleithner

first: Kristian

last: Händler

first: Kevin

last: Bassler

first: Thomas

last: Ulas

first: Marc

last: Beyer


title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Different genes, especially cytokines, have been deregulated in the inflammatory environment of intestinal mucosa in ulcerative colitis patients. The effects of differential gene expression such as immunological factors have been described before, however, there is no evidence of alarmins deregulated by microRNAs impacting on the pathophysiology of UC. Our goal is to study deregulated genes in inflamed mucosa for microRNA pairing in a Chilean cohort of patients.
We used microarrays to compare inflamed and non inflamed mucosa from chilean ulcerative colitis patients

overall_design: Inflamed and non inflamed human Intestinal biopsies were obtained in colonoscopy from Ulcerative Colitis patients and we performed gene expresion microarrays to analyze the molecular interaction between them and to determine possible relationships associated to the pathophysiology and clinical presentation

first: Karen

last: Dubois-Camacho

first: John

last: Cidlowski

first: David

last: Díaz-Jimenez


title: Expression of HPGD in regulatory T cells prevents adipose tissue inflammation and metabolic dysfunction

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

overall_design: Refer to individual Series


title: Systems-level analyses reveal a convergent pathway for progression of diffuse astrocytoma and potential role for resveratrol in delaying high-grade transformation

city: London

first: Liisi

last: Laaniste

address: 160 Du Cane Road

institute: Imperial College London

summary: We assembled genome-wide gene regulatory networks (“modules”) that are differentially co-expressed between grade II and grade III IDH1-mutated astrocytomas in order to identify drivers of astrocytoma progression. We prioritized module M2 as a candidate module regulating glioma transformation on the basis that the module was enriched for cancer predisposition genes and had a pattern of expression in human glioma samples associated with both clinical progression and genomic aberrations in known cancer genes. M2 was functionally enriched for genes related to cell cycle regulation, and a genome-wide reverse engineering approach predicted the known cell cycle regulators FoxM1, B-Myb, and E2F2 as key transcriptional regulators of this module. Using separate drug-induced transcriptional perturbation data, we predicted that the naturally occurring polyphenol resveratrol down-regulates multiple nodes of M2. Transcriptional modulation of M2 by resveratrol and its predicted growth inhibitory effects was experimentally confirmed in vitro using low-passage primary human astrocytoma cells, including at nanomolar concentrations of resveratrol achievable in human cerebral spinal fluid from oral dosing.

overall_design: Primary anaplastic astrocytoma cells (TB98) were treated with 20uM, 10nM and 2nM resveratrol for 24h

first: Prashant

last: Srivastava

first: Julianna

last: Stylianou

first: Nelofer

last: Syed

first: Kirill

last: Shkura

first: Qingyu

last: Zeng

first: Owen

last: Rackham

first: Sarah

last: Langley

first: Andree

last: Delahaye-Diurez

last: O'Neill

first: Matthew

last: Williams

first: Federico

last: Roncaroli

first: Enrico

last: Petretto

first: Michael

last: Johnson


title: Expression of HPGD in regulatory T cells prevents adipose tissue inflammation and metabolic dysfunction (data set 2)

first: Joachim

last: Schultze

overall_design: Isolation of Treg/Tconv cells from VAT of mice with Treg cell specific deletion of Hpgd (n=5) and WT control animals (n=4)

first: Lisa

last: Schmidleithner

first: Kristian

last: Händler

first: Kevin

last: Bassler

first: Thomas

last: Ulas

first: Marc

last: Beyer


title: Differential Nucleosome Spacing in Neurons and Glia

first: Razvan

last: Chereji

overall_design: Three different mouse cell types (purified primary cultures): dorsal root ganglia (DRG) neurons, oligodendrocyte progenitor cells (OPCs) and astrocytes. Two biological replicate experiments for each.

first: Sean

last: Clark

first: Philip

last: Lee

first: R

last: Fields

first: David


title: Sex hormones control muscle stem cells

status: Public on Oct 05 2019

city: Seoul

first: Ji Hoon

last: Kim

address: Kwanakro 1

country: South Korea

institute: Seoul national University, Seoul, Korea

summary: Quiescent adult muscle stem cells (MuSCs) regenerate skeletal muscle upon injury throughout life. However, aged skeletal muscles fail to maintain stem cell quiescence, leading to declines in MuSC number and functionality. Although autophagy plays an important role in the maintenance of MuSC quiescence, how quiescent MuSCs and their autophagy levels are maintained throughout life is largely unknown. The current study reveals how GnRH, a hypothalamic hormone, maintains the quiescence of adult MuSCs by preventing the onset of senescence and how the decline of sex steroids in organismal ageing is implicated in MuSC ageing.

overall_design: Gene expression profiling of WT and Pax7-CreER;Arf/y;Esr2–/– conditional knock out MuSCs.

first: Ji-Hoon

first: Young-Yun

last: Kong


title: Differentially expressed noncoding RNAs as potential biomarkers for DIPG diagnosis and prognosis

status: Public on Oct 04 2019

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

institute: Instituto Mexicano del Seguro Social

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

summary: The most fatal primary brainstem tumors in pediatric patients are diffuse intrinsic pontine gliomas (DIPGs). The identification of genetic alterations, such as the H3K27M mutation, allows a better molecular classification of these tumors. Therefore, the identification of new molecular features, mediating their formation and progression, as non-coding RNAs (ncRNAs), would be of great importance for the development of effective treatments.

overall_design: DIPGs transcriptome was analyzed with the HTA2.0 array and compared it with non-brain stem pediatric astrocytoma expression profiles obtained from the GEO database (GSE72269). Expression mRNA changes were validated by qPCR and physical interactions between lncRNAs and snoRNAs were bioinformatically predicted.

first: Miguel

middle: A

last: Velázquez-Flores

last: Esparza-Garrido


title: Functional characterization of the Differences Between Parotid and Submandibular Salivary Glands

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

summary: We applied both single cell and bulk RNA-sequencing to characterize and identify uniqueness in gene expression of the mouse Parotid gland compared to other tissues including the submandibular gland

overall_design: Bulk RNA-seq

first: Akinsola

last: Oyelakin

first: Christine

last: Song

first: Sangwon

last: Min

first: Jonathan

last: Bard


title: Affymetrix SNP array data for chicken samples

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

institute: China Agricultural University

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.

first: Pedro

last: Almeida

first: Yaxiong

last: Jia

first: Haigang

last: Bao

first: Zhonghua

last: Ning

first: Lujiang

last: Qu