title: RNA-Seq identifies condition-specific biological signatures of ischemia-reperfusion injury in the human kidney

city: Busan

first: Sang Heon

last: Song

state: Seo-gu

address: 179 Gudeok-ro

department: Internal Medicine

institute: Pusan National University Hospital

summary:
Purpose: Acute kidney injury (AKI) is defined as a sudden event of kidney failure or kidney damage occurring within a short period. Ischemia-reperfusion injury (IRI) is a critical factor to induce severe AKI and end-stage kidney disease in the kidney. However, biological mechanisms of ischemia and reperfusion are not well elucidated due to its complex pathophysiological processes. We aim to investigate key biological pathways affected by ischemia and by reperfusion separately at the transcriptome level.
Method: We analyzed steady-state gene expressions using RNA-seq transcriptome data for normal (pre-ischemia), ischemia and reperfusion conditions obtained from the human kidney tissue. A conventional differential expression analysis and self-organizing map (SOM) clustering analysis followed by pathway analysis were performed to identify the underlying biological mechanisms of ischemia and reperfusion.
Results: Differential expression analysis showed that metabolism and gap junction-related pathways were dysregulated in ischemia, whereas hypertrophy and immune response-related pathways were dysregulated in reperfusion. In addition, SOM clustering analysis revealed that metabolism, apoptosis, and fibrosis-related pathways were significantly dysregulated by ischemia compared to pre-ischemia. On the other hand, cell growth, migration, and immune response-related pathways were highly dysregulated by reperfusion after ischemia. Pro-apoptotic genes and death receptors were down-regulated during ischemia, indicating a protective process against ischemic injury. Reperfusion induced alteration of genes associated with immune components such as B-cell, neutrophil, and interleukin-15. Additionally, genes related to cell growth and migration such as AKT, KRAS, and Rho signaling were down-regulated, which might imply injury responses during reperfusion. Semaphorin 4D and plexin B1 were also down-regulated. However, further investigations are needed to identify their roles.
Conclusion: We showed that specific biological pathways were distinctively involved in ischemia and reperfusion during IRI, suggesting that condition-specific therapeutic strategies may be required to prevent severe kidney damage after IRI in clinical research.

overall_design: Five male patients mRNA profiles of pre-ischemia, ischemia and reperfusion conditions in human kidney were generated by deep sequencing, using Illumina Hiseq2500.

first: Sang

first: Meeyoung

last: Park

first: Chae

last: Kwon

first: Hong

last: Ha

first: Miyeun

last: Han


title: Interleukin-36y-producing macrophages drive IL-17-mediated fibrosis.

status: Public on Oct 10 2019

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 400 N Broadway

country: USA

institute: Johns Hopkins Univeristy

type: Expression profiling by high throughput sequencing

summary: Biomaterials induce an immune response and mobilization of macrophages, yet identification and phenotypic characterization of functional macrophage subsets in vivo remain limited. We performed single-cell RNA sequencing analysis on macrophages sorted from either a biologic matrix [urinary bladder matrix (UBM)] or synthetic biomaterial [polycaprolactone (PCL)]. Implantation of UBM promotes tissue repair through generation of a tissue environment characterized by a T helper 2 (Th2)/interleukin (IL)–4 immune profile, whereas PCL induces a standard foreign body response characterized by Th17/IL-17 and fibrosis. Unbiased clustering and pseudotime analysis revealed distinct macrophage subsets responsible for antigen presentation, chemoattraction, and phagocytosis, as well as a small population with expression profiles of both dendritic cells and skeletal muscle after UBM implantation. In the PCL tissue environment, we identified a CD9 hi+ IL-36y + macrophage subset that expressed Th17-associated molecules. These macrophages were virtually absent in mice lacking the IL-17 receptor, suggesting that they might be involved in IL-17–dependent immune and autoimmune responses. Identification and comparison of the unique phenotypical and functional macrophage subsets in mouse and human tissue samples suggest broad relevance of the new classification. These distinct macrophage subsets demonstrate previously unrecognized myeloid phenotypes involved in different tissue responses and provide targets for potential therapeutic modulation in tissue repair and pathology.

overall_design: Macrophages were sorted from mice quadriceps 1 week after undergoing volumetric muscle loss surgery with treatment of urinary bladder matrix, polycaprolactone, or saline. After sorting, cells were encapsulated using the 10x Chromium single cell RNA sequencing platform. Library prep followed the 10x 3’ v2 protocol and were sequenced using an Illumina HiSeq 2000. Alignment was performed using 10x recommendations with the CellRanger software package to generate a counts matrix. Clusters of cells were determined using Seurat. In particular, data from the three conditions were pooled, normalized, and scaled. PCA was performed and used for clustering with a graph based method (shared nearest neighbor with the Louvaine method for community detection).

first: Christopher

last: Cherry


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Pou4f3(Δ/+) Cochlear Transcriptomes

status: Public on Oct 22 2019

city: Nanjing

first: Guoqiang

last: Wan

address: 12 Xuefu Road

country: China

institute: Nanjing University

summary: We report application of RNA-seq for transcriptomic analyses of cochlear tissues from wildtype and DFNA15 deafness mouse model Pou4f3(Δ/+) to reveal gene expressions altered by Pou4f3 mutation

overall_design: Cochlear tissues (3 each genotype) were collected from 2 months old Pou4f3(Δ/+) mice and wildtype littermates and subjected to RNA-seq

first: Sihao

last: Gong


title: Transcriptome analysis of Brucella abortus S19∆per (a perosaminesynthetase gene mutant of strain S19)  immunized mice spleen revealed activation of MHC-I and MHC-II pathways

status: Public on Oct 09 2019

city: Bareilly

first: Khushal

middle: Singh

last: Solanki

state: Uttar Pradesh

address: Izatnagar

country: India

institute: ICAR-Indian Veterinary Research Institute

summary:
Goal: High-throughput sequencing-by-synthesis (Illumina) RNA sequencing technology was carried out with an aim to gain deeper understanding of immune host protective mechanisms. Here, RNA-seq was applied to understand the differential gene expression profile of mice spleen following immunization with Brucella abortus S19∆per mutant (perosamine synthetase gene mutant of Brucella abortus S19) in comparison to mock immunized mice spleen (PBS inoculated).
Methods: RNA-seq data of 15th day post immunized mice spleen (with Brucella abortus S19∆per) and PBS control mice were generated by deep sequencing ( in duplicate) using IlluminaNextSeq 500 . The sequence reads that passed quality filters were analyzed for transcript abundance using RSEM package (RNA-Seq by Expectation Maximization) (Li and Dewey, 2011). Breifly, the RSEM package generated a reference sequence based on given mouse transcript annotations (Mus_musculus.GrCm38.83.chr.gtf.gz). The Bowtie allignmet tool available within the package was used to calculate expected counts (number of mapped reads) using quality trimmed reads and reference sequence.   Finally, the expected counts estimated by RSEM were fed into different DE package tools, such as DESeq2 (Love et al., 2014), edgeR (Robinson et al., 2010) and EBSeq (Leng et al., 2013) in order to identify differentially expressed genes across spleen samples (B. abortus S19∆per versus (vs) PBS control. Functional annotation of  differently expressed genes were carried out using g:Profiler (Reimandet al., 2016; http://biit.cs.ut.ee/gprofiler/).
Results:  A mean of 37.58 million processed reads (range: 30.51 million to 51.79 million reads per individual RNA-seq library) were generated during the experiment. The expected counts generated by the RSEM package followed by differential analysis calculation using different DE packages identified a total of 1917 differentially expressed genes (DEGs), of which 968 and 949 genes were up- and down-regulated respectively. Functional annotation revealed 545 significantly enriched genes to be associated with immune system processes within the total 1917 differentially expressed genes. Further analysis revealed 21 genes showing significant expression were also in MHC-I and MHC-II antigen processing and presentation pathway during S19∆per immunization.
Conclusions:The RNA-seq data revealed the coordinated up-regulation of MHC-I and MHC-II processing pathways providing insights into the molecular mechanism of immune protection conferred by B. abortus S19∆per in mice at day 15 post immunization and might aid in the development of new attenuated vaccine strains with improved efficacy.

overall_design: Spleen RNA profiles of 15 day post immunized mice (Brucella abortus S19∆per) and control (not immunized) were generated by deep sequencing, in duplicate, using IlluminaNextSeq 500

middle: S

first: Ravi

middle: K

last: Gandham

first: Prasad

last: Thomas

first: Pallab

last: Chaudhuri


title: IGF-1-mediated microRNA profile in glioblastoma

status: Public on Nov 14 2019

city: Taipei

first: Ku-Chung

last: Chen

state: TAIWAN

address: No. 250, Wu-Hsing Street, Xinyi District

department: Department of Biochemistry and Molecular Cell Biology

country: Taiwan

institute: Taipei Medical University

summary: Insulin-like growth factor (IGF)-1 signaling and micro (mi)RNAs are relevant in mediating GBM progression. However, their roles in desensitizing GBM cells to TMZ are still unclear. We aimed to identify IGF-1-mediated miRNA regulatory networks that elicit TMZ insensitivity for GBM. By miRNA array analyses, totally 1,308 miRNAs were examined. The 93 upregulated and 148 downregulated miRNAs were identified in IGF-1-treated glioma cells.

overall_design: Establishment of microRNA profile between IGF-1-treated and untreated GBM U87-MG cells. U87-MG cells were treated with or without 200 ng/ml IGF-1 for 48 h. Total RNA was extracted for microRNA array analyses.

first: Peng-Hsu

first: Kuo-Hao

last: Ho


title: Genome wide analysis of transcripts regulated by PAX2 and Tamoxifen in MCF-7 cells

status: Public on Nov 06 2019

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

summary: The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using GRO-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 4 treatments (Veh, Tam, Dox, DoxTam) were performed in duplicates. After treatments, nuclei were isolated and used for nuclear run-on and subsequent GRO-seq library preparation. Libraries were sequenced and data analysis showed that PAX2 could repress estrogen target genes and induce genes enriched in cytokine (TNF-alpha and INF-gamma) related pathways. When combined with tamoxifen, PAX2 could further repress estrogen target genes to a higher degree, and induce genes enriched in p53 related pathway. Moreover, PAX2 could induce the transcription of some intergenic transcripts (potential enhancers) to activate the transcription of nearby genes with could predict good outcome in estrogen receptor positive breast cancer. Overall our finding suggests that PAX2 could benifit ER positive breast cancer by 1) repressing estrogen target genes, and this effect is enhanced by tamoxifen 2) activating cell death/growth arrest related pathways, which is enhanced by potential enhancer transcription induced by PAX2 itself.

overall_design: Transcriptome profiling of MCF-7 cells with PAX2 overexpression and in combination with tamoxifen

first: Henri

last: Niskanen

first: Minna

middle: U

last: Kaikkonen

first: Antoni

last: Hurtado


title: An atlas of single-base-resolution N6-methyl-adenine methylomes redefines RNA demethylase function as suppressors of disruptive RNA methylation

status: Public on Sep 20 2019

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

summary: Various methylases and demethylases catalyze methylation and demethylation of N6-methyladenosine (m6A) and N6,2?-O-dimethyladenosine (m6Am) but precise methylomes uniquely mediated by each methylase/demethylase are still lacking. Here, we developed m6A-Crosslinking-Exonuclease-sequencing (m6ACE-seq) to map m6A and m6Am at transcriptome-wide single-base-resolution. m6ACE-seq's ability to quantify relative differences in methylation levels across samples enabled the generation of a comprehensive atlas of distinct methylomes uniquely mediated by every individual known methylase/demethylase. We determined METTL16 to indirectly impact manifold methylation targets beyond its consensus target motif, and highlighted the importance of precision in mapping PCIF1-dependent m6Am. Rather than reverse RNA methylation, we found that both ALKBH5 and FTO demethylases instead maintain their regulated sites in an unmethylated steady-state. In FTO's absence, anomalous m6Am disrupts snRNA interaction with nuclear export machinery, potentially causing aberrant pre-mRNA splicing events. We propose a model whereby RNA demethylases ensure normal RNA metabolism by suppressing disruptive RNA methylation in the nucleus.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: UV crosslinking, immunoprecipitation and exonuclease treatment with anti-m6A antibodies was used to map m6A/m6Am in transcriptome-wide at single-base-resolution.

first: Wee


title: Bulk RNA-seq data from the dopaminergic neurons, MB output neurons, Kenyon cells, APL and DPM neurrons in adult Drosophila

status: Public on Nov 05 2019

city: Ashburn

first: Yoshinori

last: Aso

state: Virginia

address: 19700 Helix Drive

institute: Janelia Research Campus, Howard Hughes Medical Institute

summary: We analyzed transcriptome of the mushroom body cell types to identify cotransmitters of dopaminergic neurons. We found that the full-lengh splicing isoform of nitric oxide synthase (NOS1) is enriched in two types of dopaminergic neurons, and validated the results by in-situ hybridization and immunohistochemistry.

overall_design: Specific cell types were marked by split-GAL4 drivers, and sorted by hand or FACS

first: Robert

middle: P

last: Ray

first: Kshama

last: Aswath

first: Shannon

last: Ballard

first: Andrew

last: Lemire

first: Gerald

middle: M

last: Rubin


title: RNA-Seq data from iron-depletion experiments in Giardia WB

status: Public on Sep 04 2019

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: This study use rna-seq method to examin the effect of iron depletion.

overall_design: RNA from three conditions were extracted: Giardia WB cells growing in TYDK;  Cells growing in TYDK without ferric (less iron); Cells growing in TYDK without ferric and supplemented with 50 µM iron inhibitor (even less iron).

first: Jingyi

last: Liu


title: Metabolic regulation of BCAAs and glycogen via IRF4 in skeletal muscle

status: Public on Aug 30 2019

city: LOS ANGELES

first: Xingxing

last: Kong

state: CA

address: UCLA PEDIATRICS, 10833 LE CONTE AVE, CHS-MARION DAVIES CHILDREN CTR

institute: UCLA

summary: Skeletal muscle is not only a primary site for glucose uptake and storage, but also a reservoir for amino acids stored as protein. How the metabolism of these two fuels is coordinated in skeletal muscle is incompletely understood. Here, we demonstrate that interferon regulatory factor 4 (IRF4) integrate glucose and amino acids flux by regulating glycogen synthesis and branched-chain-amino acid (BCAA) metabolism in skeletal muscle. Mice with IRF4 specifically knocked out in skeletal muscle (MI4KO) showed elevated plasma BCAAs and skeletal muscle glycogen content, decreased adiposity and body weight, along with increased energy expenditure, remarkable improvements in glucose and insulin tolerance, and protection from diet-induced obesity (DIO). Loss of IRF4 caused downregulation of the mitochondrial branched-chain aminotransferase isozyme (BCATm) in myocytes, which encodes for the enzyme catalyzing the first step of BCAA metabolism. Lack of IRF4 also led to the upregulation of protein targeting to glycogen (PTG), which is associated with enhanced mitochondrial Complex II activity and mitochondria number. Additionally, overexpression of IRF4 in skeletal muscle caused obesity and reduced exercise capacity. Mechanistically, we found that IRF4 directly regulates both BCATm and PTG expression, and that overexpression of BCATm can partially reverse the effects of IRF4 deletion. These studies establish IRF4 as a novel driver of both glucose and BCAA metabolism in skeletal muscle.

overall_design: Examination of different gene expression in skeletal muscle of muscle-specific IRF4 knockout mice and muscle-specific IRF4 overexpression mice.

first: Tiemin


title: Transcriptomic analysis of the iron depletion in yeast

status: Public on Aug 21 2019

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: The goal of the project was to study the effects on transctiption and mRNA stability after iron depletion. We analyzed the effect of iron depletion caused by 100 μM of the Fe2+-specific chelator bathophenanthroline disulfonic acid (BPS) on the transcription rates, mRNA stabilities and mRNA levels by doing Genomic Run-On (GRO) experiments at 0, 10, 30, 90, 180 and 360 minutes after iron limitation.

overall_design: Cells were grown in YPD at 30ºC to 0.2 OD600. At the indicated times after BPS addition cells were spun-down and collected. Please note that each sample record represents three replicates (more details in the sample description field).

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

first: Antonia

last: Romero-Cuadrado

first: Sergi

last: Puig


title: Global gene expression of mesenchymal like lung cancer cell (TD) induced by TGFb with control (A549)

status: Public on Aug 06 2019

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Analysis of TGF-β induced mesenchymal type of lung cancer compared with control A549 lung cancer cell at gene expression level. In order to investigate the characteristics of mesenchymal like lung cancer cell, we established mesenchymal type of lung cancer cell (TD) with chronic exposure with TGF-β. After we established TD cell line, RNA-seq was performed with total RNA extracted from TD and parental A549 cells.

overall_design: Total RNA obtained from mesenchymal like lung cancer cells (TD) and control A549 cells

first: Hyuk-Jin

last: Cha


title: ATAC-seq profile of human oral epithelial cell line HIOEC

status: Public on Nov 02 2019

city: Iowa City

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To compare the features of nucleosome-free regions between human oral epithelial cells and zebrafish periderm, we performed ATAC-seq using immortalized human oral epithelial cells, HIOEC, with human embry palatal mesenchyme cells, HEPM, as control.

overall_design: HIOEC cells were maintained in culture medium supplemented with 1.2mM Ca2+ for 3 days, and then were disassociated with 0.25% trypsin-EDTA. Cultured HEPM cells were dissassociated with 0.25% trypsin-EDTA. For each replicates, 20000 HIOEC or HEPM cells were harvested for ATAC-seq library preparation. Three independent biological replicates were performed.

first: Huan

middle: A


title: Multi-omics profiling highlights lipid metabolism alterations of pigs fed with low-dose antibiotics

status: Public on Oct 31 2019

first: Yihe

middle: Anya

last: ZHANG

address: No. 7, Pengfei Road

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: Based on the gut-liver axis theory, to survey the effect of low-dose antibiotic (LDA) to hepatocellular functions of weight gain and metabolic imbalance by epigenetic transcription regulation, 32 weaned piglets were employed as the animal models and half were treated with Chlorotetracycline and Virginiamycin for four weeks. During the experiment, LDA showed an obviously growth-promoting effect, which was exemplified by the significantly elevated body weight and average daily gain. The DNA methylome profiling of promoter using liquid hybridization capture-based bisulfite sequencing (LHC-BS) indicated most of 745 differential methylation regions (DMRs) were hypermethylated in the LDA group, and some other DMRs were significantly enriched in genes related with fatty acids metabolic pathways, such as FABP1 and PCK1. Meanwhile, three key DEGs with the function of lipid metabolism and immunity were obtained by the liver strand-specific transcriptome analysis, including ALOX15, CXCL10 and NNMT, which were highly elevated for expressions in the LDA group. Correspondingly, the lipidome analyses of serum by LC-MS identified 38 significantly differential lipids, most of which were down-regulated in the LDA group. All these results suggest antibiotics could induce epigenetic and transcriptional changes of key genes related lipid metabolism pathway, and contributed to a more efficient metabolism of lipids.

overall_design: 32 samples for ssRNA-seq,8 samples for LHC-BS

first: Yue

last: Hu

last: Zhang

first: Rui

last: Qin

first: Ru

last: Wang

first: Du

first: Lianqiang

last: Che

first: Fei

last: Gao

first: Qi


title: HEK293 TFAM Knockout Methylation Study

status: Public on Jul 09 2019

first: Christina

last: Castellani

address: 733 N Broadway

department: McKusick-Nathans Department of Genetic Medicine

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array

summary: Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European Americans (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study using the Infinium Human Methylation 450K Beadchip (485,764 CpGs). Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5x10-8). To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1995). Meta-analysis across all cohorts identified 6 mtDNA-CN associated CpGs to be validated ac  ross cohorts at genome-wide significance (P<5x10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including CHD, CVD, and mortality. Experimental modification of mtDNA-CN through knockout via CRISPR-Cas9 of TFAM, a regulator of mtDNA replication, demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24x10-12), as well as the TFAM knockout methylation (P=4.41x10-4) and expression (P=4.30x10-4) studies. These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential gene expression of specific genes, including those acting in the ‘neuroactive ligand receptor interaction’ pathway that may impact human health and disease via altered cell signaling.

overall_design:
HEK293 cells with CRISPR KO were analyzed using Illumina EPIC Array
3 Biological Replicates of Negative Control Condition and 3 Biological Replicates of TFAM KO Condition

first: C

first: J

last: Sumpter

last: Newcomb

first: D

last: Arking


title: Cardiomyocyte Transcriptomes in Cardiac Development and Hypertrophy

status: Public on Jul 02 2019

city: Honolulu

first: Yiqiang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

summary: In this study, we aim to characterize the developmental and hypertrophy-specific, or in vitro myocyte dedifferentiation-specific genes by combining the current data set of transcriptomes in fetal cardiomyocytes (ECM, E15.5), normal adult cardiomyocytes (ACM) and hypertrophic cardioymocytes (hypertrophy induced by trans-aortic constriction; TAC; 7-days post-op), with our other data set (GSE49448 -- Transcriptomic and Epigenetic Signatures of Mouse Cardiac Progenitor Cells). Differential gene expression analysis was performed to generate cell type-specific genes, including the subsets of genes important for maturity (versus dedifferentiation, immature) and cell cycle control.

overall_design:
Transcriptomic analysis of cardiomyocytes from fetal, adult, and hypertrophic hearts. Total RNA was isolated from enriched cardiomyocytes. Illumina MouseRef-8 v2.0 Expression BeadChips were used to detect the expression of mRNA.
Total RNA was isolated using Qiagen Rneasy kit. cDNA library was prepared according to Illumina BeadChip protocols for gene expression analysis. Standard microarray hybridization, scanning, and data acquisition protocols were followed according to manufacture manuals (Illumina). Gene feature data were extracted from array images using GenomeStudio software (version 2.0; Illumina).

first: William

middle: R

last: MacLellan


title: HEK293 TFAM Knockout Expression Study

status: Public on Jul 10 2019

summary: HEK293 cells with CRISPR KO were analyzed using RNA-Seq. Abstract: Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European Americans (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study using the Infinium Human Methylation 450K Beadchip (485,764 CpGs). Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5x10-8). To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1995). Meta-analysis across all cohorts identified 6 mtDNA-CN associated CpGs to be validated across cohorts at genome-wide significance (P<5x10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including CHD, CVD, and mortality. Experimental modification of mtDNA-CN through knockout via CRISPR-Cas9 of TFAM, a regulator of mtDNA replication, demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24x10-12), as well as the TFAM knockout methylation (P=4.41x10-4) and expression (P=4.30x10-4) studies. These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential gene expression of specific genes, including those acting in the ‘neuroactive ligand receptor interaction’ pathway that may impact human health and disease via altered cell signaling.

overall_design: 3 Biological Replicates of Negative Control Condition and 3 Biological Replicates of TFAM KO Condition


title: Transcriptomic analysis of dj-1-/- zebrafish brains compared to wild type siblings

status: Public on Aug 02 2019

city: York

first: Gideon

last: Hughes

address: University of York, Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

summary: RNA-Seq comparing transcript expression in the brains of 3 dj-1-/- mutant zebrafish and 3 wild type siblings at 16 weeks post fertilisation.

overall_design: Brain mRNA profiles of 16 weeks post fertilisation wild type and park7(dj-1) -/- zebrafish were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000

middle: L

first: Betsy

last: Pownall

first: Katherine

last: Newling


title: Gene Expression data human HSCs with 2-LSD1 inhibitors

status: Public on Jun 15 2019

city: Lund

first: Agatheeswaran

last: Subramaniam

state: Skane Lan

address: BMC A12, 221 84 Lund, Sweden

institute: Lund universirty

summary: Human CB HSC enriched fractions were treated with LSD1 inhibitor 2-PCPA and UM171 to identify differntially regulated genes by these compounds.

overall_design: Human CB HSC enriched fractions were treated with LSD1 inhibitor 2-PCPA at 1.25µM for 24 hours and 6 day. 6  das after 2-PCPA treatment CD34 EPCR+ and CD34+EPCR-  populations were sorted for microarrray. Human CB HSC enriched fractions were treated with UM171 35nM for 6 days and CD90+ cells were sorted for microarray

first: Jonas

last: Larsson


title: Comparison of RhoE and RhoEα regulated pathways

status: Public on Jun 14 2019

city: Houston

first: Jiang

last: Chang

state: TX

address: 2121 W. Holcombe Blvd.

department: Center for Translational Cancer Research

institute: Texas A&M University Institute of Biosciences and Technology

summary: We identified a new RhoE isoform, RhoEα, and compared the differentially regulated signalings by these two proteins. Both RhoE and RhoEα were first knocked out via CRISPR/Cas9 in HEK 293 cells and HeLa cells (KO cells), followed by RhoE and RhoEα reintroduction (RhoE reintroduction cells and RhoEα reintroduction cells, resepectively). Wild-type cells, KO cells, RhoE reintrocution cells, and RhoEα reintroduction cells were then subjected to RNA-seq analysis.

overall_design: Examination of genes individually regulated by RhoE and RhoEα

first: Yuan

last: Dai

first: Wencai

last: Ma

first: Jing


title: Genome-wide DNA methylation analysis using next generation sequencing to reveal candidate genes responsible for boar taint in pigs

status: Public on Oct 01 2019

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: Boar taint (BT) is an offensive flavor observed in non-castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes (FAANG) for understanding the biology of complex traits and diseases can be used in the selection of breeding animals to achieve favorable phenotypic outcomes. The characterization of pig epigenomes/methylation changes between animals with high and low BT and genome-wide epigenetic markers that can predict BT are lacking. Reduced representation bisulfite sequencing (RRBS) of DNA methylation patterns based on next generation sequencing (NGS) is an efficient technology to identify candidate epigenetic biomarkers associated with BT. Three different BT levels were analyzed using RRBS data to calculate the methylation levels of cytosine. The co-analysis of differentially methylated cytosines (DMCs) identified by this study and differentially expressed (DE) genes identified by previous study found 32 significant co-located genes. The joint analysis of GO terms and pathways revealed that methylation and gene expression of seven candidate genes were associated with BT; in particular, FASN plays a key role in fatty acid biosynthesis, and PEMT might be involved in estrogen regulation and the development of BT. This study is the first to report the genome-wide DNA methylation profiles of BT in pigs using NGS and summarize candidate genes associated with epigenetic markers of BT, which could contribute to the understanding of functional biology of BT traits and selective breeding of pigs against BT based on epigenetic biomarkers.

overall_design: Reduced representation bisulfite sequencing (RRBS) of DNA methylation by Illumina HiSeq 2500 for testis of 9 Danish Landrace pigs with 3 groups (Low, Medium and High genetic merit) of boar taint (BT).

first: Xiao


title: Transcriptome Analysis of the Endometrium from Chinese Erhualian sows that differ in Calcium Ion Concentration and Litter Size

status: Public on May 31 2019

first: Xiang

state: Jiangsu

address: Weigang No.1

institute: Nanjing Agriculture University

summary: Embryonic survival rate is an important factor for the fecundity of sows, and it is affected by endometrium secreting histotroph. A higher concentration of calcium ion has been observed in the uterus of the high prolific Erhualian sows (EH) compared with low prolific ones (EL), which suggests EH sows had a greater establishment and maintenance of pregnancy, and thus increase embryonic survival rate during peri-implantation period. In order to understand the mechanisms of endometrium secreting histotroph affecting embryonic survival rate during Erhualian peri-implantation period, the expression patterns of endometrial mRNA in the EH and EL on day 12 of gestation were analyzed using RNA sequencing technology. 164 differentially expressed genes (DEGs) were identified (Padj < 0.05, |log2(FC)| ≥ 1)，including 46 upregulated and 118 downregulated genes in the EH group compared with EL group. Among these DEGs, 17 DEGs have been previously reported as DEGs in other pig breeds for litter size. Gene Ontology (GO) enrichment indicated that a subset of DEGs were involved in the calcium ion binding and cell adhesion. Solute carrier family 8 member A3 (SLC8A3) and solute carrier family 24 member 4 (SLC24A4) were upregulated genes (Padj < 0.05) in EH group and they were considered as key candidate genes expressed in endometrium to affect embryonic survival rate during peri-implantation period. The present results will aid in understanding the variation of litter size in Erhualian breed during peri-implantation period.

overall_design: Endomerium mRNA profiles at day 12 of gestation between high and low prolific Erhualian sows

first: Pinghua

last: Li

first: Qian

last: Zhang

first: Lichun

last: He

first: Guosheng

last: Su

last: Huang

first: Zhiqiang

last: Lu

first: Dongwei

last: Hu

first: Hangao

last: Ding

first: Ruihua


title: Whole-transcriptome microarray analysis of Pseudomonas syringae pv. actinidiae (Psa) treated with Gunpowder green tea extract (EGCG 0.4 mg/ml)

status: Public on Sep 23 2019

city: Verona

first: Elodie

last: Vandelle

state: Verona

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Purpose: Microarray technologies provide a unique opportunity to deeply investigate bacterial molecular responses to treatments. Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker of kiwifruit causing severe economic losses worldwide. At present, integrated control strategies include chemical treatments with copper-based products and preventive measures but the high virulence and fast spreading of the bacterium are hardly controlled by such measures, and especially copper use is questioned because of the possible appearance of copper resistant bacterial strains. The present project aims at the identification of Psa responses to green tea treatment (Gunpowder variety)  at sub-lethal concentration (0.4 mg/ml).   Methods: Psa cells were cultured in liquid KB (controls) or in KB supplemented with Gunpowder tea (Gunpowder-trateted) at 0.4 mg/ml EGCG for 24 h at 28°C. The microarray experiments on Gunpowder treated or untreated samples in biological triplicate resulted in 6 samples to be analyzed.  Conclusions: This work identified important molecular mechanisms involved in Psa responses upon Gunpowder green tea treatment.

overall_design: mRNA profiles of Psa cells treated 24 h with Gunpowder tea extract (0.4 mg/ml) were compared to mRNA profiles of untreated Psa cells. All mRNA profiles were generated from three biological replicates.

first: Arianna

last: Lovato

first: Annalisa

last: Pignatti

first: Nicola

last: Vitulo

last: Polverari


title: Differential expression of genes in HCMV-infected fibroblasts regulated by the purinergic receptor P2Y2.

status: Public on Oct 02 2019

city: Princeton

first: Thomas

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

summary: We studied changes in a whole transcriptome during HCMV infection.

overall_design: Fibroblasts (HFF) were infected transfected with control siRNA or P2Y2 siRNA, infected with HCMV and total RNA was isolated at 96 hpi. Total 4 individual samples were used. There were 2 replicates analyzed per individual sample.

first: M

middle: T

last: Nogalski

first: T


title: Dual role of CSL (RBP-Jk) and NOTCH1 in CAF

status: Public on Sep 11 2019

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

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

overall_design: Refer to individual Series


title: Functional identification of butanol-tolerant genes mediated by the transcriptional factor Rob in Escherichia coli

status: Public on Sep 17 2019

city: Tianjin

first: Tingli

last: Xue

address: Weijin Road No.92

institute: Tianjin University

summary: Butanol is a bulk chemical feedstock and a promising fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Transcript regulator factor Rob plays an important role in butanol-tolerant functional revealed by our previous study. In this study, the mutant strain DTrob (AT686-687 deletion in rob gene) could tolerate 1.25 %(v/v) butanol. And the per unit intracellular butanol concentration and transcriptome of wild-type and DTrob were further compared to understand the regulation mechanism of Rob for butanol tolerance. A total of 285 DEGs (differentially expression genes) were identified by bioinformatic analysis, and they may function in transport and localization according to the GO functional annotations and the functional annotation of gene product in NCBI database. Eighteen DEGs representing different functional categories were selected for real-time quantitative PCR (qPCR) for confirming the dependability of RNA-seq data. The deletion strains of glgS or yibT gene, which were down-regulated by Rob, had butanol-toleranct characteristic, indicating that the deletion or downregulated expression of the two genes down-regulated by Rob could improve the butanol tolerance. This study reveals the transcript regulator factor Rob could regulate and control the expression of the butanol tolerant genes, and its inactivation would result in an improved butanol tolerance.

overall_design: Examination of robgene point-mutated and wild-type strains

first: Yuanyuan

last: Ma


title: DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure.

status: Public on Jul 25 2019

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Coronary artery disease (CAD) and ischaemic cardiomyopathy are leading causes of mortality and morbidity worldwide. Currently there are only two well established biomarkers used for heart failure diagnosis and prognosis. Therefore, more research into the genetic and epigenetic mechanisms of heart failure (HF) will allow identification of biomarkers that can be used for different stages of HF. DNA methylation is an epigenetic mark that is increasingly recognised to play a critical role in cardiovascular disease. However, there are no methylation studies that specifically focus on ischaemic cardiomyopathy. Here we performed a small scale methylome wide association study to identify epigenetic markers in peripheral blood in a cohort of patients with and without HF who otherwise share a similar coronary ischaemic burden, age, sex, and ethnicity. We identified 68 significantly differentially methylated regions in our data. Of these regions, 48 occurred within gene bodies and 25 were located near enhancer elements, some within coding genes and some in non-coding genes. Our gene set enrichment analyses identified 103 significantly enriched gene sets in HF. We have demonstrated the utility of methyl-binding domain capture sequencing to evaluate DNA methylation markers in a perioperative cohort of cardiac surgical patients with ischaemic cardiomyopathy and HF. The peripheral methylation status of specific coding genes, such as HDAC9, are candidates for larger longitudinal studies. We have further demonstrated the value and feasibility of examining DNA methylation patterns from peripheral blood to highlight cellular pathways and processes that may contribute to the development of HF.

overall_design: Here we applied MBD-seq to perform a small scale methylome wide association study to identify epigenetic markers in peripheral blood in a cohort of patients with (n=10) and without HF (n=10) who otherwise share a similar coronary ischaemic burden, age, sex, and ethnicity.

first: Chris

last: Bain

first: Antony

last: Kaspi

first: Abdul

middle: W

last: Khan

first: Rachel

last: Taylor

first: Hugh

last: Trahair

first: Ishant

last: Khurana

first: Harikrishnan

last: KN

first: Sophie

last: Wallace

first: Assam

last: El-Osta

first: Paul

last: Myles

first: Kiymet

last: Bozaoglu


title: Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis (RNA-seq)

status: Public on May 23 2019

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

summary:
Background: Spermatogonial stem cells (SSCs) sustain the process of steady-state spermatogenesis in the mammalian testis, which is critical to the ongoing production of sperm and male fertility. SSCs can both self-renew to perpetuate the SSC population, and give rise to progenitors to propel the spermatogenic differentiation pathway. SSCs are detectable as a small subpopulation of undifferentiated spermatogonia that demonstrate regenerative capacity in a transplantation assay, and can be selectively recovered on the basis of expression of an Id4-eGfp sortable marker transgene. Enriched populations of SSCs and progenitors display consistent differences in gene expression patterns suggesting they represent discrete spermatogonial subtypes.
Results: Here we describe distinct spermatogonial subtype-specific epigenetic programming profiles associated with subtype-specific differential gene expression on the basis of genome-wide patterns of six different histone modifications, chromatin accessibility, and DNA methylation. We find that similarly expressed genes show no differences in epigenetic programming, whereas differentially expressed genes show distinct histone modification patterns as well as subtype-specific differences in patterns of distal intergenic low-methylated regions. Motif-enrichment analysis of differentially programmed elements predicts a set of transcription factors that may regulate this spermatogonial subtype-specific epigenetic programming, and gene-specific chromatin immunoprecipitation analyses confirm subtype-specific differences in binding of a subset of these factors to target genes.
Conclusions: Taken together, these results indicate that SSCs and progenitors are discrete spermatogonial subtypes that appear to be differentially programmed to carry out mutually exclusive functions including self-renewal and maintenance of regenerative capacity in SSCs and lineage commitment and loss of regenerative capacity in progenitors.

overall_design: mRNA profiles of P6 ID4-eGFP Bright and Dim mice spermatogonia were generated by deep sequencing, in triplicate.

first: Keren

last: Cheng

first: John

last: McCarrey


title: Androgen Receptor Signalling in Macrophages Promotes TREM-1 mediated Cell Migration and Invasion pluripotent and lineage-committed cells.

status: Public on May 18 2019

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

institute: Istituto Nazionale Tumori

summary: The Androgen Receptor (AR) is the master regulator of Prostate Cancer (PCa) development, and inhibition of AR signalling is the most effective PCa treatment. AR is expressed in PCa cells and also in the PCa-associated stroma, including infiltrating macrophages ). Macrophages play a decisive role in PCa initiation and progression, however, the role of AR in these cells remains largely unexplored. Here we show that AR signalling in macrophage-like THP-1 cell line supports PCa cell line migration and invasion in culture via increased Triggering REceptor of Macrophage-1 (TREM-1) signalling and expression of its downstream cytokines.

overall_design: THP-1 cells were  stimulated with 20ng/ml of PMA in hormone-deprived medium for 2 days, followed by stimulation with 10ng/ml of LPS and 10ng/ml of IFNɣ for 24 hrs. Cells were then stimulated for 4 hours with 10nM of R1881 (synthetic testosterone) or DMSO control. Then, cells were fixed for 10 minutes with 1% formaldehyde, quenched with glycine and lysed in LB1, LB2 and LB3 (Schmidt et al, 2009). Lysates were incubated with antibodies for AR or H3K27ac.

first: Bianca

last: Cioni

first: Anniek

last: Zaalberg

first: Judy

last: van Beijnum

first: Monique

last: Melis

first: Johan

last: van Burgsteden

first: Mauro

middle: J

last: Muraro

first: Erik

last: Hooijberg

first: Dennis

last: Peters

first: Ingrid

last: Hofland

first: Yoni

last: Lubeck

first: Jeroen

last: de Jong

first: Joyce

last: Sanders

first: Judith

last: Vivié

first: Henk

middle: G

last: van der Poel

first: Jan

last: de Boer

first: Arjan

last: Griffioen

first: Wilbert

last: Zwart

first: Andries

last: Bergman


title: Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis (ATAC-seq)

first: keren

last: cheng

first: Keren

last: Cheng

first: John

last: McCarrey


title: Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer

status: Public on May 07 2019

first: Hui

last: Yao

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

institute: MD Anderson Cancer Center

summary: The progression of conventional urothelial carcinoma (UC) of the bladder to a tumor with a mesenchymal phenotype, referred to as sarcomatoid carcinoma (SARC), is signified by a high propensity for regional and distant metastasis resulting in shorter survival. We report a comprehensive retrospective analysis of 28 cases of SARCs and 84 cases of conventional UCs. A TCGA cohort of 408 muscle-invasive bladder cancers was used as a reference cohort. SARCs showed a distinct mutational landscape with enrichment of p53, PIK3CA, and RB1 mutations. They developed from basal precursor conventional UCs and could be divided into a basal subtype and the most aggressive mesenchymal subtype. Expression analysis showed that SARCs are driven by dysregulation of cell cycle and EMT regulatory networks and nearly half exhibited an immune infiltration phenotype with PDL1 upregulation. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer.

overall_design: 28 cases of SARCs and 84 cases of conventional UCs (FFPE) profiled by Illumina HumanHT-12 DASL Expression BeadChips

first: Charles

middle: C

last: Guo

first: Tadeusz

last: Majewski

first: Li

last: Zhang

first: Jolanta

last: Bondaruk

first: Yan

last: Wang

first: Zhang

last: Shizhen

first: Ziqiao

first: June

last: Lee

first: Sangkyou

first: David

last: Cogdell

first: Miao

first: Peng

last: Wei

first: H

middle: B

last: Grossman

first: Ashish

last: Kamat

first: Jonathan

last: Duplisea

first: James

last: Ferguson III

first: He

last: Huang

first: Vipulkumar

last: Dadhania

first: Gao

last: Jianjun

first: Colin

last: Dinney

last: Weinstein

first: Keith

last: Baggerly

last: McConkey

first: Bogdan

last: Czerniak


title: Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis

first: keren

last: cheng


title: Identify the genes deregulated by the loss of GPS2 in adipocytes during obesity and metabolic activation (beta-adrenergic stimulation).

status: Public on May 20 2019

city: Paris

first: Nicolas

last: VENTECLEF

state: Ile de France

address: 15 rue de l’Ecole de Medecine

department: Physiology and Physiopathology

country: France

institute: Centre de Recherche des Cordeliers

summary: We report dysfunctional adipose tissue is linked to the loss of GPS2 in adipocyte.

overall_design: Transcriptome from Adipose Tissue of WT and GPS2 AKO upon normal chow diet, high fat diet and beta-adrenergic stimulation.

first: Mano

last: MATHEW


title: Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis (ChIP-seq)

overall_design: ChIP-seq of P6 ID4-eGFP Bright and Dim mice spermatogonia were generated by deep sequencing, in triplicate.

first: Keren

last: Cheng

first: John

last: McCarrey


title: Zonisamide facilitates survival of human iPS cell-derived dopaminergic neurons in the rat striatum

status: Public on Apr 26 2019

city: kyoto

first: yoshifumi

last: miyawaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

summary:
It is reported that the transplantation of dopaminergic (DA) progenitors derived from pluripotent stem cells improves the behavior of Parkinson's disease (PD) model animals. However, the number of survived DA neurons was reported to be about 10% of the transplanted cells. This low survivability limits the clinical application of this stem cell-based therapy for PD. Recently, it was reported that zonisamide (ZNS) increased the number of survived DA neurons upon the transplantation of mouse induced pluripotent stem (iPS) cell-derived DA progenitors in the mouse striatum. It is not known, however, whether ZNS exerts the same effect on human DA neurons.

We induced DA progenitors from human iPS cells and transplanted them into the rat striatum with daily administration of ZNS. The number of survived DA neurons was evaluated one and four months after transplantation by immunohistochemistry. To assess the mechanism of action of ZNS, we performed a microarray analysis to compare the gene expression profile in striatum treated with or without ZNS.

The immunofluorescense study at one and four months revealed that the number of survived DA neurons was significantly increased with the administration of ZNS. The microarray analysis revealed that the expression of Slitrk6 was up-regulated in rat striatum treated with ZNS. SLIT and NTRK like protein 6 (SLITRK6) was expressed by cholinergic neurons in the striatum. In addition, survival and neurite extension were enhanced when human iPS cell-derived DA progenitors were cultured on SLITRK6-expressing HEK293T cells.

ZNS promotes the survival of DA neurons after the transplantation of human iPS cell-derived DA progenitors in the rat striatum. SLITRK6 is suggested to be involved in this supportive effect of ZNS by modulating the environment of the host brain.

overall_design: In order to assess the indirect effect of ZNS, we performed a microarray analysis of the rat striatum with or without administration of ZNS for seven successive days.

first: Yoshifumi

last: Miyawaki

first: Bumpei

last: Samata

first: Tetsuhiro

last: Kikuchi

first: Kaneyasu

last: Nishimura

first: Jun

last: Takahashi


title: Single Cell mRNA Sequencing of Pca-associated CD14+CD11b+ macrophages

status: Public on Jun 21 2019

first: BIANCA

last: CIONI

summary:
Purpose: Androgen receptor (AR) is a crucial modulator of prostate cancer (PCa) cells behaviour, and AR expression has been found in several stromal cells, including macrophages, however its role in these cells in largely unknown. In this study, we described the molecular mechanims and the functional implications of AR activation and blockade in macrophages in relation to PCa progression.
Results: Analysis showed the transcriptomic landscape of PCa-associated macrophages
Conclusions: Our study represents the first detailed analysis of AR molecular function in Pca-associated macrophages

overall_design: Methods: Single cell mRNA sequencing has been performed on CD14+CD11b+ macrophages isolated from PCa biopsies of 3 untreated patients.


title: Single cell RNA sequencing analysis of fresh resected human lung tissue

status: Public on Apr 23 2019

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: Fresh resected human lung tissue (parenchymal lung and distal airway specimens) was obtained via the CPC BioArchive at the Comprehensive Pneumology Center Munich (CPC-M, Munich, Germany) and profiled using single cell RNA sequencing technology (Drop-seq). In total, we analysed parenchymal tissue of uninvolved areas of tumour resection material from four patients.

overall_design:
Fresh resected human lung tissue (parenchymal lung and distal airway specimens) was obtained from four patients and profiled using single cell RNA sequencing technology (Drop-seq).

Please note that raw data was removed on Oct 1, 2020 for privacy issues.

first: Herbert

last: Schiller


title: Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression

status: Public on Apr 05 2019

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: ON

address: 60 Murray Street

department: Cancer Biology

country: Canada

institute: Sinai Health System (LTRI)

summary:
Background: Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology.
Results: Using a CRISPR/Cas9-derived TET2-knockout prostate cell line, and through whole-transcriptome and whole-methylome sequencing, we identified seven candidate genes – ASB2, ETNK2, MEIS2, NRG1, NTN1, NUDT10, and SRPX – exhibiting reduced expression and increased promoter methylation, a pattern characteristic of tumor suppressors. Decreased expression of these genes significantly discriminates between recurrent and non-recurrent prostate tumors from the Cancer Genome Atlas (TCGA) cohort (n=423), and ASB2, NUDT10, and SRPX were significantly correlated with lower recurrence-free survival in patients by Kaplan-Meier analysis. ASB2, MEIS2, and SRPX also showed significantly lower expression in high-risk Gleason score 8 tumors as compared to low or intermediate risk tumors, suggesting that these genes may be particularly useful as indicators of PCa progression. Furthermore, methylation array probes in the TCGA dataset, which were proximal to the highly conserved, differentially methylated sites identified in our TET2-knockout cells, were able to significantly distinguish between matched prostate tumor and normal prostate tissues (n=50 pairs). Except ASB2, all genes exhibited significantly increased methylation at these probes, and methylation status of at least one probe for each of these genes showed association with measures of PCa progression such as recurrence, stage, or Gleason score. Since ASB2 did not have any probes within the TET2-knockout differentially methylated region, we validated ASB2 methylation in an independent series of matched tumor-normal samples (n=19) by methylation-specific qPCR, which revealed concordant and significant increases in promoter methylation within the TET2-knockout site.
Conclusions: Our study identifies seven genes governed by TET2 loss in PCa which exhibit association between their methylation and expression status and measures of PCa progression. As differential methylation profiles and TET2 expression are associated with advanced PCa, further investigation of these specialized TET2 targets may provide important insights into patterns of carcinogenic gene dysregulation.

overall_design: Methylation profiles of TET2-knockout RWPE-1 cells were generated by MBD-capture followed by high-throughput sequencing on the HiSeq 2500 (Illumina) in duplicate. Expression profiles of TET2-knockout RWPE-1 and parental RWPE-1 cells were generated by poly-A mRNA library preparation, followed by high-throughput RNA sequencing on the HiSeq 2500 (Illumina) in duplicate. Methylation profiles of parental RWPE-1 cells can be found under GEO accession number GSE74464.

first: Ruth

last: Isserlin

first: Theodorus

last: Van der Kwast

first: Alexandre

last: Zlotta

first: Gary

last: Bader

first: Neil

last: Fleshner

first: Bharati

last: Bapat


title: Role of lncRNA BC030870 in mammary gland cell proliferation

status: Public on Mar 12 2019

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

summary: We investigated an uncharacterized lncRNA, BC030870, that displays an epithelial cell-restricted expression, is downregulated by TGF-β in mammary gland cells, and controls —among others— Cdkn1a (p21WAF1/Cip1) gene expression at both transcriptional and post-transcriptional levels. BC030870 encodes a functionally active microptide (EPRp) that interacts with proteins belonging to apical junctional complexes. We hypothesized that: 1. BC030870 operates at multiple levels to orchestrate gene networks able to control cell fate, proliferation, and adhesion/migration in epithelial mammary gland cells and 2. the reduced expression of BC030870 in a group of breast cancer cells plays a role in tumor growth and invasiveness. Thus, we wanted to define the transcriptomic changes induced by BC030870 over-expression and to verify the contribution of the EPRp to gene expression changes.

overall_design: Comparison of the transcriptome changes caused by stable over-expression of either lncRNA BC030870 or a point mutant version unable to generate a small peptide.

first: Roberto

last: Gherzi

first: Gabriele

last: Bucci


title: Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote

status: Public on May 26 2019

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Chromatin conformation capture assays, such as 3C and Hi-C, allow for studies of three-dimensional (3D) genome structures in bulk samples through proximity ligation of DNA. However, the difference between cells can only be observed by single-cell measurements that avoid ensemble averaging3, 4,5. To study 3D chromatin organization and dynamics before and after fertilization in flowering plants, we analyzed the 3D genomes of rice egg, sperm, and unicellular zygote as well as shoot cells. We show that chromatin architectures of rice egg and sperm are comparable to that of somatic cells and are reorganized after fertilization in unicellular zygote. The rice single cell 3D genomes display specific features of chromosome compartments and configuration of telomeres/centromeres compared to those shown in mammalian single cells. Active and silent chromatin domains gather to form multiple foci in the nuclear space. Notably, the 3D genomes of egg, unicellular zygote, and shoot cells contain a compact silent center (CSC), which is absent in sperm. CSC is dynamically reorganized after fertilization and is likely to be involved in gene regulation related to zygotic genome activation (ZGA). Our results reveal specific 3D genome features of plant gametes and unicellular zygote and provide a spatial chromatin basis for ZGA and gene expression in plant.

overall_design: Single-cell Hi-C sequencing data of four eggs, four sperms, three unicellular zygotes, and two shoot cells

first: S

last: Zhou

first: D

middle: X


title: Microarray-predicted marker genes and molecular pathways indicating combined crowding and thermal stress in rainbow trout (Oncorhynchus mykiss)

status: Public on Apr 04 2019

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

summary: Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare of rainbow trout Oncorhynchus mykiss exposed to (A) a critical water temperature of 27 °C and (B) acute crowding of 100 kg/m3 combined with water temperature of 27 °C. In order to make an approximate assessment of the overall condition, we determined health index, spleen-somatic index and haematocrit and recorded the blood concentrations of haemoglobin, cortisol and glucose of rainbow trout under challenging versus control conditions. Moreover, we analysed the transcriptomic profiles of the spleen of the two stress-treatment and the reference groups to identify gene sets, which are specific for temperature stress alone or combined temperature and crowding stress.

overall_design:
Please see a diagram of treatments in the file Overall_design_diagram.pdf available at the foot of this record.
Spleen transcriptomes from reference fish at 16C, fish given temperature stress at 27C and fish given temperature and crowding stress and 27C.

first: Marieke

last: Verleih

first: Andreas

last: Borchel

first: Tomáš

last: Korytář

first: Tom

last: Goldammer


title: Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis (MeDIP-seq)

first: keren

last: cheng

first: Keren

last: Cheng

first: John

last: McCarrey


title: Glucocorticoid Exposure During Hippocampal Neurogenesis Primes Future Stress Response by Inducing Long-Lasting Changes in DNA Methylation [expression_acute]

status: Public on Mar 01 2019

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: Prenatal stress exposure is associated with the risk for psychiatric disorders later in life. This may be mediated via enhanced exposure to glucocorticoids (GCs), known to impact neurogenesis. We aimed to identify molecular mediators of these effects, focusing on long-lasting epigenetic changes. In a human hippocampal progenitor cell (HPC) line, we assessed the short- and long-term effects of GC exposure during neurogenesis on mRNA expression and DNA methylation (DNAm) profiles. GC exposure induced changes in DNAm at 27,812 CpG sites and in the expression of 3,857 transcripts at FDR ≤ 0.1 and an absolsute change in expression of 1.15. HPC gene expression and GC-affected DNAm profiles were enriched for changes observed during human fetal brain development. Differentially methylated sites (DMSs) with GC exposure clustered into four trajectories over HPC-differentiation, with transient as well as long-lasting DNAm changes. Lasting DMSs mapped to distinct functional pathways and were selectively enriched for poised and bivalent enhancer marks. Lasting DMSs had little correlation with lasting gene expression changes, but were associated with a significantly enhanced transcriptional response to a second acute GC challenge. A significant subset of lasting DMSs was also responsive to an acute GC-challenge in peripheral blood. These tissue-overlapping DMSs were used to compute a poly-epigenetic score that predicted exposure to conditions of excessive prenatal GC in newborn cord blood. Overall, our data suggest that early exposure to GCs can change the set point of future transcriptional responses to stress by inducing lasting DNAm changes. Such altered set points may relate to differential vulnerability to stress exposure later in life.

overall_design: The immortalized, multipotent human fetal HPC line HPC03A/07 provided by ReNeuron Ltd, UK was used. HPC03A/07 cells proliferated in the presence of growth factors (EGF, FGF) and 4-hydroxytamoxifen (4-OHT), while differentiation is initiated upon growth factor and 4-OHT removal. Cells were exposed to an additional challenge of dexamethosone (dex) for 4 hours at a lower dose (100 nM) after the Pro-diff+WO treatments (Pro-diff+WO +acute, dex n=5). To assess the effects of the acute dex challenge alone on differentiated cells, 4 hours of 100 nM dex or vehicle was applied to cells treated with only vehicle during proliferation and differentiation stages followed by 20 days of washout (veh+acute, veh n=5, dex n=5).

first: Nadine

last: Provençal

first: Elisabeth

last: Binder


title: Glucocorticoid Exposure During Hippocampal Neurogenesis Primes Future Stress Response by Inducing Long-Lasting Changes in DNA Methylation [methylation]

overall_design: The immortalized, multipotent human fetal HPC line HPC03A/07 provided by ReNeuron Ltd, UK was used. HPC03A/07 cells proliferated in the presence of growth factors (EGF, FGF) and 4-hydroxytamoxifen (4-OHT), while differentiation is initiated upon growth factor and 4-OHT removal. Cells were first treated with either 1 μM of dexamethasone (dex) or vehicle (ETOH) in four different experiments with independent replicates. Cells were treated during 3 days of proliferation (Pro, veh n=6, dex n=6) or during both proliferation and 7 days of differentiation induced by the removal of growth factors and 4-OHT (Pro-diff, veh n=7, dex n=7). Next, treatments were applied during both proliferation (3 days) and differentiation (7 days) and cells were cultured for an additional 20 days of washout without dex or vehicle (Pro-diff+WO, veh n=8, dex n=8) to assess the lasting effects of the treatment. Lastly, cells were treated after proliferation and differentiation for 10 days followed by 20 days of washout (Post+WO, veh n=9, dex n=9) to compare lasting effects between treatments applied before and after differentiation.


title: Glucocorticoid Exposure During Hippocampal Neurogenesis Primes Future Stress Response by Inducing Long-Lasting Changes in DNA Methylation [expression]

overall_design: The immortalized, multipotent human fetal HPC line HPC03A/07 provided by ReNeuron Ltd, UK was used. HPC03A/07 cells proliferated in the presence of growth factors (EGF, FGF) and 4-hydroxytamoxifen (4-OHT), while differentiation is initiated upon growth factor and 4-OHT removal. Cells were first treated with either 1 μM of dexamethasone (dex) or vehicle (ETOH) in four different experiments with independent replicates. Cells were treated during 3 days of proliferation (Pro, veh n=6, dex n=6) or during both proliferation and 7 days of differentiation induced by the removal of growth factors and 4-OHT (Pro-diff, veh n=6, dex n=6). Next, treatments were applied during both proliferation (3 days) and differentiation (7 days) and cells were cultured for an additional 20 days of washout without dex or vehicle (Pro-diff+WO, veh n=5, dex n=6) to assess the lasting effects of the treatment. Lastly, cells were treated after proliferation and differentiation for 10 days followed by 20 days of washout (Post+WO, veh n=6, dex n=6) to compare lasting effects between treatments applied before and after differentiation.


title: lncRNA and mRNA expression analysis of lung adenocarcinoma and adjacent non-tumor tissues

city: Fuzhou

first: Fei

last: He

address: No.1 Xuefubei Road

institute: Fujian Medical University

summary: Genome wide lncRNA and mRNA expression profiling of lung adenocarcinoma and non-tumor adjacent tissues. The Agilent microarray was used to obtain gene expression profiles. Samples included eight lung cancer and adjacent non-tumor tissues excised from a cohort of 8 patients with lung adenocarcinoma.

overall_design: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacture's protocol. The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading. Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray

first: He

last: Fei


title: Glucocorticoid Exposure During Hippocampal Neurogenesis Primes Future Stress Response by Inducing Long-Lasting Changes in DNA Methylation

overall_design: Refer to individual Series


title: Widespread and Functional RNA Circularization in Localized Prostate Cancer.

status: Public on Feb 07 2019

first: Housheng

middle: Hansen

state: Ontario

address: 101 College Street

institute: University of Toronto

type: Non-coding RNA profiling by high throughput sequencing


title: Genome-wide analysis of gene changes caused by chemotherapy

status: Public on May 01 2019

city: London

first: Andrew

last: Gravett

address: Cranmer Terrace

institute: SGUL

summary: The human colorectal cancer cell line HCT116 was cultured in media alone, with gemcitabine (GEM), oxaliplatin (OXP), docetaxel (DOC), Artesunate (ARS), Lenalidomide, camptothecin (CAM) or interferon-γ for 4 hours. RNA was then isolated from from the cells by Trizol.  Total RNA was labelled and hybridised to Illumina Human HT-12v3 arrays.

overall_design:
compound_treatment_design
Experimental Factor Name: COMPOUND
Experimental Factor Type: compound
Quality Control Type: # none

middle: M

first: Jayne

last: Dennis

middle: P

last: Copier

first: Angus

last: Dalgleish

first: Wai

last: Liu


title: A 5' fragment of Xist can sequester the RNA of adjacent genes on chromatin

city: Chapel Hill

first: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: Xist requires Repeat-A, a protein binding module in its first two kilobases (2kb), to repress transcription. We report that in mouse embryonic stem cells (ESCs), when expressed as a standalone transcript, the first 2kb of Xist (Xist-2kb) represses the expression of adjacent genes not at the transcriptional level, but by sequestering their mRNA on chromatin. Sequestration does not spread beyond adjacent genes, requires the same sequence elements in Repeat-A that full-length Xist requires to repress transcription, and can be induced by lncRNAs whose sequence composition is related to Xist-2kb. We did not detect local sequestration by full-length Xist, but did detect it by mutant forms of Xist with attenuated transcriptional silencing capability. SPEN and RBM15, Repeat-A binding proteins required for Xist-induced transcriptional silencing, also bound Repeat-A in Xist-2kb, but neither protein was necessary for sequestration. Thus, in mouse ESCs, expression of a 5¢ fragment of Xist that contains Repeat-A can repress gene expression by sequestering nearby mRNAs on chromatin, but it does not induce transcriptional silencing. Rather, Xist-induced transcriptional silencing requires synergy between Repeat-A and additional sequence elements in Xist. These results highlight an important gap in our understanding of the mechanisms through which Repeat-A functions within Xist. We discuss how the mechanisms that underpin sequestration may be relevant to the biology of Xist and of other lncRNAs.

overall_design: RNA-seq data compare relative gene expression and transcript subcellular localization upon expression of Xist

first: J

first: David

last: Lee


title: Neutrophils Escort Circulating Tumor Cells to Enable Cell Cycle Progression

status: Public on Feb 06 2019

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: Circulating tumor cells (CTCs) are precursors of metastasis in several cancer types, and are occasionally found within the bloodstream in association with non-malignant cells such as white blood cells (WBCs). The identity and function of these CTC-associated WBCs, as well as the molecular features that define the interaction between WBCs and CTCs are unknown. Here, we achieve the isolation and interrogation of individual CTC-associated WBCs, alongside with corresponding cancer cells within each CTC-WBC-cluster, from multiple breast cancer patients and mouse models.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA-Seq from CTCs and CTC-WBC-clusters obtained from multiple breast cancer patients and mouse models were used to identify CTC-associated WBCs cell types and differential expression between CTCs alone and CTC-associated to WBC.

first: Barbara

last: Szczerba

first: Marcus

last: Vetter

first: Sofia

last: Gkountela

first: Julia

last: Landin

first: Ilona

last: Krol

first: Cinzia

last: Donato

first: Ramona

last: Scherrer

first: Jochen

last: Singer

first: Christian

last: Beisel

last: Kurzeder

first: Walter

last: Weber

first: Christoph

last: Rochlitz

first: Viola

last: Heinzelmann-Schwarz

first: Niko

last: Beerenwinkel

first: Nicola

last: Aceto


title: Transcriptional profiling of Brucella ovis strains cultivated in the presence of high (5%) and low (0.04%) CO2

status: Public on May 04 2019

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

country: USA

institute: Michigan State University

summary: Wild-type Brucella ovis ATCC 25840 requires the addition of 5% CO2 to the atmosphere to grow on either nutrient agar plates or in liquid broth culture. The goal of this study was to measure the transcriptional response of two Brucella ovis strains under high (5%) and low (0.04%) CO2. The two strains assayed were 1) wild-type and 2) a spontaneous mutant that can be cultivated in standard atmospheric levels of CO2 (~0.04%). Wild-type B. ovis harbors a single nucleotide insertion at the 3' end of a beta carbonic anhydrase gene, bcaA, which renders it non-functional. The spontaneous mutant lost this nucleotide insertion, which restored the consensus reading frame and results in a functional BcaA protein.

overall_design: Triplicate samples of wild-type B. ovis and bcaA1 mutant strains were grown to equivalent OD and the effect of incubation in an atmosphere containing either 5% CO2 or 0.04% CO2 on transcription was measured

first: Lydia

last: Varesio

first: Aretha

last: Fiebig


title: Characterization of a novel potential peptide import system of Treponema denticola

status: Public on Jan 01 2019

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

summary: Treponema denticola is a major etiologic agent of chronic periodontitis. On the outer sheath of T. denticola, several proteins such as the major outer sheath protein were detected, and among them, a 95 kDa protein has not yet been characterized. The aim of this study was to characterize the function of this 95 kDa protein. A gene encoding this 95 kDa protein (TDE_1072) of T. denticola was inactivated by homologous recombination. We compared growth curves between the TDE_1072 mutant and wild-type strains as well as differences in gene expression by DNA microarray analysis. Differentially expressed genes identified by microarray analysis were confirmed by quantitative reverse transcription-polymerase chain reaction. The proteins encoded by TDE_1072, TDE_1073, TDE_1074, TDE_1075, and TDE_1076 shared respective similarities to the substrate-binding domain (DppA) of an ABC-type dipeptide/oligopeptide/nickel transport system, and to the permease component (DppB and DppC) and ATPase component (DppD and DppF) of an ABC-type dipeptide/oligopeptide/nickel transport system.　Inactivation of dppA attenuated the growth of T. denticola and down-regulated expression of dppB-dppF. In contrast, expression of oppB-oppF was upregulated in the mutant. Our findings indicate that TDE_1072 may be a potential periplasmic solute binding protein encoded by dppA that is involved in the organization of a peptide uptake system with dppB-dppF.

overall_design: Comparison of 2 strains of T. denticola.  Treponema denticola ATCC 35405 and I-1 was cultured in TYGVS medium for 24-48 h. Profile of gene expression of T. denticola I-1 was compared to that of ATCC 35405.

first: Tomohiro

last: Asai

first: Kazuko

last: Okamoto-Shibayama

first: Yuichiro

last: Kikuchi


title: OCT6 uniquely replaces OCT4 in inducing human pluripotency

status: Public on Jan 17 2019

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

country: China

institute: tongji university

summary: Somatic cells can be reprogrammed into pluripotent stem cells by the ectopic expression of OCT4, SOX2, KLF4, and c-MYC. Although SOX2, KLF4, and c-MYC (SKM) can be substituted by their respective family members, OCT4 is considered to not be interchangeable with any octamer-binding POU proteins. Through a screening with 102 candidate genes, here we have identified that the POU protein OCT6 (also known as SCIP, TST-1, and POU3F1), in conjunction with SKM, is capable of functionally replacing OCT4 and inducing pluripotency. OCT6-mediated reprogramming works with any human cell type, but not with mouse cells. The reprogramming process involving OCT6 is relatively inefficient and slow. This is mainly due to either inefficient formation of OCT6-SOX2 heterodimers onto canonical SOX-OCT sites or lower transactivation activity of OCT6. We demonstrate that modulating either the DNA-binding propensity or the transactivation activity of OCT6 enhances iPSC generation to the efficiency of OCT4. These results thus provide the first evidence that a POU factor other than OCT4 can induce human pluripotency.

overall_design: The TRA1-60+ cells in the two induction system at day 2, 4, 6, 8, 10, 12, and 16, which were isolated by FACS using APC anti-human CD13 (BioLegend), PE anti-human TRA-1-60 (BioLegend). The sorted TRA1-60+ cells during reprogramming were washed several times in 0.5% BSA-PBS (Sigma) solution and subsequently picked and transferred into lysate buffer by a mouth pipette with 50 cell for each tube. At least 3 replicates were set for each time point.

first: Kee-Pyo

last: Kim

first: Yawei

last: Gao

first: Chuan

last: Chen

first: Shiyang

last: Zeng

first: Shenen

last: Hu


title: Microarray of young shoot of Populus trichocarpa under abiotic stresses

status: Public on Dec 30 2018

city: Sapporo

first: Chiaki

last: Hori

state: Hokkaido

address: Kita13, Nishi8

department: Research Faculty of Engineering

institute: Hokkaido University

summary:
We identified 1251 and 1509 significantly up-regulated and down-regulated genes, respectively (FDR<0.05) by drought-treatment. In contrast, in response to salt stress, only 133 genes and 309 genes were significantly up- and down-regulated (FDR<0.05) respectively.
Of these, 55% of the up-regulated and 75% of the down-regulated genes were also identified in the drought data set.

overall_design: To explore the mechanism by which poplar cell wall responses occur, we collected microarray data for young shoot (Ys) tissue in response to drought and salinity exposure

last: Hor

first: Xiang

last: Yu

first: Ryosuke

last: Sano


title: Analysis of physiological and gene expression changes related to Vibrio harveyi adaptation in the time of global warming

status: Public on Feb 05 2019

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

institute: University of the Basque Country

summary: Vibrio species represent one of the most diverse genera of marine bacteria known for their ubiquitous presence in natural aquatic systems. Several members of this genus including Vibrio harveyi are receiving increasing attention lately because they are becoming a source of health problems, especially for some marine organisms widely used in sea food industry. To learn about adaptation changes triggered by V. harveyi during its long-term persistence at elevated temperatures, we studied adaptation of this marine bacterium in sea water microcosms at 30 oC that closely mimicks the upper limits of sea surface temperatures recorded around the globe.

overall_design: Total RNA was isolated from Vibrio harveyi ATCC 14126 cultures by triplicate. To carry out this analysis, total RNA was isolated from the initial inoculate grown in marine broth at 26ºC (control) and from V. harveyi cells after their permanence in sterile seawater at 30ºC for 12 hours, 3 and 6 days (Stress). RNA samples were submitted for sequencing. Read were aligned to Vibrio harveyi ATCC 43516 genome.

first: Itxaso

last: Montánchez

first: Elixabet

last: Ogayar

first: Anna

last: Esteve-Codin

first: Jèssica

last: Gómez Garrido

first: Maite

last: Orruño

first: Inés

last: Arana

first: Vladimir

last: Kaberdin


title: Gene expression changes in cord blood-derived ECFCs in response to in vitro senescence stimuli for the identification of novel reference genes

status: Public on Mar 27 2019

city: Belfast

first: Kiran

middle: John

last: Mcloughlin

address: Jubilee Road

department: Centre for Experimental Medicine

institute: Queen's University Belfast

summary: To identify the most suitable reference genes for ECFC senescence studies, we analysed a microarray dataset, which compared the gene expression between proliferating and senescent ECFCs. In addition to replicative senescence, the data included X-ray-induced and Etoposide-induced senescence. We used the geNorm algorithm to identify the most stable genes across all studied conditions.

overall_design: In this study, three biological replicates of cord-blood derived ECFCs were exposed to three different senescence-associated stimuli to identify the most stable mRNA transcripts for use as novel housekeeping genes in downstream rt-qPCR studies

first: Jasenka

last: Guduric-Fuchs

first: Edoardo

last: Pedrini

first: Reinhold

last: Medina


title: Gene expression profile of human primary pericytes and colorectal cancer HCT-116 cells from co-cultures or monocultures

status: Public on Dec 31 2018

city: Majadahonda

first: Laura

last: Sanz

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology

institute: Hospital Puerta de Hierro

summary: Cancer growth and metastasis are regulated to a great extent by stromal cells within the tumor microenvironment. Tumor blood vessel components (endothelial cells and mural cells) are also ubiquitous within tumors, and yet, the impact of these tumor-resident cells is scarcely understood beyond oxygen and nutrients supply. Our hypothesis is that the interaction between stromal cells and tumor cells is bidirectional: tumor cells can modulate their peripheral environment that in turn becomes more favorable to tumor growth. To test this hypothesis, we analyzed the transcriptome of human pericytes and colon cancer cells after being cocultured for 48h in comparison with the same cells in monoculture.

overall_design: Human primary pericytes and CRC cell line HCT-116 were cocultured for 48h before sorting and RNA isolation. Three complete biological replicates of heterotypic co-cultures and corresponding monocultures were set up in parallel.

first: Rocio

last: Navarro


title: Transcriptional response to PORCN inhibition using an in vitro model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)

status: Public on Dec 04 2018

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

summary: SRP136961 - PRJNA448457 - RNA-seq of response to PORCN inhibition, using ETC-159, in vitro of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).

overall_design: Drug response in an in vitro model of RNF43 mutant PDAC (HPAF-II) following 24 h and 48 h of treatment.

first: Nathan

last: Harmston

first: Babita

last: Madam

first: Enrico

last: Petretto

first: David

last: Virshup


title: Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

city: New York

first: Eleni

last: Mimitou

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Multi-modal single-cell assays provide high-resolution snapshots of complex cell populations but are mostly limited to transcriptome plus an additional modality. Here, we describe Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct sgRNA capture and to clonotype-aware multimodal phenotyping of cancer samples.

overall_design:
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq  with additional profiling of protein surface markers and sgRNAs (when present). Antibody oligo counts are listed in the ADT and HTO tables and sgRNAs counts in the GDO tables.

>>>The raw data for the samples GSM3596095, GSM3596098, GSM3596099, GSM3596100, GSM3596103, and GSM3596104 are being submitted to dbGaP due to patient privacy concerns<<<

first: Peter

last: Smibert


title: RNA-Seq with and without RNase treatment in PCa cell lines

city: Toronto

first: Housheng

last: He

summary: Standard RNA analyses using microarrays and low-coverage polyadenylation enriched RNA-Sequencing (RNA-Seq) cannot fully characterize the complexity of the cancer transcriptome. To fully elucidate the transcriptome of prostate tumours, we performed ultra-deep total RNA-Seq on 144 localized prostate tumours with long-term clinical follow up. Analysis of linear RNAs identified a transcriptomic subtype associated with the aggressive intraductal carcinoma subhistology, and a fusion gene profile that differentiates localized from metastatic prostate cancers. Analysis of back-splicing events identified widespread RNA circularization, with the average tumour expressing 7,140 distinct circular RNAs. The degree of aberrant circRNA production is correlated to disease progression in multiple clinical cohorts. Loss of function screens identified 11.3% of the screened circRNAs as essential to prostate cancer proliferation, and for 93.6% of these, their parental linear genes are not required for proliferation. Follow-up studies on circCSNK1G3 revealed its role in regulating cell cycle progression. Ultra-deep transcriptome sequencing thus provides a more comprehensive view of the linear and circular transcriptional and functional landscapes of localized prostate cancer.

overall_design: RNA-seq with rRNA depletion and random reverse transcription (RT) primer was performed with or without RNase R treatment in five PCa cell lines: LNCap, 22Rv1, V16A, PC-3 and 42D

first: Sujun

last: Chen

first: Xin

last: Xu

first: Fraser

last: Sores

last: Hansen He


title: Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer [RT-PCR]

status: Public on Mar 14 2019

city: Houston

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

summary: The progression of conventional urothelial carcinoma (UC) of the bladder to a tumor with a mesenchymal phenotype, referred to as sarcomatoid carcinoma (SARC), is signified by a high propensity for regional and distant metastasis resulting in shorter survival. We report a comprehensive retrospective analysis of 28 cases of SARCs and 84 cases of conventional UCs. A TCGA cohort of 408 muscle-invasive bladder cancers was used as a reference cohort. SARCs showed a distinct mutational landscape with enrichment of p53, PIK3CA, and RB1 mutations. They developed from basal precursor conventional UCs and could be divided into a basal subtype and the most aggressive mesenchymal subtype. Expression analysis showed that SARCs are driven by dysregulation of cell cycle and EMT regulatory networks and nearly half exhibited an immune infiltration phenotype with PDL1 upregulation. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer.

overall_design: 52 cases of SARCs and 80 cases of conventional UCs profiled using TaqMan® Array Human MicroRNA A Card v2.0, which contains 384 TaqMan® MicroRNA Assays enabling accurate quantitation of 377 human microRNAs.

first: Charles

last: Guo

first: Tadeusz

last: Majewski

first: Li

last: Zhang

first: Hui

last: Yao

first: Jolanta

last: Bondaruk

first: Yan

last: Wang

first: Zhang

last: Shizhen

first: Ziqiao

first: June

last: Lee

first: Sangkyou

first: Miao

first: Peng

last: Wei

first: H

last: Grossman

first: Ashish

last: Kamat

first: Jonathan

last: Duplisea

first: James

middle: E

last: Ferguson III

first: He

last: Huang

first: Vipulkumar

last: Dadhania

first: Gao

last: Jianjun

first: Colin

last: Dinney

first: John

last: Weinstein

first: Keith

last: Baggerly

last: McConkey

first: Bogdan

last: Czerniak


title: A Persistence Detector for Metabolic Network Rewiring in an Animal

status: Public on Dec 08 2018

city: Worcester

first: Amy

last: Holdorf

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

institute: Univesity of Massachusetts Medical School

summary: Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental inputs. Caenorhabditis elegans has two breakdown pathways for the short-chain fatty acid propionate: a canonical, vitamin B12-dependent pathway and a propionate-shunt that is used when vitamin B12 levels are low. The shunt pathway is kept off when there is sufficient flux through the canonical pathway, likely to avoid generating shunt-specific toxic intermediates. Here, we discover a transcriptional regulatory circuit that activates shunt gene expression upon propionate buildup. The nuclear hormone receptors NHR-10 and NHR-68 function together as a ‘persistence detector’ in a type 1, coherent feed-forward loop with an AND-logic gate to delay shunt activation upon propionate accumulation, and to avoid spurious shunt activation in response to a non-sustained pulse of propionate. Together, our findings identify the first persistence detector in an animal, which transcriptionally rewires propionate metabolism to maintain homeostasis.

overall_design: C. elegans RNA-sequencing in wild type, nhr-10 deletion, or nhr-68 deletion animals treated with nothing, 20 nM vitamin B12, or 20 nM vitamin B12 and 40 mM propionate for 48 hours in duplicate.

first: Jote

last: Bulcha

first: Albertha

last: Walhout


title: The effect of circadian rhythm on gene expression in human skin

status: Public on Nov 13 2018

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of human epidermal samples collected in a time-ordered fashion. We also determined whether this circadian patterning could be applied to unordered (i.e., randomly collected) human epidermal samples. The purpose of this study was to gain insight into the evolutionarily-conserved rhythmic patterns of the circadian transcriptome in human skin and how it relates to published transcriptomes from other human tissues.

overall_design: For the time-ordered data,  2mm punch biopsies from the forearm were collected from 20 healthy male subjects over the course of 24 hours (12pm, 6pm, 12am, and 6am the following day). As controls, saliva samples were also collected every 3 hours to measure fluctuations in known circadian oscillators. For the unordered data, single 4mm punch biopsies were collected from the forearms of 152 Caucasian and 67 African-American healthy female subjects  All biopsy samples were subjected to laser capure microdissection to isolate the epidermal compartments for subsequent gene expression profiling using Affymetrix U219 array plates.

first: Kevin

last: Mills

last: Oblong

last: Hogenesch


title: Transcriptional response to PORCN inhibition using an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)

first: NATHAN

last: HARMSTON

summary: Timecourse RNA-seq of response to PORCN inhibition, using ETC-159, in an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).

overall_design: Timecourse to investigate drug response in an orthotopic model of RNF43 mutant PDAC. RNA-seq performed at multiple timepoints (0 hrs, 3 hrs, 8 hrs, 16 hrs, 32 hrs, 56 hrs and 7 days)

first: Nathan

last: Harmston

first: Babita

last: Madam

first: Enrico

last: Petretto

first: David

last: Virshup


title: Genome-wide expression profiling of Candida albicans transcription factor Crz2p

status: Public on Nov 20 2018

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

summary: Candida albicans is part of the human gastrointestinal (GI) microbiota. To better understand how C. albicans efficiently establishes GI colonisation, we competitively challenged growth of 572 signature-tagged strains (~10% genome coverage), each conditionally overexpressing a single gene, in the murine gut. We identified CRZ2, a transcription factor whose overexpression and deletion respectively increased and decreased early GI colonisation. Using clues from genome-wide expression and gene-set enrichment analyses, we found that the optimal activity of Crz2p occurs under hypoxia at 37°C, as evidenced by both phenotypic and transcriptomic analyses following CRZ2 genetic perturbation. Consistent with early colonisation of the GI tract, we show that CRZ2 overexpression confers resistance to acidic pH and bile salts, suggesting an adaptation to the upper sections of the gut. Genome-wide location analyses revealed that Crz2p directly modulates the expression of many mannosyltransferase- and cell-wall protein-encoding genes, suggesting a link with cell-wall function. We show that CRZ2 overexpression alters cell-wall phosphomannan abundance and increases sensitivity to tunicamycin, suggesting a role in protein glycosylation. Our study reflects the powerful use of gene overexpression as a complementary approach to gene deletion to identify relevant biological pathways involved in C. albicans interaction with the host environment.

overall_design:
Two-condition experiments:
1) Samples 1-6: Comparison of Candida albicans TETp-CRZ2 strain treated (+Dox, Cy5-labeled) or untreated (-Dox, Cy3-labeled) with 40 µg/mL of doxycyline during 2h and 4h in Yeast Peptone Dextrose medium, 30ºC, 3 biological replicates for each time-point.
2) Samples 7-12: Comparison of a Candida albicans wild-type strain (Cy3-labeled) to a crz2-/- mutant (Cy5-labeled) grown under normoxia at 30ºC (standard lab growth conditions, Samples 7-9) or under hypoxia at 37ºC (BBL GasPak anaerobic jar in an incubator at 37ºC, Samples 10-12).
3) Samples 13-18: Comparison of Normoxia 30ºC-grown (Norm30C, Cy3-labeled) wild-type or crz2-/- mutant strains to hypoxia 37ºC-grown (Hyp37C, Cy5-labeled) wild-type (Samples 13-15) or crz2-/- mutant (Samples 16-18) strains, respectively.
4) Samples 19-22: Comparison of Candida albicans TETp-only (empty vector) strain treated (+Dox, Cy5-labeled) or untreated (-Dox, Cy3-labeled) with 40 µg/mL of doxycyline during 4h in Yeast Peptone Dextrose medium, 30ºC, 4 biological replicates.

last: Znaidi


title: Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Insights into the role of immunomodulation of ZIKV-infected UCMSC by using transcriptomic analysis.

status: Public on Nov 06 2018

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

institute: Korea Univ.

summary: RNA profiles of UCMSC infected with various ZIKV strains were generated by High-throughput sequencing using Illumina Hi-seq 2500

overall_design: Investigation of host immunesuppression effect differences in response to infection with ZIKV two strains.

first: Ok

middle: S

first: Rak-Kyun

last: Seong


title: The SOG1 transcriptional activator and the MYB3R repressors control a complex gene network in response to DNA damage in Arabidopsis

status: Public on Nov 15 2018

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies