title: Temporal Transcriptomic Landscape of Interorgan Crosstalk between Islets and Liver in High-fat Diet Model

status: Public on Jun 26 2020

first: Rui

last: Gao

address: Old Road

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

institute: Churchill Hospital

summary:
Purpose: Hyperinsulinemia and insulin resistance are co-existing characteristics of type 2 diabetes, whereas the forerunner initiating the deleterious cycle remains elusive. The temporal transcriptomic landscape of islets (responsible for hyperinsulinemia) and liver (involved in insulin resistance) could provide new insights.
Methods: C57BL/6N mice were fed a 60% high-fat diet (HFD) or control diet (CD) for 24 weeks. RNA-sequencing of islet and liver samples were respectively performed in quadruplicates at six consecutive time points of diet treatments (week 4, 8, 12, 16, 20 and 24), using BGISEQ-500 sequencing platform by the Beijing Genomics Institute (Shenzhen, China).The sequencing raw reads were filtered for low-quality, adaptor-polluted, high content of unknown base reads by SOAPnuke (v1.5.2). We used Trinity (v2.0.6) to perform de novo assembly, and Tgicl (v2.0.6) on cluster transcripts to remove redundancy and get unigenes. The high-quality clean reads were then mapped to the mouse reference genome (GRCm38) via HISAT2 (v2.0.4) and full-length transcriptome database via Bowtie2 (v2.2.5). The gene expression levels were then quantified by RSEM (v1.1.12) and were normalized by the method of fragments per kilobase of exon model per million reads mapped (FPKM). To interpret the functional significance of differentially expressed genes (DEGs), pathway analyses was conducted to determine enriched canonical pathways.
Results: Combined analyses of all 96 samples yielded the identification of 21990 annotated genes. Differentially expressed genes (DEGs) between the two groups (HFD vs. CD) at each time point were identified using the criteria of fold change ≥2 and adjusted P-value ≤0.05. In total, 3844 DEGs were found in islets, of which 33 were shared among all six time points. With regard to liver, 4101 DEGs were discovered throughout 24 weeks of feeding, of which 39 were overlapped. Our islet and liver RNA-sequencing datasets outlined the impact of HFD on dynamics of molecular network at different stages. Correlation analyses of islet and liver modules with metabolic phenotypes illustrated that these two tissues jointly program β-cell adaption to irreversible impairment. Top scored networks combining islet and liver transcriptomes showed potential interactions of genes implicated in cell cycle during week 4, organismal development around week 12, and immune cell trafficking at week 24.
Conclusions: Our data provide a comprehensive landscape of crosstalk between islets and liver in diet-induced diabetes, linking to the development of islet dysfunction and insulin resistance.

overall_design: Islet and liver mRNA profiles of C57BL/6N mice fed a 60% HFD or CD for 24 weeks (including 48 islets samples and 48 liver samples, quadruplicates for each group and each time point)

first: Qi

last: Fu

first: Quan

last: Zhang

first: Tao

last: Yang


title: Intratumoral CD4+ T cells mediate anti-tumor cytotoxicity in human bladder cancer

status: Public on Jun 01 2020

city: San Francisco

first: David

last: Oh

state: CA

address: 513 Parnassus Ave, HSE301, Box 0519

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: Responses to anti-PD-1 immunotherapy occur but are infrequent in bladder cancer. The specific T cells that mediate tumor rejection are unknown. T cells from human bladder tumors and non-malignant tissue were assessed with single-cell RNA and paired T cell receptor (TCR) sequencing of 30,604 T cells from 7 patients. We find that the states and repertoire of CD8+ T cells are not altered in tumors compared with non-malignant tissues. In contrast, single-cell analysis of CD4+ T cells demonstrates several tumor-specific states, including multiple distinct states of regulatory T cells. Surprisingly, we also find multiple cytotoxic CD4+ T cell states that are clonally expanded. These CD4+ T cells can kill autologous tumor in an MHC class II-dependent fashion and are suppressed by regulatory T cells. Further, a gene signature of cytotoxic CD4+ T cells in tumors predicts a clinical response in 244 metastatic bladder cancer patients treated with anti-PD-L1.

overall_design: Fresh bladder tumors and adjacent normal bladder tissue were obtained from surgical resection (cystectomy). These were treated before surgery with anti-PD-L1 therapy, chemotherapy, or no systemic therapy. Fresh tissues were digested to single cells and subjected to droplet-based single-cell RNA sequencing (scRNA-seq, 10X Genomics). Libraries for T cell receptor (TCR sequencing) were generated using consensus TCR primers from the full-length cDNA generated during 10X Genomics RNAseq library preparation.

middle: Y

first: Lawrence

last: Fong


title: Multi-omic analysis provide insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600

status: Public on May 22 2020

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Background: Wood-decay basidiomycetes are effective for the degradation of highly lignified and recalcitrant substrates. Brown-rot strain produces carbohydrate-active enzymes involved in the degradation of lignocellulosic materials, along with a non-enzymatic mechanism, via Fenton reaction. Differences in the lignocellulose metabolism occurring even among closely related brown-rots are not completely understood, bringing attention to a multi-omics study of brown-rot L. sulphureus.  Results: To evidence the oxidative-hydrolytic mechanism, the Laetiporus sulphureus ATCC 52600 genome was sequenced and the response to lignocellulosic substrates was analyzed by transcriptomics and proteomics. The transcriptomic profile in response to a short cultivation period on in natura sugarcane bagasse revealed 128 out of 12,802 upregulated transcripts. The high upregulated transcripts included a set of redox enzymes along with hemicellulases. The exoproteome in response to extended-time cultivation with Avicel, and steam-exploded sugarcane bagasse, sugarcane straw, and Eucalyptus grandis revealed 121 proteins. Contrasting to the mainly oxidative profile observed in the transcriptome, the secretomes showed a diverse hydrolytic repertoire including constitutive cellulases and hemicellulases, in addition to 19 proteins upregulated relative to glucose. The secretome produced on sugarcane bagasse was evaluated in the saccharification of pretreated sugarcane straw by supplementing a commercial cocktail. Additionally, growth analysis revealed that L. sulphureus ATCC 52600 has higher efficiency to assimilate glucose than other mono and disaccharides.  Conclusion: This study shows the singularity of L. sulphureus ATCC 52600 relative to other Polyporales brown-rots, regarding the presence of cellobiohydrolase and peroxidase class II. The multi-omic analysis reinforces the oxidative-hydrolytic metabolism involved in lignocellulose deconstruction, providing insights into the overall mechanisms as well as specific proteins of each step.

overall_design: Pre-inoculum, consisting of 15 discs (8 mm diameter) of L. sulphureus ATCC 52600 pre-cultivated on agar plates, was inoculated into 100 mL of liquid medium and incubated under 180 rpm for 7 days at 30 °C. Mycelia were then filtered and washed with water and then transferred to liquid medium containing 1.0 g of in natura sugarcane bagasse and 100 mL of medium pH 7.0 composed of 6 g/L (NH4)2SO4, 1 g/L KH2PO4, 1 g/L KCl and 1 g/L MgSO4. Cultivation was performed under 180 rpm for 24 h at 30 °C. Mycelia and substrate mixtures were collected by filtration, washed with sterile water, manually dried in filter paper, and stored at -80 °C before RNA extraction. Mycelium from pre-inoculum was used as a reference before induction (T0).Three biological replicates of L. sulphureus were used for RNAseq analysis.

first: Ana

middle: P

last: Oliveira

first: Fernanda

middle: L

last: Figueiredo

first: Thiago

middle: A

last: Gonçalves

first: Cesar

last: Terrasan

first: Geizecler

last: Tomazetto

first: Marcelo

middle: V

last: Rubio

first: Jaqueline

last: Gerhardt

first: Maria

middle: C

last: Silvello

first: Rosana

last: Goldbeck

first: Fabio

middle: M

last: Squina

first: André

middle: R

last: Damasio


title: Microarray  Sequencing Analysis of microglia from Wild Type and AIM2-/-  mice with EAE

status: Public on Jun 03 2020

city: Nanjing

first: Chunmei

last: Ma

address: 101 Longmian road,Nanjing

country: China

institute: Nanjing medical university

summary:
We identified that AIM2 protected against MOG-induced EAE, and AIM2 deficiency in microglia promoted the development of EAE.
The purpose of this experiment was to identify how AIM2 protected against MOG-induced EAE.

overall_design: Microglia mRNA profiles of wild type (WT) and AIM2-/- mice with EAE were generated by microarray

first: Shuo


title: A Distinct Role for GLUT3 in Glioblastoma Invasion

status: Public on Jul 01 2020

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

summary: In a study of GLUT1 and GLUT3, we used RNA-sequencing to assess the affects of GLUT1 and GLUT3 knockdown in the D456 glioblastoma cell line.

overall_design: RNA-sequencing after overexpression of GLUT1 and GLUT3 in D456 neuroblastoma cell lines

middle: J

first: Anita

middle: B

last: Hjelmeland


title: Gene expression variability in human and chimpanzee populations share common determinants

status: Public on May 29 2020

city: Chicago

first: Benjamin

middle: Jung

last: Fair

state: IL

address: 920 E. 58th Street, CLSC 317

department: Section of Genetic Medicine

institute: University of Chicago

summary: Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative expression quantitative trait loci (eQTL) mapping study in humans and chimpanzees, using gene expression data from primary heart samples. While expression variability in both species is strongly determined by non-genetic sources, such as cell type heterogeneity, we found evidence that the degree of inter-individual variation in gene regulation is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of genes associated with eQTLs in the two species. We conclude that humans and chimpanzees share sources common determinants of gene expression variability, including genetically regulated constraints from stabilizing and diversifying selection pressures.

overall_design: 38 chimpanzee primary heart tissues samples subjected to RNA-seq. One replicate per individual. Analyzed in conjunction with previously published human primary heart tissue RNA-seq samples and chimpanzee samples in (Pavlovic et al. 2018 [PMID 30333510]). Only the 38 novel chimpanzee samples are included as raw data with this GEO project. Processed data also include a chimpanzee sample ("4x373") from which raw data was sourced from Pavlovic et al 2018 (GEO accession GSE110471)

first: B

first: L

middle: E

last: Blake

first: C

last: Chavarria

first: A

last: Sarkar

last: Pavlovic

first: Y

last: Gilad Y


title: Transcriptional analysis of early and late generation nuclear RNAi deficient animals

city: Chapel Hill

first: Shawn

last: Ahmed

state: North Carolina

address: 216 Fordham Hall, 133 Medical Drive

institute: UNC Genetics Department

summary: Germ cells deficient for Piwi and associated small RNA genome silencing factors transmit a form of heritable stress that induces sterility after growth for several generations. The cause of this transgenerational sterility phenotype is not understood but has been attributed to progressive deterioration of heterochromatin and associated DNA damage. Sterile small RNA genome silencing mutants displayed inconsistent increases in DNA damage signaling but consistently altered perinuclear germ granules. Germ granule dysfunction was sufficient to induce phenotypes associated with sterile small RNA genome silencing mutants, including germline atrophy, reproductive diapause and univalents in oocytes. Genes that perturb germ granule structure were not compromised in sterile small RNA mutants, suggesting a post-transcriptional reproductive arrest mechanism. We conclude that the integrity of germ granules, which are intimately associated with Piwi silencing factors, orchestrates the sterility of Piwi deficient mutants and could be generally relevant to regulation of reproductive arrest in response to stress.

overall_design: Sequencing of ribosome-depleted total RNA from wild-type, nrde-1, nrde-2 and nrde-4 L4 worms.

first: S

last: Frenk


title: Gene expression profiles in BV2 cells with or without PGC-1α overexpression after LPS stimulation

status: Public on Jun 19 2020

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: PGC-1α overexpression in microglia protects against ischemia-induced brain damage in mice. To investigate the underlying mechanism of PGC-1α in vitro, we have employed whole mRNA microarray expression profiling as a discovery platform to identify genes with the potential to change the BV2 cells function. Indeed,  PGC-1α overexpression alters the gene expression profiles of BV2 cells, this revealed that PGC-1α could inhibit the production of IL-1β and pro-inflammatory cytokines.

overall_design: BV2 cells with or without PGC-1α overexpression were treated with LPS, then the samples were processed to perform microarray analysis.

first: Junwei

last: Hao


title: Muscle transcriptome analysis identifies genes involved in ciliogenesis and in the molecular cascade associated with intramuscular fat content in Large White heavy pigs.

status: Public on May 28 2020

city: Bologna

first: Martina

last: Zappaterra

address: viale Fanin 46

department: Department of Agricultural and Food Science

country: Italy

institute: University of Bologna

summary: Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analysing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs in order to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 ± 0.09% in low IMF vs. 6.81 ± 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analysed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and in G-protein and ERK signalling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes comprised in the significant modules confirmed the results obtained for the DEGs, and the analysis with CytoHubba indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation.

overall_design: Illumina RNAs sequencing for mRNAs discovery, quantification, characterisation, and differential expression evaluation on 12 RNA samples collected from Italian Large White pigs.

first: Silvia

last: Gioiosa

first: Giovanni

last: Chillemi

first: Paolo

last: Zambonelli

first: Roberta

last: Davoli


title: Single-cell RNA-sequencing of adult mouse urethra

status: Public on May 19 2020

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

summary: Single-cell RNA-sequencing was conducted on heterogeneous mouse urethra on the 10x Genomics platform.

overall_design: Fresh mouse urethral specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.

first: Douglas

middle: W

last: Strand

middle: H


title: Single-cell RNA-sequencing of adult human prostates from BPH patients

summary: Single-cell RNA-sequencing was conducted on heterogeneous human prostates FACS sorted for viability from BPH patients on the 10x Genomics platform.

overall_design: Fresh human prostate specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.


title: Meiotic double-strand break mapping in spo11 mutants by S1Seq

status: Public on May 12 2020

city: New York

first: Sam

last: Tischfield

state: NY

address: 1275 York Ave

department: Center for Molecular Oncology

institute: Memorial Sloan-Kettering Cancer Center

summary: The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are non-randomly distributed across the genome. Here, we use S1Seq mapping to map the distribution of meiotic DSBs in spo11 mutant strains of Saccharomyces cerevisiae.

overall_design: 4 samples total: two biological replicate Spo11-oligo maps of S. cerevisiae spo11-F260A and wildtype

first: Eleni

last: Mimitou

first: Scott

last: Keeney


title: Exploration of fine root gene expression relating to root pressure magnitude in Sorghum bicolor

status: Public on Jun 10 2020

city: Fort Collins, CO

first: Sarah

middle: Tepler

last: Drobnitch

state: Colorado

address: C106 Plant Sciences

institute: Colorado State University

summary: After experiencing drought, Sorghum bicolor generates substantial root pressure, which varies with genotype and re-watering amount.

overall_design: Two biological replicates were analyzed for each level of root pressure expression (watered + low pressure; deficit + low pressure; deficit + mid pressure)

middle: T

first: Louise

last: Comas


title: Metabolism of primary colorectal tumor facilitate MDSC infiltration in pre-metastatic liver

status: Public on Apr 30 2020

city: Guangzhou

first: Dongqiang

last: Zeng

state: Guangdong

address: NO.1838 North Guangzhou Avenue

department: Medical oncology

institute: Southern Medical University

summary: Through an integrated transcriptome analysis of orthotopic colorectal cancer tumor-bearing mice and sham-operation mice, we showed the distinct immune microenvironment of pre-metastatic liver and identified MDSCs as the dominated cell type mediating pre-metastatic niche formation. MDSCs instead of other immune cell types were highly infiltrated in the pre-metastatic liver when compared with normal liver. Notably, immunosuppressive factors released by MDSCs such as HIF1α, iNOS, TGFβ were significantly up-regulated in the pre-metastatic liver. Increasing immune checkpoint molecules expression also reflected an immunosuppressive condition of pre-metastatic liver. The primary tumor may induce MDSCs accumulation via metabolic mechanism including glycolysis/gluconeogenesis, HIF-1 signaling pathway, and CCL28 chemokine axis. This study depicts the immune cell landscape of pre-metastatic cancer and primary CRC tumor, and provides insights into how MDSCs reshape the pre-metastatic niche facilitating circulating cancer cells colonization.

overall_design: Integrated transcriptomic analysis of orthotopic colorectal cancer tumor-bearing mice and sham-operation mice to identify immune landscape of pre-metastatic liver in comparison with normal liver. The corresponding metabolism and signaling pathways that potentially mediates pre-metastatic niche formation are explored.

first: Miaohong

last: Wang

first: Jiani

last: Wu

first: Zilan

last: Ye

first: Min

last: Shi

first: Wangjun

last: Liao

first: Siheng

last: Lin


title: Chromatin profiling of the relationship between EWS/FLI, LSD1, and the enhancer landscape - H3K4 methylation

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The purpose of this study was to define the genome-wide functional relationship between LSD1 and EWS/FLI in Ewing sarcoma cells. We found EWS/FLI and LSD1 co-localize throughout the genome and that EWS/FLI induces a large change in the chromatin occupancy of LSD1.

overall_design: A673 cells were assayed with either wildtype ("A673") or depleted ("EFKD") levels of EWS/FLI. For knockdown, shRNAs were retrovirally delivered targeting either EWS/FLI ("EFKD") or luciferase as a negative control ("A673") and cells were selected in 2 µg/mL puromycin (Sigma P8833). For histone H3K4 methylation marks, three replicates of 50-bp single end sequencing were performed with input controls for each replicate. Bigwigs for H3K4 methylation marks were generated by MACS2 and represent the fold-enrichment over control; replicates are combined when present.

first: Stephen

last: Lessnick


title: Spo11-oligo mapping of double-strand breaks in spo11 mutants

summary: The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are non-randomly distributed across the genome. Here, we use Spo11-oligonucleotide complexes to map the distribution of meiotic DSBs in a spo11 mutant strain of Saccharomyces cerevisiae.

overall_design: 4 samples total: two biological replicate Spo11-oligo maps of S. cerevisiae SK1 spo11-F260A and wildtype


title: Double-strand breaks in spo11 mutants

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

overall_design: Refer to individual Series


title: An embryo lethal transgenic line manifests global expression changes and elevated protein/oil ratios in heterozygous soybean plants

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: Understanding the molecular processes of seed development is important especially in agronomic crops that produce large amounts of nutrient reserves.  Because soybean is a vital source of vegetable protein worldwide, producers are concerned about increasing the total amount of protein in the seed without substantially lowering the amount of oil, another economically important product. Here we describe a transgenic soybean line with increased protein and protein/oil ratio, containing an average of 42.2% protein vs. 38.5% in controls and with a protein/oil ratio of 2.02 vs. 1.76 in controls over several generations of greenhouse growth.  Other phenotypic data show that the seeds are heavier, although there are overall lower yields per plant. We postulate these effects result from insertion site mutagenesis by the transgenic construct. As this line never achieves homozygosity and appears to be embryo lethal when homozygous, one functional copy of the gene is most likely essential for normal seed development. Global transcript analyses using RNA-Seq for 88,000 gene models over two stages of cotyledon development revealed that more genes are over-expressed in the transgenic line including ribosomal protein related genes and those in the membrane protein and transporters families. Localization of the insertion site should reveal the genes and developmental program that has been perturbed by the transgenic construct, resulting in this economically interesting increase in protein and the protein/oil ratio.

overall_design: 26 RNA-Seq samples from two stages of immature cotyledons, 10-25mg and 100-200mg, across 2 generations of plants. They include Jack control plants; mutants positively identified as having the transgenic construct (transformed transgenic); and mutant offspring that nonetheless did not contain the transgenic construct (transformed non-transgenic), indicating the lines did not become homozygous. There were 3 replicates per stage for the Jack controls; 3 replicates per stage for the transformed but non-transgenic plants; and 7 replicates per stage for the transformed transgenic plants.

middle: I

last: Jones

first: Matt

last: Hunt

middle: O


title: Transcriptome profiling of cultured primary recessive dystrophic epidermolysis bullosa (RDEB) squamous cell carcinoma (SCC)

status: Public on Apr 22 2020

city: Salzburg

first: Roland

last: Zauner

state: Salzburg

address: Muellner Hauptstrasse 48

department: University Hospital of Dermatology  Salzburger Landeskliniken (SALK) | Paracelsus Medical University Salzburg (PMU)

country: Austria

institute: EB House Austria

summary:
Recessive dystrophic epidermolysis bullosa (RDEB) is a monogenetic skin disorder caused by mutations in the COL7A1 gene. Missing type VII collagen leads to severe blister formation and frequent chronic wounds. Patients suffering from RDEB are prone to develop particulary aggressive squamous cell carcinoma (SCC), representing the major cause of mortality.  This dataset provides Affymetrix microarray (ClariomD) based whole transcriptome data on RNA isolated from cultured primary RDEB keratinocytes (RDEB-KC) as well as RDEB squamous cell carcinoma (RDEB-SCC).
Cells were derived from punch biopsies or tumor resections from patients with confirmed diagnosis recessive dystrophic epidermolysis bullosa (RDEB). Primary KC and SCC were cultivated in fully defined medium till subconfluency. Total RNA was isolated and microarray assay performed.

overall_design: A case-control study design of cultured primary cells representing RDEB-SCC and RDEB-KC.

first: Monika

last: Wimmer

first: Verena

last: Wally


title: Single-cell RNA-sequencing of adult human prostates and urethra (normal and diseased)

first: Gervaise

last: Henry


title: RNAseq analysis of resting and TDM-stimulated DGCR8-deficient macrophages

status: Public on Apr 28 2020

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

summary: Pathogenic mycobacteria subvert immune responses to survive and replicate in macrophages. Mycobacterial cell wall components are sensed by several C-type lectin receptors, including MINCLE, the receptor for the cord factor trehalose-6,6-dimycolate (TDM). Regulation of innate immune cells relies on miRNAs, some of which are induced by mycobacterial ligands. Thus, MTB may exploit host miRNAs to establish its niche in macrophages. Here, we have employed conditional knockout mice for the microprocessor component DGCR8 to investigate the impact of miRNAs on the macrophage response to the mycobacterial cord factor. Deletion of DGCR8 during differentiation of macrophages from bone marrow progenitors significantly reduced the cell yield, but did not interfere with macrophage differentiation as determined by typical surface marker expression and phagocytic capacity. DGCR8-deficient macrophages expressed reduced levels of constitutive and TDM-inducible miRNAs, yet in turn accumulated primary miRNA transcripts. RNAseq revealed a modest type I interferon (IFN) signature in resting DGCR8-deficient macrophages. Stimulation of DGCR8-deficient macrophages with TDM induced overshooting and prolonged expression of interferon response genes, which was associated with enhanced expression of IFNb and could be largely prevented by antibodies to type I interferon. In turn, exogenous IFNb upregulated CXCL10 and CD69 to similar levels in control and DGCR8-deficient macrophages, indicating that signaling downstream of the type I IFN receptor was unaltered. Infection with live Mycobacterium bovis Bacille Calmette-Guerin (BCG) replicated the enhanced interferon response of DGCR8-deficient macrophages. Together, our results reveal an essential role for DGCR8 in curbing IFNb expression and IFN-dependent macrophage activation by mycobacteria.

overall_design: Comparisons of 12 samples belonging to 6 categories were performed with 2 replicates per category.

first: Barbara

last: Killy

last: Lang

first: Arif

last: Ekici


title: Gene expression profile of SoNar-high and SoNar-low B-cell acute lymphoblastic leukemia (B-ALL) cells

status: Public on May 25 2020

city: shanghai

first: Chiqi

last: Chen

address: 上海市黄浦区重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

summary: To dissect the metabolic state of B-ALL cells, we have developed a genetically encoded fluorescent sensor (SoNar) for tracking cytosolic NADH and NAD+ redox states and constructed the transgenic mouse. Based on the NADH/NAD+ ratio, we have sorted SoNar-high and SoNar-low B-ALL cells to employ whole genome microarray expression profiling as a discovery platform to identify genes with the potential to regulate the metabolism of B-ALL cells.

overall_design: SoNar-high and SoNar-low two population B-ALL cells from bone marrow were sorted to measure gene expression.

first: Junke

last: Zheng


title: miRNA profiling of cultured primary recessive dystrophic epidermolysis bullosa (RDEB) squamous cell carcinoma (SCC)

summary:
Recessive dystrophic epidermolysis bullosa (RDEB) is a monogenetic skin disorder caused by mutations in the COL7A1 gene. Missing type VII collagen leads to severe blister formation and frequent chronic wounds. Patients suffering from RDEB are prone to develop particulary aggressive squamous cell carcinoma (SCC), representing the major cause of mortality.  This dataset provides Affymetrix microarray (miRNA4.1) based whole transcriptome data on RNA isolated from cultured primary keratinocytes (KC) as well as squamous cell carcinoma (SCC).
Cells were derived from punch biopsies or tumor resections from either healthy donors or SCC patients with or without the diagnosis recessive dystrophic epidermolysis bullosa (RDEB). Primary KC and SCC were cultivated in fully defined medium till subconfluency. Total RNA was isolated and microarray assay performed.

overall_design: A case-control study design of cultured primary cells representing RDEB-SCC, RDEB-KC, non-EB SCC, healthy control KC.


title: Chromatin profiling of the relationship between EWS/FLI, LSD1, and K27ac in multiple Ewing sarcoma cell lines

summary: The purpose of this study was to define the genome-wide functional relationship between LSD1 and EWS/FLI in Ewing sarcoma cells. We found EWS/FLI and LSD1 co-localize throughout the genome and that EWS/FLI induces a large change in the genomic distribution of LSD1, and that this also occurs for the LSD1 interacting partner, REST.

overall_design: A673, EWS502, SKNMC, and TC71 cells were collected for CUT&RUN. Two independent replicates were performed for each sample including EWS/FLI, LSD1, and H3K27ac, with a non-specific IgG control. Samples were submitted for 150-bp paired end sequencing. Bigwigs for LSD1 and EWS/FLI were generated by MACS2 and represent the fold-enrichment over control; replicates are combined when present. Bigwigs for H3K27ac and relevant non-specific control are spike-in normalized representations of the aligned reads.

middle: L


title: The PPAR agonist Rosiglitazone induces paracrine signaling in melanoma cells that activate stromal cells and enhances tumor growth.

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Besides improving insulin sensitivity in type 2 diabetes, the thiazolidinedione family of compounds and the pharmacologic activation of their best characterized target PPARg has been proposed as a therapeutic option for cancer treatment. In the present study, we reveal a new mechanism by which the thiazolidinedione rosiglitazone contributes to tumorigenesis, which limits its therapeutic potential in cancer. We provide evidence that rosiglitazone activates a tumorigenic paracrine communication program in a subset of human melanoma cells, that involves the secretion of cytokines, chemokines and angiogenic factors. This complex blend of paracrine signals activates non-malignant fibroblasts, endothelial cells and macrophages in a tumor-friendly way. In agreement with these data, we show that rosiglitazone promotes human melanoma development in xenografts, through enhanced angiogenesis and inflammation. Together, these findings establish an important tumorigenic action of rosiglitazone in melanoma cells. While studies conducted on cohorts of diabetic patients report overall benefits of TZDs in cancer prevention, we show that exposure of an established tumor to rosiglitazone may be deleterious.

overall_design: A375 melanoma cells were treated for 24h with 5μM RGZ, 2μM T007 or a combination of both; three independent experiments were performed and in each of these 3 experiments, RNA samples from technical replicates of the same condition were pooled.

first: Christine

last: Pich

first: Patrick

last: Meylan

first: Beatris

last: Mastelic-Gavillet

first: Romain

last: Loyon

first: Catherine

last: Moret

last: Goepfert

first: Pedro

last: Romero

first: Camilla

last: Jandus

first: Liliane

last: Michalik


title: Single-cell RNA-sequencing of adult mouse lower urinary tracts

last: Henry


title: Comparative transcriptome analysis between two tomato materials under drought stress

status: Public on Apr 13 2020

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary:
RNA sequencing was performed to investigate the the response mechanism of tomato response to drought stress.

C2H2-type zinc finger proteins are classic and extensively studied members of the zinc finger family. C2H2-type zinc finger proteins participate in plant growth, development and stress responses. In this study, 99 C2H2-type zinc finger protein genes were identified and classified into four groups, and many functionally related cis-elements were identified. Differential C2H2-ZFP gene expression and specific responses were analyzed under drought, cold, salt and pathogen stresses based on RNA-Seq data. Thirty-two C2H2 genes were identified in response to multiple stresses. Seven, 3, 5, and 8 genes were specifically expressed under drought, cold, salt and pathogenic stresses, respectively. Five glycometabolism and sphingolipid-related, pathways and the endocytosis pathway were enriched by KEGG analysis. The results of this study represent a foundation for further study of the function of C2H2-type zinc finger proteins and will provide us with genetic resources for stress tolerance breeding.

overall_design:
mRNA profiles of different tomato leaf samples were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript .
Please note that the 'Micro-TOM-EX' is the 'Micro-TOM' plants overexpressing a GATA transcription factor gene.
CK0*_0h = Micro-TOM_control
CK3*_3h = Micro-TOM_drought stress for 3hrs
CK6*_6h = Micro-TOM_drought stress for 6hrs
EX0*_0h = Micro-TOM-EX_control
EX3*_3h = Micro-TOM-EX_drought stress for 3hrs
EX6*_6h = Micro-TOM-EX_drought stress for 6hrs

first: Tingting

last: Zhao

first: Xiangyang

last: Xu


title: An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability

city: Kensington

first: Zsuzsanna

last: Nagy

address: Lowy Cancer Research Centre, C25/9 High St

country: Australia

institute: Children's Cancer Institute

summary: To achieve the very high oncoprotein levels required to drive the malignant state, cancer cells utilise the ubiquitin proteasome system to regulate proteins involved in growth signalling pathways. Here we identify a transcriptional coactivator, ALYREF, expressed from the most common genetic copy number variation in childhood neuroblastoma, chromosome 17q21-ter gain. We show strong co-operativity between ALYREF and MYCN from transgenic models of neuroblastoma in vitro and in vivo. MYCN induced ALYREF transcription, and the two proteins formed a nuclear coactivator complex which stimulated transcription of the ubiquitin specific peptidase 3, USP3. We found that increased USP3 levels markedly reduced K-48- and K-63-linked ubiquitination of MYCN, thus driving up MYCN protein stability. In the MYCN-ALYREF-USP3 signal, ALYREF was required for MYCN effects on the malignant phenotype in vitro and that of USP3 on MYCN stability. Our data define a novel MYCN oncoprotein dependency state which provides rationale for future pharmacological studies.

overall_design: SK-N-BE(2)-C cells (1x10^7) were subjected to chromatin immunoprecipitation with a mouse anti-ALYREF antibody (11G5, ImmunoQuest) or control mouse IgG (Santa Cruz). After immunoprecipitation, ChIP DNA and genomic inputs were purified and sequencing libraries were created using an Illumina TruePrep DNA Library Prep Kit (TD501) and were then sequenced using an Illumina HiSeq X-Ten (Paired End; 150x2).

first: Yanhua

last: Du

first: Janith

middle: A

last: Seneviratne

first: Cizhong

last: Jiang

first: Glenn

last: Marshall


title: Expression data for C. elegans blunt force trauma

status: Public on Apr 09 2020

first: Peter

middle: M

last: Douglas

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

summary:
C. elegans exhibit an age-dependent mechanical stress response to blunt force injury.
Stress responses are often defined in part by an elicited cellular transcriptional response. We find in C. elegans that mechanical stress by blunt trauma induces a distinct and age-dependent transcriptional program.

overall_design: Age-synchronized C. elegans were given paralytic injury or sham (buffer incubation) and collected for RNA processing 1 hour after. We aimed to determine how mechanical injury affects gene transcription and further to what extent the process is age-dependent.


title: Regulation of the transcriptional response to mechanical trauma by vhp-1

summary: Mechanical stress by blunt force trauma elicits a distinct and reproducible transcriptional response in C. elegans. Vhp-1, a MAPK phosphatase, regulates a significant portion of these stress-inducible transcripts.

overall_design: mRNA profiling from whole worms: 1 hour following stress and with or without vhp-1 RNAi.

first: Nathan

last: Egge


title: Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted therapies in colon cancer

status: Public on Apr 18 2020

city: Beijing

first: ZIyi

last: Li

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Single cell RNA sequencing (scRNA-seq) is a powerful tool for defining cellular diversity in tumors, but its application towards dissecting mechanisms underlying immune-modulating therapies is scarce. We performed scRNA-seq analyses on immune and stromal populations from colorectal cancer patients, identifying specific macrophage and conventional dendritic cell (cDC) subsets as key mediators of cellular cross-talk in the tumor microenvironment. Defining comparable myeloid populations in mouse tumors enabled characterization of their response to myeloid-targeted immunotherapy. Treatment with anti-CSF1R preferentially depleted macrophages with an inflammatory signature but spared macrophage populations that in mouse and human expresses pro-angiogenic/tumorigenic genes. Treatment with a CD40 agonist antibody preferentially activated a conventional dendritic cell population and increased Bhlhe40+ Th1-like cells and CD8+ memory T cells. Our comprehensive analysis of key myeloid subsets in human and mouse identifies critical cellular interactions regulating tumor immunity and defines mechanisms underlying myeloid-targeted immunotherapies currently undergoing clinical testing.

overall_design:
For Patient P0104, P0305, P0309, P0411, P0720, P0728, P1212, P1228, P0413, and P0825, single-cell RNA-seq were performed by the SMART-seq2 platform. Single cell suspensions collected from CRC samples were stained with antibodies against CD45 for FACS sorting, performed on a BD Aria III instrument. To enrich myeloid cells, single cells were further enriched either by gating CD3-, CD3-CD19-/CD79A- or CD3-CD19-CD56- cells to exclude lymphoid cells. For B cells and NK cells, single cells were enriched by gating 7AAD-CD45+CD3-CD19+CD56- and 7AAD-CD45+CD3-CD19-CD56+. For non-immune cells, single cells were enriched by gating 7AAD-CD45-.
For Patient P0104, P0123, P0202, P0305, P0323, P0408, P0410, P0613, P1025, P1026, single-cell RNA-seq were performed by the 10x Genomic single cell 3’ library platform. Single cell suspensions collected from CRC samples were stained with antibodies against CD45 for FACS sorting, performed on a BD Aria III instrument. To enrich myeloid cells, single cells were further enriched either by gating CD3- or CD3-CD19-/CD79A-CD56-, cells to exclude lymphoid cells. For T and monocyte-lineage cells, single cells were enriched by gating 7AAD-CD45+CD3+ and 7AAD-CD45+CD3-CD14+ cells, respectively.
*** Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (under accession HRA000056 https://bigd.big.ac.cn/gsa-human/browse/HRA000056).

first: Lei

last: Zhang

first: Ziyi

first: Katarzyna

last: Skrzypczynska

first: Qiao

last: Fang

first: Wei

first: Sarah

last: O’Brien

first: Yao

last: He

first: Lynn

first: Qiming

first: Aeryon

last: Kim

first: Ranran

last: Gao

first: Jessica

last: Orf

first: Tao

first: Deepali

last: Sawant

first: Jiajinlong

last: Kang

first: Dev

last: Bhatt

first: Daniel

last: Lu

first: Chi-Ming

first: Aaron

last: Rapaport

first: Kristy

last: Perez

first: Yingjiang

last: Ye

first: Shan

first: Xueda

last: Hu

first: Xianwen

last: Ren

first: Wenjun

last: Ouyang

first: Zhanlong

last: Shen

first: Jackson

middle: G

last: Egen

first: Zemin

first: Xin

last: Yu


title: microRNAs array of livers from three different lifestyle modification mice models

status: Public on Apr 07 2020

first: Huan

last: Gong

address: No.1 Dahua Road, Dong Dan,

institute: Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology

summary: To investigate the microRNAs involved in the processes of beneficial and detrimental lifestyles, including caloric restriction(CR), exercise and high-fat diet(HF), we performed a comprehensive and thorough comparison of microRNAs expression profiles in liver among these lifestyle modifications.

overall_design: We set male C57BL/6 mice at two months of age into the following groups and treated for 3 months: ad libitum, normal-fat diet group (AL); ad libitum, high-fat diet group (HF); normal-fat diet and 30~35% caloric restriction as in AL group (CR); and ad libitum, normal-fat diet with exercise (EX). After the treatment, we applied the microRNA array detection of livers.


title: Disrupting ATF4 expression mechanisms provides an effective strategy for BRAF-targeted melanoma therapy (Knockdown Series)

status: Public on Apr 06 2020

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research (JFCR)

summary: BRAF V600 mutation influences cellular signaling pathways for melanoma development. Here, we show that mutated BRAF plays an essential role in the adaptive stress response following activation of general control non-derepressible 2 (GCN2) kinase. In parallel with GCN2, BRAF ensures ATF4 induction by utilizing mTOR and eIF4B as downstream regulators during nutrient stress and BRAF-targeted, therapeutic stress. Upon pharmacological BRAF inhibition, this signaling pathway exhibits temporal resistance, compared with the MEK-ERK pathway, thereby enabling transient induction of ATF4 under GCN2 activation. Notably, the prevention of GCN2 activation, using a chemical inhibitor that we identified, produces synergistic cell killing with BRAF inhibition. Thus, oncogenic BRAF can collaborate with the GCN2–ATF4 pathway, promoting stress adaptation for cell survival.

overall_design: We examined the gene expression change in BRAF-mutated melanoma A375 cells transfected with siRNA specific for BRAF and cultured in glutamine-free medium for 18 h, or A375 cells transfected with siRNA specific for ATF4 and then treated with vemurafenib for 4 h.

first: Ikuko

last: Nagasawa

first: Masaru

last: Koido

first: Yuri

last: Tani

first: Satomi

last: Tsukahara

first: Kazuhiro

last: Kunimasa


title: Single-cell RNA-sequencing of adult mouse prostates

first: Gervaise

last: Henry

summary: Single-cell RNA-sequencing was conducted on heterogeneous mouse prostates on the 10x Genomics platform.

overall_design: Fresh mouse prostate specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.

first: Douglas

last: Strand


title: Disrupting ATF4 expression mechanisms provides an effective strategy for BRAF-targeted melanoma therapy (Drug Treatmant Series)

overall_design: We compared gene expression patterns in BRAF-mutated melanoma A375 cells treated with vemurafenib, AT9283, or in combination with vemurafenib and AT9283 for 6  or 16 hours.


title: Disrupting ATF4 expression mechanisms provides an effective strategy for BRAF-targeted melanoma therapy

status: Public on Apr 05 2020

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of adult human prostates from organ donors

summary: Single-cell RNA-sequencing was conducted on heterogeneous human prostates FACS sorted for viability from organ donors (with no known prostatic diseases) on the 10x Genomics platform.

overall_design: Fresh human prostate specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.


title: Nfil3, a target of the NACA transcriptional coregulator, affects osteoblast and osteocyte gene expression differentially

status: Public on Mar 17 2020

city: Montreal

first: Hadla

last: Hariri

state: Quebec

address: 1003 Decarie Boulevard, Shriners Hospital For Children

department: Human Genetics

country: Canada

institute: Shriners Hospital for Children, Canada-Montreal, Department of Human Genetics, McGill University, Montreal,Quebec,Canada

summary: Using ChIP-Seq, we show that Nfil3 is a transcriptional target of the PTH-NACA axis in osteoblasts. We also show that Nfil3 transcription is, by part, regulated by NACA and CREB. Finally, we show that Nfil3 has a distinct role in osteoblasts vs osteocytes

overall_design: Examination of NACA binding to the Nfil3 promoter in Vehicle versus PTH(1-34)-treated MC3T3-E1 osteoblast like cells.

first: Rene

last: St-Arnaud


title: Transcriptional profile of CAOV2 ovarian cancer cells with YAP silencing

status: Public on Mar 05 2020

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

summary: We performed RNAseq to study the transcriptional changes of human CAOV2 ovarian cancer cells with or without YAP silencing by siRNAs to understand the genetic determinants of ferroptosis response

overall_design: Human ovarian cancer cell line CAOV2 were transfected by siRNA targeting YAP (siYAP) and compared to the control with non-targeting siRNA (siNT).

first: Wen-Hsuan

last: Yang


title: Interleukin-33 induces the enzyme tryptophan hydroxylase 1 to promote inflammatory group 2 innate lymphoid cell-mediated immunity

status: Public on Apr 21 2020

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

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


title: Interfering with DNA replication improves beta cell differentiation and maturation from human pluripotent stem cells

status: Public on Feb 28 2020

city: Tarrytown

first: Sandra

last: Kleiner

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Tarrytown, New York, USA

summary: Cell cycle progression plays an important role in mediating the transition from a differentiated state to a pluripotent stem cell. Conversely, establishing limitations in proliferative potential may be important to achieve functional maturity as well as to prevent abnormal growths after transplantation of stem cell derived products. Here we induced exit from the cell cycle in pancreatic progenitors by interfering with the progression of DNA replication and determined growth potential, differentiation and maturation to insulin producing endocrine cells. Treatment with the DNA polymerase inhibitor aphidicolin, as well as with antineoplastic agents, etoposide and cisplatin arrested cell cycle progression in G1 and promoted differentiation of pancreatic progenitor cells towards C-peptide positive cells. G1 arrest by aphidicolin did not induce DNA damage response or apoptosis, improved the functional maturity of stem cell-derived cells and protected mice from diabetes, without the formation of cystic growths. Therefore, induction of G1 arrest is an efficient way to promote precursor cell differentiation and generate insulin-producing cells with a stable identity and predictable growth potential after transplantation.

overall_design: Gene expression differences between differentiated ECs with and without APH

first: Lina

last: Sui

first: Yurong

last: Xin

first: Daniela

last: Georgieva

first: Giacomo

last: Diedenhofen

first: Leena

last: Haataja

first: Yong

last: Wang

first: Qi

last: Su

first: Jinrang

last: Kim

first: Jiayu

last: Fu

first: Danielle

last: Baum

first: Robin

middle: S

last: Goland

first: Peter

last: Arvan

first: Dieter

last: Egli


title: Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, mcm functions, and iron homeostasis.

status: Public on Apr 15 2020

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

institute: University of Adelaide

summary: Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal models. In a previous study, we generated an EOfAD-like mutation, psen1Q96_K97del, in zebrafish and performed a transcriptome analysis comparing entire brains from 6-month-old wild type and heterozygous mutant fish. We identified predicted effects on mitochondrial function and endolysosomal acidification. Here we aimed to determine whether similar effects occur in 7 day post fertilization (dpf) zebrafish larvae that might be exploited in screening of chemical libraries to find ameliorative drugs. We generated clutches of wild type and heterozygous psen1Q96_K97del 7 dpf larvae using a paired-mating strategy to reduce extraneous genetic variation before performing a comparative transcriptome analysis. We identified 228 differentially expressed genes and performed Goseq analysis and gene set enrichment analysis (GSEA). This predicted a significant effect on oxidative phosphorylation, consistent with our earlier observations of predicted effects on ATP synthesis in adult heterozygous psen1Q96_K97del brains. The dysregulation of minichromosome maintenance protein complex (MCM) genes strongly contributed to predicted effects on DNA replication and the cell cycle and may explain earlier observations of genome instability due to PSEN1 mutation. The upregulation of crystallin gene expression may be a response to defective activity of mutant Psen1 protein in endolysosomal acidification. Extracellular matrix (ECM) related genes were downregulated, consistent with previous studies of EOfAD mutant iPSC neurons and postmortem late onset AD brains. Also, changes in expression of genes controlling iron ion transport were observed without identifiable changes in the prevalence of transcripts containing iron responsive elements (IREs) in their 3’ untranslated regions. These changes may, therefore, predispose to the apparent iron dyshomeostasis previously observed in 6-month-old heterozygous psen1Q96_K97del EOfAD-like mutant brains.

overall_design: 12 samples were from 6 pairs of larvae cluches. Each pair consisted of one wild-type cluch and one heterzygous mutant cluch from the same wild-type male parent.

first: Yang

last: Dong

first: Michael

last: Lardelli


title: Fasciola hepatica miRNAs in mouse peritoneal Ago2

status: Public on Feb 21 2020

city: Sydney

first: Sheila

last: Donnelly

state: NSW

address: Corner Thomas St & Harris St

department: School of Life Sciences

institute: University of Technology Sydney

type: Non-coding RNA profiling by high throughput sequencing

summary:
Helminths, or worms, are multicellular parasites that can live for many years within their vertebrate hosts. Of prime importance is the regulation of the host immune cell signalling pathways to prevent the parasite’s elimination before they can produce their off-spring in the form of eggs.  Fasciola hepatica, a global worm parasite of humans and their livestock, regulates host innate immune responses within hours of infection. Host macrophages, essential to the first-line defence mechanisms, are quickly restricted in their ability to initiate a classic protective pro-inflammatory immune response. To determine the role of both host miRNAs and parasite-derived miRNAs in this outcome to infection with F. hepatica, peritoneal macrophages were harvested from the peritoneal cavity of BALB/c mice at various timepoints during infection and subject to RNASeq.
Sequenced Ago2 extracted from peritoneal macrophages of fasciola infected mice

overall_design: RNA extracted from infected mouse peritoneal macrophages sequenced after library prepartion for miRNAs

first: Nham

last: Tran

first: Tania

last: Marques

first: Alison

last: Ricafrente


title: Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in root

status: Public on Feb 27 2020

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

institute: University of Bologna

summary: Nitrogen (N) is an essential macronutrient for crops. Plants developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main N inorganic forms taken up by plants and act as both nutrients and signals, affecting gene expression and plant development.   In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. To assess the physiological response to these nutrients the shoot and root growth, the leaf pigment content and the amino acid amount in root and shoot were assessed. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. NH4+ activates the response to stress, while NO3- acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while reduces biomass and chlorophyll and flavonoids accumulation. The profiles observed for hydrolysed and free amino acids highlighted common and distinct features in response to the two nitrogen forms.

overall_design: Illumina RNA-Seq analysis of maize root apexes samples collected from seedlings grown for 24 h in nutrient solution supplied with 1mM NO3- or 1mM NH4+ compared to negative controls grown in a N-deprived nutrient solution. 3 days old maize B73 inbreed seedlings were treated for 24 h prior to roots collection and RNA extraction.  3 biological replicates per condition were produced, each composed by 10-15 plants.

first: Laura

last: Ravazzolo

first: Sara

last: Trevisan

first: Serena

last: Varotto

first: Stefania

last: Sut

first: Stefano

last: Dall'Acqua

first: Mario

last: Malagoli

first: Silvia

last: Quaggiotti


title: Genome-wide analysis of mouse glial cell gene expression by  Sgk1 inhibition.

status: Public on Feb 19 2020

city: Seoul

first: Oh-Chan

last: Kwon

address: 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea

department: Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

summary: Analysis of stem cell functions of mouse glial cell at gene expression level. The hypothesis tested in the present study was that Sgk1 inhibiton potentiates neurotrophic functions of glial cells. Results provide important information  of neural stem cell fuctions like glutamate uptake, inflamamtion, neurotrophic activity.

overall_design: Total RNA obtained from primary mouse glial cell culture, Sgk1 inhibited glial cells compared to control glial cells.

first: Jae-jin

last: Song


title: Gene expression changes in Corynebacterium glutamicum during iron limitation [Set I]

status: Public on Feb 24 2020

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: Iron is the fourth most abundant element in the Earth’s crust. However, the poor solubility of iron due to oxidation of ferrous iron to the almost insoluble ferric iron under aerobic conditions constitutes a considerable challenge for living organisms to obtain sufficient amounts of the iron available. In the present study, we set out to characterize the global gene expression of C. glutamicum under iron limitation in comparison to iron-replete conditions.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: C. glutamicum cells were cultured under iron deplete (1 µM) or replete (36 µM) conditions and were harvested at early exponential phase (OD600 4–5).

first: Andreas

last: Küberl

first: Aliye

last: Mengus-Kaya

first: Jochem

last: Gätgens

last: Bott


title: Genome-wide analysis of mouse glial cell gene expression by overexpression of certain genes

summary: Analysis of stem cell functions of mouse glial cell at gene expression level. The hypothesis tested in the present study was that Nurr1 and Foxa2 overexpression potentiates neurotrophic functions of glial cells. Results provide important information  of neural stem cell fuctions like glutamate uptake, inflamamtion, neurotrophic activity.

overall_design: Total RNA obtained from mouse glial cell culture,  Nurr1+Foxa2 gene overexpression glial cells compared to untreated control glial cells.


title: Gene expression changes in Corynebacterium glutamicum during iron limitation [Set II]

overall_design: C. glutamicum cells were cultured under iron deplete (1 µM) or replete (36 µM) conditions and were harvested at late exponential phase (OD600 12–15).

first: Michael


title: Whole transcriptomes analyses of gastric tumor tissues derived from Mst4F/F UBCcre (Mst4 KO) mice and wildtype (WT) mice

status: Public on Apr 02 2020

city: Shanghai

first: Liwei

last: AN

address: Yanchang Road

institute: Shanghai Tenth People's Hospital

summary: To explore whether Mst4 limits YAP signaling and suppresses GC development in vivo, RNA sequencing was performed to analyze the genome-wide RNA change in gastric tumors from MST4 KO mice and those from WT mice induced by chemical MNNG.

overall_design: Total mRNA was extracted from gastric tumors of Mst4 KO and WT mice in duplicate. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina Hiseq X10.

last: An

first: Shi

last: Jiao


title: Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks

status: Public on Feb 12 2020

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

type: Methylation profiling by high throughput sequencing

summary: Meiotic recombination is initiated by the formation of double-strand breaks (DSBs), which are repaired as either crossovers (COs) or noncrossovers (NCOs). In most mammals, PRDM9-mediated H3K4me3 controls the nonrandom distribution of DSBs; however, both the timing and mechanism of DSB fate control remain largely undetermined. Here, we generated comprehensive epigenomic profiles of synchronized mouse spermatogenic cells during meiotic prophase I, revealing spatiotemporal and functional relationships between epigenetic factors and meiotic recombination. We find that PRDM9-mediated H3K4me3 at DSB hotspots, coinciding with H3K27ac and H3K36me3, is intimately connected with the fate of the DSB. Our data suggest that the fate decision is likely made at the time of DSB formation: earlier formed DSBs occupy more open chromatins and are much more competent to proceed to a CO fate. Our work highlights an intrinsic connection between PRDM9-mediated H3K4me3 and the fate decision of DSBs, and provides new insight into the control of CO homeostasis.

overall_design:
We have applied chromatin ChIP-seq (Chromatin immunoprecipitation and sequencing) to spermatogenic cells for six critical histone modifications, including H3K4me3, H3K9me2, H3K9me3, H3K27me3, H3K36me3, and H3K27ac, and NOMe-seq (Nucleosome Occupancy and Methylome Sequencing) for the chromatin state, nucleosome positioning, and DNA methylation for each sample with two biological replicates. We also performed ChIP-seq and NOMe-seq for synchronous leptotene and zygotene from Prdm9-/-, Spo11-/-, and Dmc1-/- mice.
Examination of 6 different histone modifications in homogenous synchronous spermatogenic cells of 8 stages during meiotic process.

first: Yao

last: Chen

first: Ruitu

last: Lyu

first: Bowen

last: Rong

first: Zhen

last: Lin

first: Ruofei

last: Dai

first: Xi

last: Zhang

first: Nannan

last: Xie

first: Siqing

last: Wang

first: Fuchou

last: Tang

first: Fei

last: Lan

first: Ming-Han

last: Tong


title: Gene expression changes in Corynebacterium glutamicum during iron limitation

first: Tino

last: Polen


title: Genome-wide identification of Foxf2 transcriptional target genes in palate development

status: Public on Feb 11 2020

city: Cincinnati

first: Jingyue

last: Xu

state: Ohio

address: 3333 burnet avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Cleft palate is among the most common structural birth defects in humans. Previous studies have shown that mutations in FOXF2 are associated with cleft palate in humans and mice and that Foxf2 acts in a Shh-Foxf-Fgf18-Shh molecular network controlling palatal shelf growth. In this study, we generated mice carrying 3xFLAG epitope-tagged endogenous Foxf2 protein using the CRISPR/Cas9-mediated genome editing technology and characterized genome-wide Foxf2 binding sites in the developing palatal shelves using chromatin immunoprecipitation and genome sequencing (ChIP-seq). By combined analysis of ChIP-seq and RNA-seq datasets we identified a large list of Foxf2 target genes. Further analyses demonstrate that Foxf2 directly regulate expression of several genes encoding ECM or ECM modifiers during palate development. Moreover, our ChIP-seq and RNA-seq datasets provide an excellent resource for comprehensive understanding of the molecular network controlling palate development.

overall_design: We generated mice carrying 3xFLAG epitope-tagged endogenous Foxf2 protein using the CRISPR/Cas9-mediated genome editing technology. 50 pairs of palatal shelves were dissected from Foxf2FLAG/FLAG embryos at E13.5. ChIP was performed by using anti-FLAG antibodies (Sigma). Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI). Sequencing was performed on an Illumina HiSeq2500 (Illumina, San Diego CA). Raw FASTQ files were aligned to mm9 reference genome. Peak calling was performed using the HOMER (Hypergeometric Optimization of Motif EnRichment) software. The input samples were used as the control for calling peaks from the Foxf2-FLAG ChIP-seq data set.

first: Han

last: Liu

first: Joo-seop

last: Park

first: Rulang

last: Jiang


title: Commensal Microbial Interactions Alter Streptococcus mutans Transcriptome Profile and Cell-Cell Signaling

status: Public on Mar 24 2020

city: Columbus

first: Justin

middle: Ray

last: Kaspar

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

summary:
BACKGROUND: Hundreds of bacterial species coexist within the human oral cavity, where complex interactions can occur. Recent evidence has shown that the commensal oral streptococci that populate supragingival biofilms on the tooth surface produce extracellular proteases that degrade cell-cell signaling molecules of their disease-causing competitors, Streptococcus mutans. To further explore these interactions, we performed transcriptome analysis of S. mutans cocultured with different oral streptococci and found that cell-cell signaling was complety inhibited, but only when the bacteria were directly cocultured together.
METHODS: RNA-Seq was utilized to compare the transcriptomes of S. mutans wild-type strain UA159 cocultured in its own supernatant (3 replicates), UA159 cocultured in S. sp. A12 supernatant (3 replicates) and directly cocultured with S. sp. A12 (3 replicates). Strains were grown to OD600 nm = 0.5 in CDM medium before harvest. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 15 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores, the resulting sequences were mapped onto the reference genome of strain UA159 (GenBank accession no. AE014133) using the short-read aligner.  Mapped short-read alignments were then converted into readable formats using SAMTOOLS.
RESULTS: Using an optimzed data analysis workflow, we mapped 13-16 million reads per sample to the genome of UA159. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). When comparing the growth of S. mutans in its own spent supernatant against competitor spent supernatants, we found 88 genes differentially expressed (Log2 fold change > (-)1.5, -log10 P-value > 4) which included upregulation of the zinc transport system and several amino acid ABC transporters, along with downregulation of the TnSmu1 genomic island. A more substantial effect was seen when we compared growth of S. mutans in competitor spent supernatant compared to growth directly with a competitor. Here, 140 genes were differentially expressed and included upregulation of one of the CRISPR genetic clusters as well as downregulation of the entire genetic competence regulon, as expected. Principal component analysis (PCA) of transcriptome data from these three conditions displayed a wide variation and separation among the tested groups, further confirming a unique transcriptome response for S. mutans between growth in the supernatant of a competitor and directly with a competitor.
CONCLUSIONS: We believe that these measured transcriptomic changes represent a conserved S. mutans response to competitors that has not been previously captured in RNA-Seq experiments of monocultures alone. Together, these results highlight a previously undocumented transcriptomic alteration by S. mutans when challenged by health-associated oral streptococci.

overall_design: To determine if the proximity-dependent effects of S. mutans encountering oral competitor streptococci was limited to only ComRS signaling and genetic competence activation, we performed transcriptome profiling by RNA-Seq of S. mutans grown in CDM medium under three different conditions: (i) growth in its own spent supernatant, (ii) growth in spent supernatants of competitor (S. sp. A12; treated similarly to Figure 6A), and (iii) cocultured directly with competitor (S. sp. A12).


title: Stabilization of Heterochromatin by CLOCK Counteracts hMSC Senescence and Articular Degeneration

first: ji

middle: qian

last: zhao

address: 15 Datun Road Chaoyang District

institute: institute of zoology ,CAS

summary: Accumulating evidence indicates the close association between the circadian clock and the aging process. However, it is unclear whether and how the circadian clock proteins regulate stem cell aging. Here, we identified a noncanonical transcriptional activator-independent role of CLOCK, a core component of the molecular circadian clock machinery, in counteracting human mesenchymal stem cell (hMSC) senescence. CLOCK expression was decreased during hMSC aging. In addition, CLOCK deficiency accelerated hMSC senescence, whereas CLOCK overexpression attenuated physiological and pathological hMSC senescence. Mechanistic studies revealed that CLOCK formed complexes with nuclear lamina proteins and KAP1, thus maintaining heterochromatin architecture and stabilizing genomic repetitive sequences. Finally, gene therapy with lentiviral vectors encoding CLOCK promoted cartilage regeneration and attenuated age-related osteoarthritis in mice. These findings reveal a novel role of CLOCK independent of its transcriptional activation activity in the stabilization of heterochromatin and alleviation of hMSC senescence, providing a potential therapeutic target for treating aging-associated articular degeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Multi-omics sequencing of WT and CLOCK defecient hMSCs.

first: Guanghui


title: Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria

status: Public on Feb 01 2020

city: Oxford

first: Satish

last: Adhikari

state: MS

address: 415 Shoemaker Hall

institute: University of Mississippi

overall_design: Refer to individual Series


summary: Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.

overall_design: RNA-seq was performed in WT, gcrA and ccrM mutant of B. subvibrioides. All experiments were carried out in triplicates.

first: Patrick

middle: D

last: Curtis


title: Expression profile of RCC4 cells with YAP silencing

first: Jen-Tsan

last: Chi

summary: YAP is the one of the effectors of Hippo pathway. YAP promotes organ size growth as well as tumor metastasis. In this study, YAP is silencing in clear cell carcinoma cell line RCC4 to elucidate the downstream targets that promotes the resisntance toward erastin-induced ferroptosis.

overall_design: Human clear cell renal carcinoma cell line RCC4 were transfected with siRNA targeting YAP(siYAP) and compared with non-targeting siRNA control (siNT). All samples were prepared as biological triplicates. Total RNA was collected after 2 days of reverse transfection for cDNA synthesis. The influence of silencing YAP on gene expression was derived by zero transformation process, in which we compared the gene expression level with siYAP to the average of gene expression level in control (siNT) samples.

first: Wen-Hsuan

last: Yang


overall_design: ChIp-seq was performed in 3 biological replicates of gDNA of WT before (input DNA/control) and after immunoprecipitation.


title: Human ESC-embryoid body sorted populations: TMRM-hi and ALCAM-low vs. TMRM-hi and ALCAM-hi

status: Public on Mar 01 2020

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Signal differences between  TMRM-hi and ALCAM-low vs. TMRM-hi and ALCAM-hi  in representative cardiac and hepatic gene expression in mRNA microarray analysis.
INTRODUCTION: Non-genetic purification methods for pluripotent stem cell-derived hepatocyte-like cells are useful for liver regenerative therapy and pharmaceutical applications.   METHODS: Fluorescent activated cell sorting (FACS) was used to separate cells by combining two parameters: cellular mitochondrial content evaluated by the mitochondrial membrane potential-dependent fluorescent probe (TMRM) and immunocytochemical detection of activated leukocyte cell adhesion molecule (ALCAM). This method was applied to murine fetal, human embryonic stem cell (ESC)-derived, and human induced pluripotent stem cell (iPSC)-derived cell-mixtures. Separately sorted cell fractions were evaluated by quantitative PCR, immunohistochemistry, and cytochemistry for HNF4a, AFP, and albumin mRNA and/or protein expression.   RESULTS: Hepatocyte-like cells were highly segregated into the high TMRM signal and ALCAM-positive population. The purity of hepatocyte-like cells derived from human iPSCs was 97 ± 0.38% (n = 5).   CONCLUSIONS: This hepatocyte-like cell purification method may be applicable to quality control of cells for liver regenerative cell therapy and pharmaceutical development.

overall_design: comparison of each one sample

first: Hiromi

last: Yamashita

first: Fumiyuki

last: Hattori


title: Transcriptional analysis of sodium valproate and lithium in a serotonergic cell line

status: Public on Mar 07 2020

city: Christchurch

first: Martin

last: Kennedy

state: Canterbury

address: 2 Riccarton Avenue

department: Pathology and Biomedical Science

country: New Zealand

institute: University of Otago

summary: Sodium valproate (VPA) and lithium are mood stabilizers, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for these drugs are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression but no changes with lithium. Analysis by multiple pipelines revealed that as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated in response to VPA exposure.

overall_design: Differentiated RN46A cells were treated with 0.5mM each of VPA and lithium for 72 hours. Total RNA was extracted and polyA-enriched unstranded mRNA sequencing was carried out on Illumina HiSeq 2500.

first: Priyanka

last: Sinha


title: Next-generation sequencing study in multiple sclerosis white matter brain lesions

status: Public on Jan 21 2020

city: Odense M

first: Tobias

last: Frisch

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: Total RNA seq on human brain tissue samples.

overall_design: RNA-Sequencing of MS white matter lesions based on 10 MS and 5 control patients.

first: Maria

last: Elkjaer

first: Richard

last: Reynolds

first: Tim

last: Kacprowski

first: Mark

last: Burton

first: Torben

last: Kruse

first: Mads

last: Thomassen

first: Jan

last: Baumbach

first: Zsolt

last: Illes


title: MicroRNA profiling in different types,grades and stages of breast cancer

status: Public on Jan 30 2020

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

country: India

institute: Centre for cellular and molecular biology

summary: MicroRNA  profiling was done using Taqman Low Density Arrays (TLDA)  platform consisting of 667 microRNAs covering Sanger miRBase version10  cross 50  samples along with their adjacent normals consisting of different types (ER+ and ER-ve), grades (grade 2 and grade 3) with their different stages (I to III). The above isolated RNA which displayed good RIN value and linearity (R2>0.96), were used for  reverse transcription (RT) reactions  with the help of TaqMan MicroRNA Reverse Transcription Kit followed by real time PCR Reactions (ABI 7900 HT) as per manufacturer's instructions.A pre -amplification step of cDNA with pre-amp megaplex pool primers was carried out to significantly enhance the ability to detect highly down regulated miRNAs. The TaqMan human microRNA arrays consists of two plates, pool A and pool B. RNU 46 and RNU 48 were used as endogenous controls for data normalization. Another control not related to human was also included as a negative control. Each TaqMan Assay was run in quadruplicate. RNU 46 and RNU 48 expression was consistent in all the samples and displayed good range of CT values (22–24 ) where as in ‘No Template’ Control (NTC) CT value was  above 38. The average CT values of total profiled miRNAs in all samples were normalized with RNU 46 & RNU 48 using spotfire (statminer) software and fold changes were represented in terms of 2 - Δ Δ CT  (RQ ) and log10RQ. Only valid and significant miRNAs were picked up for further analysis.

overall_design: Taqman Low Density Arrays (TLDA) were performed across 50 samples along with their adjacent normals consisting of different typs (ER+/ER-ve), grades (grade 2 and grade 3) and stages (stages I,II,III) of breast cancer samples. Another control not related to human is also included as a negative control.

first: Rekha

last: Nair


title: The influence of acetate in the medium to the global gene expression of  C. glutamicum wild type (WT) and the C. glutamicum ΔcyaB mutant (ΔcyaB)

status: Public on Jan 09 2020

first: Tino

last: Polen

summary: The cAMP-dependent transcriptional regulator GlxR serves as a central hub in the regulatory network of the actinobacterial model organism Corynebacterium glutamicum and controls expression of ~10% of all genes. The consequences of a lowered cAMP level are mostly unkown. A single gene (cyaB) for a cAMP-synthesizing adenylate cyclase was identified and it had been reported that a cyaB mutant grows like the wild type on glucose, but has a strong growth defect in the presence of acetate. Our work aimed to understand the molecular basis for the acetate sensitivity of a ΔcyaB mutant and improve our knowledge on the physiological function of cAMP. Our results indicate that a diminished expression of the GlxR-activated genes for the cytochrome bc1-aa3 supercomplex in the ΔcyaB mutant causes a reduced capacity to build up membrane potential. This deficiency becomes evident in the presence of acetate or the protonophore CCCP, which increase the proton permeability of the cytoplasmic membrane, and has systemic effects on transport processes including oxidative phosphorylation. The acetate sensitivity of the ΔcyaB mutant could be abolished by a single amino acid exchange in GlxR. Our results demonstrate a key role of cAMP and GlxR in the control of energy metabolism in corynebacteria.

overall_design: DNA microarray analyses of the ΔcyaB mutant and the wild type (WT), grown in minimal medium with glucose and acetate (100 mM each) were performed. For this purpose RNA was isolated from exponentially growing cells cultivated in CGXII medium containing glucose and acetate (each 100 mM) as carbon source. Three biological replicates of both strains were performed.

first: Natalie

last: Wolf

first: Michael

last: Bussmann

first: Abigail

last: Koch-Koerfges

first: Nino

last: Katcharava

first: Julia

last: Schulte

first: Johannes

last: Hartl

last: Vorholt

first: Meike

last: Baumgart

last: Bott


title: Chromatin accessiblity of influenza-specific memory CD8 T cells in the lung airways, lung parenchyma, and spleen

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To examine differences in chromatin accessibility of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung parenchyma, and spleen were FACS sorted and DNA isolated for ATAC-seq.

overall_design: C57Bl/6 mice were infected with influenza x31 and rested for 35 days to establish T cell memory. Five minutes prior to euthanasia mice were injected with anti-CD45.2-PE to discriminate between tissue resident and circulating cells, and cells were isolated from the airways by bronchoalveolar lavage, from the lung parechyma by enzymatic digestion, and from the spleen by mechanical disruption. Cells were sorted on CD8+ CD44Hi FluNP 366-374 Db tetramer+ populations, and cells from the airways and parenchyma were further sorted on intravital label negative (i.e. tissue resident) cells.

first: C

first: J

middle: E

last: Kohlmeier


title: A multiparametric extraction method for the molecular characterization of Vn96-isolated plasma extracellular vesicles

status: Public on Jan 08 2020

city: Moncton

first: Rodney

last: Ouellette

address: 35 Providence St.

institute: ATLANTIC CANCER RESEARCH INSTITUTE

summary: We demonstrate a method for the DNA, RNA and Protein extraction of plasma extracellular vesicles.

overall_design: Plasma Extracellular Vesicles were isolated using Vn96 from Control donor plasma.

first: Jeremy

middle: W

last: Roy

first: Catherine

last: Taylor

first: Annie-Pier

last: Beauregard

first: Daniel

middle: C

last: Ayre

first: Sheena

last: Fry

first: Simi

last: Chacko

first: Gabriel

last: Wajnberg

first: Andrew

middle: P

last: Joy

first: Ngoc-Neu

last: Mai-Thi

first: Nicolas

last: Crapoulet

first: David

last: Barnett

first: Anirban

last: Ghosh

first: Stephen

last: Lewis

middle: J


title: SMARCA4 reads PRMT1-mediated H4R3me2a to promote colorectal cancer progression II

status: Public on Jan 07 2020

city: Nanjing

first: Bing

last: Yao

state: Jiangsu

address: Longmian Road 101

department: Department of Medical Genetics

institute: Nanjing Medical University

summary: To further investigate the functional associations between PRMT1 and SMARCA4 and explore the biological significance of these interactions, we conducted expression profiling on the Agilent SurePrint G3 Human Gene Expression v3 (8*60K,Design ID:072363) using knockdown of PRMT1 or SMARCA4’s RNA in HCT116 cells.

overall_design: Total RNA was extracted from HCT116-PRMT1-NC, HCT116-PRMT1-KD1, HCT116-PRMT1-KD2, HCT116-SMARCA4-KD1 and HCT116-SMARCA4-KD2 cell lines.  Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

first: Quan

last: Zhao


title: A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

status: Public on Mar 30 2020

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Transcription factor (TF)-mediated gene regulation is critical to cellular development and function, an understanding of which has been promoted by the advent of genome-wide TF profiling methodologies. While traditional TF profiling methods in a variety of cell lines have made clear that TF binding is highly diverse amongst cell types, these techniques become challenging to interpret in vivo in complex tissues, such as the brain, which are composed of numerous, distinct cell types. Here we present FLEX calling cards, a virally-mediated system for genome-wide, longitudinal, cell type-specific recording of TF occupancy. We generated cell type-specific TF occupancy profiles in multiple cell types of the mouse brain and demonstrated the ability of this system to record and integrate historical TF binding events across time. FLEX calling cards is now ready for adaptation to any AAV-tractable animal model to investigate cell type-specific, TF-mediated gene regulation in vivo.

overall_design: C57bl6J injected with Cre-independent viruses. Cre lines and replicate numbers indicated in sample names. For SRT libraries, 10 "barcodes" per replicate were pooled and used in creation of .ccf files. Each barcode is listed as a separate sample, each with a unique .combination of .fastq file and 5' primer.

first: Alexander

last: Cammack


title: SMARCA4 reads PRMT1-mediated H4R3me2a to promote colorectal cancer progression I


title: LncRNA and mRNA expression profile of peripheral blood mononuclear cells in primary Sjögren’s syndrome patients

city: Beijing

first: Yu

last: Peng

address: No. 1, Shuaifu yuan

institute: Peking Union Medical College Hospital

summary: RNA-seq technology was used to detect the differentially expressed LncRNAs and mRNAs between five paired pSS patients and healthy control PBMCs. In this study, 44 out of 1772 LncRNAs and 1034 out of 15424 mRNAs were expressed differentially in the PBMCs of pSS patients.

overall_design: Examination of LncRNA and mRNA expression profile of 5 pSS patients and 5 healthy controls.

first: Xuan

last: Luo

first: Yingying

last: Chen

first: Linyi

first: Chuiwen

last: Deng

first: Wen

last: Zhang

first: Yunyun

last: Fei

first: Yan


title: Gene expression signatures in blood and muscle biopsy after intramuscular immunization of healthy adult humans with adjuvanted vaccines (BIOVACSAFE protocol 305E)

status: Public on Jan 06 2020

city: London

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

summary: The gene expression in whole blood and simultaneous muscle biopsy (site of immunization and control contralateral non-injected leg) was measured in healthy adult male humans attending a research unit (CRC, University of Surrey, UK), who were randomized to receive a single immunization with an adjuvanted licensed vaccine or saline placebo control.

overall_design: Participants, all males, were randomized into the following groups (characteristics: treatment) to receive one of the following vaccines: FENDRIXE: intramuscular AS04C-alum-adjuvanted Fendrix, Hepatitis B (rDNA) vaccine (adjuvanted, adsorbed) supplied as a 0.5 mL suspension pre-filled syringe as a booster dose given to participants who were hepatitis B seropositive as a result of previous HBV immunization but negative for markers of HBV infection; FLUADE: intramuscular Fluad, MF59C-adjuvanted subunit vaccine supplied as a 0.5 ml pre-filled syringe containing influenza virus; PLACEBOE: intramuscular 0.5 mL normal saline. Participants attended on day 0 when pre-immunization baseline blood samples were drawn and vaccine or saline placebo intramuscularly administered into the anterolateral thigh of a designated leg (characteristics: injected side). The contralateral leg was not injected. The depth and angle of the injection was standardised and the injection site marked. Participants were randomized into groups (n = 5 per group) to undergo muscle biopsy and simultaneous blood draw on one of the following time points: 3 hours after immunization on day 0, days 1, 3, 5 or 7. For convenience a characteristics: hour value has been calculated for each array but this is only accurate at 0 and 3 hours, participants being free to attend at any time during the morning of the designated biopsy day after day 0. All whole blood samples were collected into PaxGene tubes. Muscle biopsies were obtained using an Abrahams suction / cutting needle under local anaesthetic. The needle was engraved at the same depth as the vaccine/placebo injection to facilitate accurate location of the injection site. A second biopsy was obtained from the same anatomical site in the contralateral non-injected control leg. Comments by the operator on the biopsy, quality, size, blood or adipose tissue presence have been included (characteristics: biopsy comments). A biopsy from the non-injected control leg was inadequate for RNA extraction in participant CRC305E9042 and so no array data are present.  Biopsies were placed immediately into RNAlater for storage at 4°C overnight before freezing at -20°C and shipping on dry ice to the processing centre.

first: January

last: Weiner

first: Jeroen

last: Maertzdorf


title: miRNA seq of sperm RNA after olfactory stress

status: Public on Jan 01 2020

first: Brian

middle: George

last: Dias

address: 954 Gatewood Rd NE

department: Psychiatry and Behavioral Sciences

summary: We profile miRNA in sperm obtained from adult male C57 mice that had either been exposed to an Odor (F0-Exposed) or been conditioned with the Odor (Odor+mild foot-shock) (F0-Trained)

overall_design: Examination of miRNA in mouse sperm RNA after olfactory-related treatments.


title: The transcriptional responses of C. glutamicum to the secretory production of two different heterologous proteins

status: Public on Feb 03 2020

first: Tino

last: Polen

address: Wilhelm-Johnen-Str 1

institute: Forschungszentrum Jülich GmbH

summary: High level secretion of proteins via the Sec protein export pathway leads to secretion stress, a phenomenon that is thought to be caused by the accumulation of incompletely or misfolded proteins at the membrane-cell envelope interface. We have analyzed the transcriptional responses of C. glutamicum to the secretory production of two different heterologous proteins and found that, in both cases, the expression of the gene encoding a homologue of the extracytosolic HtrA protease was highly upregulated.

overall_design: Transcriptional responses of C. glutamicum to the secretory production of heterologous proteins were determined in 3 sets. Set 1 comprises 3 biological replicates of C.glutamicum WT carrying plasmid for expression of AmyE without signal peptide. Set 2 comprises 3 biological replicates of C.glutamicum WT carrying plasmid for expression of AmyE fused with signal peptide. Set 3 comprises 3 biological replicates of C.glutamicum WT carrying plasmid for expression of cutinase fused with NprE signal peptide. In all sets/replicates the induced culture was compared to the uninduced culture.

first: Sarah

last: Jurischka

first: Roland

last: Freudl


title: vasc1-bravo-Transciptome of VASC1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 4plex_brachy_2016_01 - vasc1-bravo - Are hormone signaling genes misregulated in VASC1. - During a screening of the Brachypodium mutant collection at Versailles, a line was identified with a marked vascular phenotype. The causal locus segregates Mendelian way (a recessive locus). A candidate gene was identified by ILLUMINA sequencing at the Joint Genome Institute (JGI) and by the ShoreMAP technique. The objective is to identify which genes whose expression is deregulated in this mutant explain the observed phenotype.

overall_design:
4 dye-swap - genotype and ecotype comparison

Vasc1_He = Vasc1 heterozygote
Vasc1_Ho = Vasc1 homozygote

first: Richard

last: Sibout

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Temporal profile of brain gene expression associated with learning in an anuran amphibian

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

institute: Carleton University

summary: Reported here are the transcriptomic changes resulting from learning, in the brain of an anuran amphibian. RNA sequencing was utilized to investigate temporal  gene expression patterns resulting from conditioned learning in the fire-bellied toad, Bombina orientalis. As a basal tetrapod lineage, B. orientalis represents a robust candidate for investigating the evolution of molecular mechanisms underlying learning in vertebrates. Differential expression following learning reveled activity in molecular pathways related to immediate early gene expression, cytoskeletal modification, axon guidance activity, and apoptotic processes. Learning in the fire-bellied toad is characterized by early IEG activity coinciding with transcriptional activity and structural modification, followed by axon guidance and adhesion activity, and late neural pruning.

overall_design: Experiment consisted of three treatments + control with three replicates each. Treatments represent post-training sacrifice timing (2 hours, 4 hours, and 24 hours), with an unmanipulated control. n=12.

first: Frederic

last: Laberge

first: Andreas

last: Heyland


title: Total, polysome and monosome RNAseq of Caenorhabditis elegans strains ppp-1(wrm10), ppp-1(wrm15) and wild type

city: Cologne

first: Martin

last: Denzel

address: Joseph-Stelzmann-Str. 9b

institute: Max Planck Institute for Biology of Ageing

summary: We compared the ratio of polysome-associated mRNAs (>3 ribosomes/mRNA) normalized to total mRNA levels between WT and ppp-1 animals. We found a significant de-enrichment of 336 mRNAs and an enrichment for 72 mRNAs in ppp-1 polysome fractions.

overall_design: Examination of the combined translatome (polysomal mRNA levels normalized to total mRNA levels) of ppp-1 mutants wrm10 (= mutA) and wrm15 (= mutB) compared to wild type

first: Maxime

last: Derisbourg

first: Laura

last: Wester

first: Ruth

last: Baddi


title: Genome-wide maps of DNA methylation and gene expression for  multiple  regions  within  a  breast tumor [RNA-Seq]

city: Harbin

first: Xishan

last: Wang

address: Xue Fu Road 246

institute: The Second Affiliated Hospital of Harbin Medical University

summary: As the differentiation state of the cells is affected by epigenetic modification regulation, the abnormal epigenetic modification is an important factor leading to the intratumoral heterogeneity. To further understand of the intratumoral epigenetic heterogeneity, we performed Reduced Representation Bisulfite Sequencing and RNA sequencing for multiple regions within a breast tumor and exhibited the epigenetic maps of different regions. We detected intratumoral heterogeneity-related molecular features and further explored the correlation between tumor heterogeneity and tumor hypoxic microenvironment.

overall_design: Our  tumor  samples  were  derived  from  a  patient  with  HER2  breast  invasive  ductal carcinoma  at  stage  II.  The  size  of  tumor  was  45  mm×22  mm  and  the  patient  was without  prior  neoadjuvant  therapy.  For  RNA  and  DNA  libraries  preparation,  the tissues  of  tumor  center,  12  o'clock,  3  o'clock,  6  o'clock  and  9  o'clock  of  tumor periphery as well as adjacent of the tumor were taken for 0.6 mg, respectively. Another case of normal breast tissue was used as a control. Totally, 7 samples were examined by RRBS and RNA sequencing.

first: Yan

last: Zhang

first: Yihan


title: Genome-wide maps of DNA methylation and gene expression for  multiple  regions  within  a  breast tumor

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

overall_design: Refer to individual Series


title: Identification of cis-regulatory elements affecting pancreatic Islet maturation using chromatin accessibility variations

status: Public on Dec 31 2019

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of science

summary: we were able to find several known and unforeseen key transcriptional regulators acting at cis-regulatory sites and promoters which depicted a differential accessibility and induced differential gene expression along maturation.

overall_design: ATAC-seq of Post natal 10 days  (P10) and adults rats (N=3)

first: Claudiane

last: Guay

first: Veronique

last: Menoud

first: Adriana

last: Rodriguez-Trejo

first: Lisa

last: Stoll

first: Romano

last: Regazzi