title: Altered thymic selection in Themis-deficient mice leads to expansion of an unusual virtual memory and bystander-competent CD8+ subpopulation bearing Va3.2 TCR

city: Singapore

first: Nicholas

last: Gascoigne

address: 1E Kent Ridge Road

department: Microbiology and Immunology

country: Singapore

institute: National University of Singapore

summary: This study aimed to compare the TCRab repertoires from CD8 T cell subsets in a different T cell progression stage in Themis-sufficient and Themis-deficient mice. Analysis of the NGS-derived data revealed an overall reduction of the TCRa repertoire diversity in Themis's absence. In contrast, the CD8 compartment bearing the Va3.2 TCRs in the Themis-deficient model retains higher diversity than the repertoire from the Themis-sufficient counterpart. Furthermore, analysis of CDR3 peptide sequences of Va3.2+ and Va3.2- TCRs disclose the greater contribution of the hydrophobic residues in the former repertoires, indicating enhanced self-reactivity within this CD8+ T cell fraction.

overall_design: Examination of the TCRab repertoires from two mice models:  Themis+/+ and :Themis-/-. Each genotype and cell subset is represented by the two data sets derived from two individual mouse.

first: Mukul

last: Prasad

first: Lukasz

last: Wojciech

first: Joanna

last: Brzostek

first: Jianfang

last: Hu

first: Yen

last: Chua

first: Desmond

last: Tung

first: Vasily

last: Rybakin


title: A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation

status: Public on Dec 10 2020

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The evolution of alternative splicing in glioblastoma under therapy.

city: San Francisco

first: Aaron

last: Diaz

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

summary: Alternative splicing is a rich source of tumor-specific neoantigen targets for immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary tumors of the adult brain, which are resistant to standard-of-care therapy. Although most clinical trials enroll patients at recurrence, most preclinical studies have been done with specimens from primary disease. There are limited expression data from GBMs at recurrence and surprisingly little is known about the evolution of splicing patterns under therapy. We profiled 29 primary-recurrent paired human GBM specimens via RNA sequencing. We describe the landscape of alternative splicing in GBM at recurrence and contrast that to primary and non-malignant brain-tissue specimens. By screening single-cell atlases, we identify cell-type specific splicing patterns and novel splicing events in cell-surface proteins that are suitable targets for engineered T-cell therapies. We identify recurrent-specific isoforms of mitogen-activated kinase pathway genes that enhance invasiveness and are preferentially expressed by stem-like cells. These studies shed light on gene expression in recurrent GBM and identify novel targets for therapeutic development.

overall_design:
We combined de novo RNA sequencing (RNA-seq) of paired GBM clinical specimens with public RNA-seq of non-malignant adult and fetal brain tissues to construct an integrated model of AS during GBM malignant progression.  RNA-seq of non-malignant human brain tissues were obtained from the GTEx portal (https://www.gtexportal.org/home/datasets); see Supplementary file thirdparty-reanalysis_of_GTExSamples.txt.  We screened the AS events we detected in suitable single-cell RNA-seq (scRNA-seq) data from human GBM specimens to determine their cell-type specificity. We identified an exon-retention event up-regulated in recurrent GBM in mitogen-activated protein 4 kinase 4 (MAP4K4).
*** Raw data not available due to privacy concerns.

first: Lin

last: Wang

first: Karin

last: Shamardani

first: Husam

last: Babikir

first: Francisca

last: Catalan

first: Takahide

last: Nejo

first: Susan

last: Chang

middle: J

last: Phillips

first: Hideho

last: Okada

middle: A


title: Changes in Gene Expression Profiling and Phenotype in Aged Multidrug Resistance Protein 4-Deficient Mouse Retina

status: Public on Dec 01 2020

city: Kobe

first: Sentaro

last: Kusuhara

state: Hyogo

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Department of Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

summary: Multidrug resistance related protein 4 (MRP4) belongs to the C subfamily of ABC transporters and maintains cellular environment by functioning as an efflux pump. We aimed to obtain insights into the coeffects of MRP4 deficiency and ageing on the retina, and gene expression profiling using DNA microarray were performed. To find out genes significantly up- or downregulated in aged Mrp4-null mice, the comparison of microarray data using retinal samples was carried out between aged Mrp4-null mice and aged wild-type mice.

overall_design: Eight arrays are included. We isolated whole retina from aged (aged 46-55 weeks) Mrp4 knockout mice and wild-type mice. Then, RNA extracts were hybridized to Agilent SurePrint G3 Mouse Gene Expression Arrays 8x60K Ver. 2.0 in quadruplicate.

first: Kyong

middle: W

last: Kim

first: Noriyuki

last: Sotani

first: Megumi

last: Kitamura


title: Single cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristics.

status: Public on Dec 12 2020

city: Jinan

first: Yaxiao

last: Liu

state: Shandong

address: Wenhuaxi Road 107

country: China

institute: Qilu hospital of Shandong University

summary:
Objectives: Much of the information to date in terms of subtypes and function of bladder urothelial cells were derived from anatomical location or by the expression of a small number of marker genes. To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single-cell RNA-sequencing to thoroughly characterize mouse bladder urothelium.
Materials and methods: A total of 18,917 single cells from mouse bladder urothelium was analyzed by unbiased single-cell RNA sequencing. The expression of the novel cell marker was confirmed by immunofluorescence using urinary tract infections models.
Results: Unsupervised clustering analysis identified 8 transcriptionally distinct cell subpopulations from mouse bladder urothelial cells. We discovered a novel type of bladder urothelial cells marked by Plxna4 that may be involved with host response and wound healing. We also found a group of basal-like cells labeled by ASPM that could be the progenitor cells of adult bladder urothelium. ASPM+ urothelial cells are significantly increased after injury by UPEC. In addition, specific transcription factors were found to be associated with urothelial cell differentiation. At the last, a number of interstitial cystitis/bladder pain syndrome-regulating genes were found differentially expressed among different urothelial cell subpopulations.
Conclusions: Our study provides a comprehensive characterization of bladder urothelial cells, which is fundamental to understanding the biology of bladder urothelium and associated bladder disease.

overall_design: One sample from murine urothelium. A total of 18,917 single cells from mouse bladder urothelium was analyzed by unbiased single-cell RNA sequencing.

first: Benkang

last: Shi

first: Yan


title: Hepatokine Fetuin-A  disrupts functional maturation of pancreatic β-cells

status: Public on Dec 07 2020

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: Neonatal beta-cells undergo a maturation process to acquire glucose responsiveness. We hypothesize that in later life, a partial reversal of this maturation might promote beta-cell dysfunction. We previously ascertained that fetuin-A, a fetal glycoprotein downregulated at birth but increasingly secreted when fatty liver develops, inhibits insulin secretion. Here, we evaluate fetuin-A’s impact on beta-cell maturation. In vitro maturation of neonatal porcine islet cell clusters (NICCs) promoted expression of beta-cell markers and TGFBR/SMAD signaling. Fetuin-A reduced both functional and proliferative gene expression and SMAD phosphorylation. Consequently, fetuin-A impaired glucose- and forskolin-dependent secretion, and reduced adaptive beta-cell proliferation. In adult human islets, fetuin-A abolished glucose responsiveness, diminished SMAD phosphorylation and downregulated functional and proliferative genes. Our findings suggest that perinatal decline of fetuin-A relieves TGFBR signaling in neonatal beta-cells, thereby facilitating the onset of postnatal maturation. However, this program remains revocable during adulthood, since fatty liver-derived fetuin-A reverses beta-cells’ maturity, conferring them a neonatal-like phenotype and contributing to their failure.

overall_design: 24 samples derived from porcine neonatal pancreatic islets. The neonatal islets were subjected to in vitro maturation for 10 days. Maturation was conducted in standard culture medium or in the presence of five different treatment conditions. The experiment was replicated in four idependent islet preparations.The immature islets (islets at culture day 6; HSA/day 6) represent the control for the maturated islets in standard culture medium (islets at culture day 10; HSA/day 10). The maturated islet in standard medium (HSA/day 10) represents the control for the different treatment conditions (fetuin-A, HSA + SB, HSA + LDN and HSA + SB + LDN) during the maturation process.

first: Felicia

last: Gerst

first: Marie

last: Gauder

first: Andreas

last: Dahl

first: Susanne

last: Ullrich


first: Yanqiang

last: Li

summary: Overactivated ribosome biogenesis is a common feature of cancer. However, the underlying molecular mechanism remains elusive. Herein, we report enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, could interact with fibrillarin (FBL) directly in the nucleolus. While loss of EZH2 does not impact FBL-mediated histone H2AQ104 methylation (H2AQ104me) and 18S rRNA processing, EZH2 is proved to be involved in rRNA 2′-O methylation in a manner dependent of its interaction with FBL. Mechanistically, EZH2 strengthens the fibrillarin (FBL)-NOP56 interaction by binding to both proteins and thus facilitates the assembly of box C/D small nucleolar ribonucleoprotein (box C/D snoRNP). Strikingly, EZH2 deficiency alters translational efficiency and reduces internal ribosome entry site (IRES) activity of key oncogenes in prostate cancer. In summary, our findings reveal a novel non-methyltransferase role of EZH2 that mediates FBL functions, which may provide more options for the development of EZH2-targeting curative strategies in cancer.

overall_design: Examination of transcription and translational efficiency in replicative  analysis with RNA-seq and Ribo-seq with 2 replicates at shCTRL, shEZH2 and shFBL

first: Yang

last: Yi

first: Qingshu

last: Meng

first: Wei

last: Zhao

first: Kaifu

last: Chen

first: Qi

last: Cao


title: Cranberry proanthocyanidins and dietary oligosaccharides synergistically modulate Lactobacillus plantarum physiology

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

summary: Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their gut microbiome. Based on previous observations, we hypothesized thatprobiotic Lactobacillus plantarum interact with cranberry polyphenols and dietary oligosaccharides to synergistically impact its physiology. In this study, L. plantarum ATCC BAA-793 was grown on dietary oligosaccharides including cranberry xyloglucans, fructooligosaccharides, and human milk oligosaccharidesin conjunction with proanthocyanidins (PACs) extracted from cranberry. As a result, L. plantarum exhibits a differential physiological response to cranberry PACs dependent on the carbohydrate source and polyphenol fraction introduced. Of two extracts evaluated, the PAC1 fraction increased growth regardless of oligosaccharide whereas PAC2 positively modulates growth during xyloglucan metabolism. Interestingly, PAC1 enables ATCC BAA-793 to utilize fructooligosaccharides efficiently as it is unable to ferment this substrate ordinarily. Relative to glucose, oligosaccharide metabolism increases the ratio of secreted acetic acid to lactic acid. The PAC2 fraction differentially increases this ratio during cranberry xyloglucan fermentation compared with PAC1. RNA-seq transcriptomics link expression of putative polyphenol degradation genes, polyphenol degradation profiles, and physiological phenotypes.

overall_design: Examination of genes expressed by L. plantarum during fermentations of xyloglucans, human milk oligosaccharides and fructooligosaccharides in combination with two extracts of cranberry proanthocyanidins

last: Özcan

first: Michelle

middle: R

last: Rozycki

first: David

last: Sela


title: Higher-order chromatin structures of chromosomally-integrated HHV-6A predict Integration Sites

status: Public on Dec 09 2020

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 106 Carrigan Drive

department: Biomedical and Health Sciences

institute: University of Vermont

summary: We used 4C sequencing technology for high-throughput profiling of HHV6A integration in both HEK293T cells and SMC cells. We identified genome-wide host-virus and virus-virus interactions profiles.

sample_organism:
Homo sapiens
Human betaherpesvirus 6
Human betaherpesvirus 6A

overall_design: Identification of HHV6A integration sites as well as virus-virus and host-virus interactions.

first: Michael

last: Mariani

first: Cosima

last: Zimmerman

first: Ellie

last: Hasenohr

first: Andrea

last: Dest

first: Princess

last: Rodriguez

first: Alyssa

last: Richman

first: Louis

last: Flamand

first: Benedikt

last: Kaufer


title: maize DDM1 targets RNA-directed DNA methylation on active chromatin

status: Public on Dec 05 2020

city: Beijing

first: Jincheng

last: Long

state: Beijing

address: Hai Dian district ,Yuanmingyuan Road.Beijing

department: National Maize improvement center

institute: China Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this work, we used chromatin immunoprecipitation coupled with high throughput sequencing (ChIP-seq) to ascertain the genome-wide occupancy of ZmDDM1 in maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites (TSSs) and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 could be co-purified with ZmAGO4 proteins, providing further evidence that ZmDDM1 is a component of RdDM complex in planta.

overall_design: ZmDDM1 and ZmAGO4 ChIP-seq in maize developing embryo

first: Yan

last: He


title: Transcriptomic Similarities and Differences in Host Response between SARS-CoV-2 and Other Viral Infection

city: Burlingame

first: Yehudit

last: Hasin-Brumshtein

address: 863 Mitten Road

department: Computational Biology

institute: Inflammatix

summary: COVID-19 is a pandemic that shares only certain clinical characteristics with other acute viral infections. Here, we studied the whole-blood transcriptomic host response to SARS-CoV-2 and compared it with other viral infections to understand similarities and differences in host response. We profiled peripheral blood from 24 healthy controls and 62 prospectively enrolled patients with community-acquired lower respiratory tract infection by SARS-Cov-2 within the first 24 hours of hospital admission using RNA-seq. We also collected 23 independent studies that profiled 1,855 blood samples from patients with one of six viruses (influenza, RSV, HRV, Ebola, Dengue, and SARS). We identified differentially expressed genes that change in patients with COVID-19 or other viral infections. We show changes in gene expression in peripheral blood from patients with COVID-19 are highly correlated with changes in response to other viral infections (r=0.74, p<0.001). However, two genes, ACO1 and ATL3, show significantly different changes in expression. Pathway analysis of differentially expressed genes in patients with COVID-19 or other viral infections versus healthy controls also identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection, and cytokine production for over-expressed genes, as well as lymphocyte differentiation and T cell activation for under-expressed genes. When comparing transcriptome profiles of patients with COVID-19 directly with those with other viral infections, we found 114 and 302 genes were over- and under-expressed, respectively during COVID-19. Pathways analysis did not identify any significant pathways in these genes. Statistical deconvolution using immunoStates found that M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells, and total B cells showed changes consistently in the same direction across all viral infections including COVID-19. Those that increased in COVID-19 but decreased in non-COVID were CD56bright NK cells, M2 macrophages, and total NK cells. The concordant and discordant responses mapped out via such a comparison provides a window to explore the underlying biology of why COVID-19 is so different from other viral infections encountered so far. Together, results from pathway and immunoStates analyses help dissect major shifts in cellularity and activation of signaling pathways as part of host response to SARS-CoV-2

overall_design:
Total RNA sequencing from whole blood of 62 COVID-19 patients and 24 healthy controls was compared to publicly available expression data from other infections.
Please note that raw data is not provided as consent forms do not allow for public access to raw data.

first: Simone

last: Thair

first: Yudong

middle: D

last: Hasin

first: Rushika

last: Pandya

first: Suraj

last: Sakaram

first: Jiaying

last: Toh

last: Rawling

first: Melissa

last: Remmel

first: Sabrina

last: Coyle

first: Purvesh

last: Khatri

first: Evangelos

last: Giamarellos-Bourbolis

first: Timothy

middle: E

last: Sweeney


title: Epithelial miR-141 regulates IL-13-induced airway mucus production

first: Srilaxmi

last: Nerella

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

summary: We performed RNA sequencing of gene expression in primary human bronchial epithelial cells that have undergone CRISPR/Cas9-based targeting of MIR141. The goal was to identify the role of miR-141 in goblet cell mucus production. CRISPR-targeted cells were differentiated at air-liquid-interface and stimulated with IL-13 to induce goblet cell hyperplasia.

overall_design: An electroporation-based dual guide RNA (gRNA; cRNA:tracrRNA) CRISPR protocol enabled MIR141 gene repression in primary human bronchial epithelial cells (HBECs) grown in monolayer cultures. Subsequent transfer to air-liquid-interface generated a fully differentiated airway epithelium. We harvested IL-13-stimulated HBECs that received either MIR141 gene-targeting gRNA (n=4) or non-targeting (NT) gRNA control (n=4) and untreated HBECs that received either MIR141 gene-targeting gRNA (n=3) or NT gRNA control (n=3).

first: Prescott

middle: G

last: Woodruff

first: Sana

last: Siddiqui

first: Kristina

last: Johansson


title: RNA sequencing analysis of EBF1 overexpression in cholangiocarcinoma cell line

city: Nai-Muang, Muang District

first: Napat

last: Armartmuntree

state: Khon Kaen

address: Mittapap Rd.

department: Biochemistry, Faculty of Medicine

country: Thailand

institute: Khon Kaen University

summary: To investigate the molecular mechanism of EBF1 in cholangiocarcinoma cell line, RNA sequencing analysis was performed to investigate the differential gene expression profiles between EBF1 overexpression group and control group in KKU-213A cells.

overall_design: To investigate the differential gene expression profiles between EBF1 overexpression group and control group in KKU-213A cells.

first: Raynoo

last: Thanan


title: Biomarkers for aristolochic acid nephrotoxicity

status: Public on Nov 27 2020

city: Tianjin

first: Yuhong

last: Bian

address: 10 Poyanghu Road, West Area,  Tuanbo New Town, Jinghai District

institute: Tianjin University of Traditional Chinese Medicine

summary:
Aristolochic acid (AA) is a major ingredient in several Chinese herbs that exhibits a wide range of pharmacological effects. Recently, clinical reports and experimental studies have demonstrated that AA causes renal toxicities, acute renal failure and interstitial fibrosis.However, the molecular mechanism underlying AA nephrotoxicity is not yet fully understood. Embryonic stem cells (ESCs) are pluripotent cells isolated from early embryos, which have highly undifferentiated potential and are capable of differentiating into all kinds of body tissues and organs. It has been reported that ESCs are sensitive to drug stimulation, and thus may serve as important tools for in vitro assessment of drug toxicity.
We aimed to identify accurate biomarkers of AA-induced renal toxicity on ESCs. Genomics analysis was performed to screen the changes in gene expression levels of ESCs following treatment with AA, in order to determine the potential biological processes in which AA induces renal toxicity.

overall_design: MTT assay was performed to determine the cytotoxicity of aristolochic acid in ESCs. Differentially expressed genes (DEGs) were identified using the DNA-Chip Analyzer following microarray analysis. Gene Ontology analysis was performed to determine representative categories of biological processes. Cellular component and molecular function were assessed to further understand the gene functions. DEGs were subjected to Kyoto Encyclopedia of Genes and Genomes analysis to determine representative pathways, and the network was constructed using Cytoscape 3.2 software. PERP, cation transport regulator-like 1 (Chac1), Adrb2 and Wnt6 were selected for reverse transcription-quantitative (RT-q)PCR analysis

first: Li

last: Wang

first: Shanshan

last: Man


title: The Candida albicans MEKK Ste11 has both structural and enzymatic functions in opaque cells under pheromone stimulation

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

country: Canada

institute: Western University

summary: In this study, we investigated the relationships among the pheromone components to identify how the MAPK proteins are coordinated through a scaffold that lacks a key domain. An attempt to bypass other components by artificially driving either Cst5 or Ste11 to the plasma membrane suggested that the interactions among the proteins are more complex than the linear cascade characterized in S. cerevisiae. Moreover, the findings suggest the MAPK proteins Hst7 and Ste11 regulate the translocation of Cst5 within the cytoplasm. Indeed, it appears that Ste11 interacts with Cst5 to generate a complex node to tether the downstream kinases where Ste11 can both act enzymatically on Hst7 as well as make the MAPK Cek1 available for phosphorylation and activation by Hst7.

overall_design: Liquid cultures of wild-type (WT) opaque cells (SN148aa) and opaque cells of ste11Δ/Δ were adjusted to OD600 at 0.8 in 10 mL liquid SC-GlcNac medium and incubated at room temperature for 6 hours with shaking at 220 rpm. The wild-type strain was cultivated in two tubes: untreated and treated with 10 µg/mL α-pheromone. The mutant strain was untreated. We conduted RNAseq profiling for 2 replicates in each condition (untreated WT , treated WT and untreated ste11Δ/Δ).

first: Anna

middle: C

last: Pereira Costa

first: Malcolm

last: Whiteway


title: Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster

status: Public on Nov 30 2020

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: The architectural protein Pita is critical for Drosophila embryogenesis and predominantly binds to gene promoters and insulators. In particular, Pita is involved in the organization of boundaries between regulatory domains, controlled by the expression of three hox genes in the Bithorax complex (BX-C). The best-characterized partner for Pita is the BTB/POZ-domain containing protein CP190. Here, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. The deletion of the CP190-interacting regions did not significantly affect the binding of the mutant Pita protein to most chromatin sites. The expression of the mutant protein completely complemented the null pita mutation. However, the mutant Pita protein does not support the ability of multimerized Pita sites to prevent cross-talk between the iab-6 and iab-7 regulatory domains that activate the expression of Abdominal-B (Abd-B), one of the genes in the BX-C. The recruitment of the Pita region and the interaction with CP190 and the polytene chromosomes of larvae induces the formation of a new interband, which is a consequence of the formation of open chromatin in this region. These results suggested that the interaction with CP190 is required for the primary Pita activities, but other architectural proteins may also recruit CP190 in flies expressing only the mutant Pita protein.

overall_design: ChIP-seq signal of the Flag and CP190 architectural/insulator proteins occupancy in whole embryo during embryonic development at 0-12h after egg-laying in Pita wt and Pita ΔCP1+2 lines.

first: O

last: Maksimenko

first: N


title: Gene expression of autopsy samples from small cell lung cancer patients

status: Public on Nov 25 2020

city: Kagoshima

first: Shunsuke

last: Misono

address: 8-35-1, Sakuragaoka

department: Pulmonary Medicine

institute: Kagoshima University Hospital

summary: To identify gene expression in patients with treatment-resistant small cell lung cancer.

overall_design: Twelve samples (4 normal lung tissues, 2 primary tumors, 4 lymph node metastases, 1 liver metastasis, 1 lung metastasis) were collected from autopsy specimens of three treatment-resistant small cell lung cancer patients.

first: Naohiko

last: Seki


title: Feeding a Saccharomyces cerevisiae fermentation product improves udder health and immune response to a Streptococcus uberis mastitis challenge in mid-lactating dairy

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

summary: Supplementation of a Saccharomyces cerevisiae fermentation product modulates dairy cows health by reducing incidence and severity of mastitis, one of the most common and economically important diseases of the dairy industry. However, mechanisms remain unclear. We conducted a comprehensive molecular analysis, along with physiological data, on dairy cows supplemented for 45 days with NutriTek, a commercially available S. cerevisiae fermentation product, and then subjected to a mastitis challenge . NutriTek supplementation improved cow’s responses to a mastitis challenge by stimulating influx of immune cells to the mammary gland  , enhancing their bactericidal capacity, and protecting mammary tissues from the side effect of an immune response allowing faster and more complete recovery from milk production drop

overall_design: Sixteen mid-lactation multiparous Holstein cows (n = 8/group) were used to determine the effects of a Saccharomyces cerevisiae fermentation product (NTK, NutriTek®, Diamond V, Cedar Rapids, IA) on the response to a mastitis challenge. Cows were fed the control diet (CON) or CON supplemented with 19 g/d NTK for 45 d (phase 1, P1) and then infected in the right rear quarter with 2,500 CFU of Streptococcus uberis (phase 2, P2). After 36-h, mammary gland (the infected quarter) and liver biopsies were collected and antibiotic treatment was started until the end of P2 (9 d post challenge). Cows were then followed until day 75 (phase 3, P3). On day 73 (30 days post challenge) a second mammary gland (previously infected quarter) and liver biopsy was collected.

middle: V

last: Riboni

first: Danielle

middle: N

last: Coleman

first: Vincenzo

last: Lopreiato

first: Abdulrhaman

last: Alharthi

first: Ryan

last: Bucktrout

first: Ehman

last: Abdel-Hamied

first: Ismael

middle: M

last: Cortes

first: Erminio

last: Trevisi

first: Ilkyu

last: Yoon

first: Juan

last: Loor


title: Comparative expression analysis of the Arabidopsis CK-signaling ahp4-1 mutant and wild type (WT) plants (Col-0) under dehydration conditions

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

summary: To understand the role of CK-signaling components in water stress response, we have carried out comparative expression analysis of the CK-signaling ahp4-1 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and ahp4-1 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 5 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Chien

last: Van Ha

first: Maho

last: Tanaka

first: Motoaki

first: Lam-Son

last: Phan Tran


title: Paternal obesity and epigenetic inheritance of breast cancer: The role of systemic effects and transmission to the second generation

status: Public on Nov 20 2020

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

type: Non-coding RNA profiling by high throughput sequencing

summary: Mammary gland from F1 CO female offspring exhibited enhanced development when transplanted into OID females [OID(CO-MG)], as shown by higher mammary gland area, epithelial branching and epithelial elongation, compared to CO females that received a CO mammary gland [CO(CO-MG)]. Similarly, mammary tumors from F1 CO female offspring transplanted into OID females [OID(CO.T)] displayed improved growth with higher proliferation index and lower apoptotic rates. We also found that granddaughters (F2) from the OID grand-paternal germline showed accelerated tumor growth compared to COxCO granddaughters (F2). Transmission of breast cancer predisposition to the F2 generation through OID male germline was associated with alterations in sperm tRNA fragments (tRF) in both F0 and F1 males.

overall_design: Male mice (F0) were fed either a control (CO) diet or an obesity-inducing diet (OID) for seven weeks and then mated with female mice (F0) reared on a CO diet only. The resulting offspring (F1), also fed exclusively with CO diet, were either used for mammary gland or tumor transplantation surgeries or to generate the F2 generation. To induce the mammary tumors, F1 and F2 female offspring were treated with 7,12 dimethylbenz[a]anthracene (DMBA). Total RNA extracted from F0 or F1 male’s sperm was used for small RNA-Seq analysis.

first: Camile

last: Fontelles

first: Raquel

middle: S

last: da Cruz

first: Alexandra

last: Krebs

first: Ersilia

last: Barin

first: Volkan

last: Tekman

first: M

middle: I

last: Cruz

first: Olivier

last: Loudig

first: Anni

last: Warri

first: Sonia

last: de Assis


title: Maternal antioxidant treatment prevents the adverse effects of prenatal stress on the offspring's brain and behavior [NanoString nCounter rat miRNA]

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

type:
Expression profiling by array
Other

summary:
Maternal exposure to stress during pregnancy is associated with an increased risk of psychiatric disorders in the offspring in later life. The mechanisms through which the effects of maternal stress are transmitted to the fetus are unclear, however the placenta, as the interface between mother and fetus, is likely to play a key role. Using a rat model, we investigated a role for placental oxidative stress in conveying the effects of maternal social stress to the fetus and the potential for treatment using a nanoparticle-bound antioxidant to prevent adverse outcomes in the offspring.

Maternal psychosocial stress increased circulating corticosterone in the mother, but not in the fetuses. Maternal stress also induced oxidative stress in the placenta, but not in the fetal brain. Blocking oxidative stress using an antioxidant prevented the prenatal stress-induced anxiety phenotype in the male offspring, and prevented sex-specific neurobiological changes, specifically a reduction in dendrite lengths in the hippocampus, as well as reductions in the number of parvalbumin-positive neurons and GABA receptor subunits in the hippocampus and basolateral amygdala of the male offspring. Importantly, many of these effects were mimicked in neuronal cultures by application of placental-conditioned medium or fetal plasma from stressed pregnancies, indicating molecules released from the placenta may mediate the effects of prenatal stress on the fetal brain. Indeed, both placenta-conditioned medium and fetal plasma contained differentially abundant microRNAs following maternal stress, and their predicted targets were enriched for genes relevant to nervous system development and psychiatric disorders.

The results highlight placental oxidative stress as a key mediator in transmitting the maternal social stress effects on the offspring's brain and behaviour, and offer a potential intervention to prevent stress-induced fetal programming of affective disorders.

overall_design: Samples that underwent microRNA analysis were foetal plasma, pooled per litter, collected from pregnant rats (gestational day 20) or culture medium conditioned by placentae collected from the pregnant rats. Pregnant rats had been exposed to chronic social stress while control rats were left undisturbed. Both stressed rats and control rats had been injected with nanoparticle bound MitoQ (MitoQ-NP) or saline prior to the stress episode. n = 3 pregnant rats in each of 4 experimental groups.

first: Thomas

last: Phillips

first: Ying

last: Sze

first: Alessio

last: Alfieri

first: Mark

middle: F

last: Rogers

first: Viola

last: Volpato

first: Charles

middle: P

last: Case

first: Paula

last: Brunton


title: Brassinosteroids application affects maize growth and gravitropic response by regulating gene expression in roots, shoots and leaves

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

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

country: Italy

institute: University of Bologna

summary:
Brassinosteroids (BRs) are a class of plant-specific steroid hormones which play key roles in plant physiology and seem to actively participate to the regulation of plant responses to stress. For this reason, these compounds are also grouped among the category of plant biostimulants which could be provided to crops to improve their performances and induce abiotic stress tolerance.
In this study, thanks to a combined physiological and molecular approach new insight on the effects of 24-epibrassinolide (EBL), a synthetic BR, on hydroponically grown maize seedlings were gained. To this aim, a preliminary assessment of the effect of different EBL concentrations and time of treatment on root elongation was conducted to identify the concentration to be used in subsequent experiments. A treatment with EBL 1nM and a time exposure of 48 hours were then selected to better assess the effects of this molecule also on shoot growth and on root gravitropic response. Afterwards, a RNAseq based untargeted approach was applied to obtain an overview of the transcriptomic regulation occurring in roots, shoot and leaves upon exogenous brassinosteroids applications. Our outcomes highlight a deep influence exerted by this molecule on plant growth and on root gravitropic response of maize seedlings. Moreover, thanks to the functional characterization of differentially regulated genes by means of Gene Ontology (GO) and pathway analyses, new knowledge on the BR response and signalling in plants were gained. Globally, this study provides useful information which could help for future agriculture applications of these categories of substances.

overall_design: Illumina RNA-Seq analysis of maize leaves, shoots and roots samples collected from Epibrassinolide treated or control plants (3 biological replicates per condition). 3 days old maize B73 inbreed seedlings were treated with 1nM EBL for 48h prior to samples collection and RNA extraction.

first: Sara

last: Trevisan

first: Silvia

last: Brojanigo

last: Quaggiotti

first: Serena

last: Varotto


title: Transcriptome analysis to SARS-CoV-2 infection in Vero E6 cells

status: Public on Nov 21 2020

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: RNAseq was used to identify host and viral transcriptome changes in SARS-CoV-2 infection in Vero E6 cells at 8hpi.

overall_design: Vero E6 cells were mock infected or infected with SARS-CoV-2 at a moi of 2. At 8 hours post infection, total RNAs were extracted and subjected to RNAseq analysis.

first: Yuchen

last: Zhang

first: Benjamin

last: Gewurz


title: Single cell transcriptomics reveals lineage trajectory of the retinal ganglion cells in wild-type and Atoh7-null retinas

status: Public on Nov 24 2020

city: Buffalo

first: Xiuqian

last: Mu

state: NY

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

overall_design: 10x scRNA-Seq and bulk-rna-seq of retinal ganglion cell development

first: Fuguo

last: Wu

first: Jonathan

last: Bard

first: Julien

last: Kann

first: Donald

last: Yergeau

first: Darshan

last: Sapkota

first: Yichen

last: Ge

first: Zihua

last: Hu

first: Jie

last: Wang

first: Tao

last: Liu


title: Single cell sequencing defines a branched progenitor population of stable medullary thymic epithelial cells

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary: Medullary thymic epithelial cells (mTECs) play a critical role in central immune tolerance by mediating negative selection of autoreactive T cells through the collective expression of the peripheral self-antigen compartment, including tissue-specific antigens (TSAs). Recent work has shown that gene expression patterns within the mTEC compartment are remarkably heterogenous and include multiple differentiated cell states. To further define mTEC development and medullary epithelial lineage relationships, we combined lineage tracing and recovery from transient in vivo mTEC ablation with single cell RNA-sequencing in Mus musculus. The combination of bioinformatic and experimental approaches revealed a non-stem transit-amplifying population of cycling mTECs that preceded Aire expression. Based on our findings, we propose a branching model of mTEC development  wherein a heterogeneous pool of transit-amplifying cells gives rise to Aire- and Ccl21a-expressing mTEC subsets. We further use experimental techniques to show that within the Aire-expressing developmental branch, TSA expression peaked as Aire expression decreased, implying Aire expression must be established before TSA expression can occur. Collectively, these data provide a higher order roadmap of mTEC development and demonstrate the power of combinatorial approaches leveraging both in vivo models and high-dimensional datasets.

overall_design: Lineage trace and ablation-recovery of medullary thymic epithelial cells to determine lineage relationships

middle: L


title: Hippocampal neurons respond to brain activity with functional hypoxia

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann Rein Straße 3

department: Clinical Neuroscience

institute: Max Planck Institute of Experimental Medicine

summary: Physical activity and cognitive challenge are established non-invasive methods to induce comprehensive brain activation and thereby improve global brain function including mood and emotional well-being in healthy subjects and in patients. However, the mechanisms underlying this experimental and clinical observation and broadly exploited therapeutic tool are still widely obscure. Here we show in the behaving brain that physiological (endogenous) hypoxia is likely a respective lead mechanism, regulating hippocampal plasticity via adaptive gene expression. A refined transgenic approach in mice, utilizing the oxygen-dependent degradation (ODD) domain of HIF-1α fused to CreERT2 recombinase, allows us to demonstrate hypoxic cells in the performing brain under normoxia and motor-cognitive challenge, and spatially map them by light-sheet microscopy, all in comparison to inspiratory hypoxia as strong positive control. We report that a complex motor-cognitive challenge causes hypoxia across essentially all brain areas, with hypoxic neurons particularly abundant in the hippocampus. These data suggest an intriguing model of neuroplasticity, in which a specific task-associated neuronal activity triggers mild hypoxia as a local neuron-specific as well as a brain-wide response, comprising indirectly activated neurons and non-neuronal cells.

overall_design: 4 mice (2 Normoxia, 2 Hypoxia), sacrificed after 5 days with 6h/day of normoxia/hypoxia (6%) + daily tamoxifen injections, hippocampus isolated

first: Umer

middle: J

last: Butt

first: Agnes

middle: A

last: Steixner-Kumar

first: Constanze

last: Depp

first: Ting

last: Sun

first: Imam

last: Hassouna

first: Liane

last: Wuestefeld

first: Sahab

last: Arinrad

first: Matthias

last: Zillmann

first: Nadine

last: Schopf

first: Laura

last: Fernandez Garcia-Agudo

first: Leonie

last: Mohrmann

first: Ulli

last: Bode

first: Anja

last: Ronnenberg

first: Martin

last: Hindermann

first: Sandra

last: Goebbels

first: Stefan

last: Bonn

first: Dörthe

last: Katschinski

first: Kamilla

last: Miskowiak

first: Klaus-Armin

last: Nave


title: Direct exposure to SARS-CoV-2 and cigarette smoke increases infection severity and alters the stem cell-derived airway repair response

status: Public on Nov 17 2020

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: To study the effect of cigarette smoke exposure on Sars-Cov2 infection, we directly exposed mucociliary air-liquid interface (ALI) cultures derived from primary human nonsmoker airway basal stem cells (ABSCs) to short term cigarette smoke and infected them with live SARS-CoV-2. We set out to examine the underlying mechanisms governing the increased susceptibility of cigarette smoke exposed ALI cultures to SARS-CoV-2 infection by usingle cell profiling of the cultures, which showed that interferon response genes were induced in SARS-CoV-2 infected airway epithelial cells in ALI cultures but smoking exposure together with SARS-CoV-2 infection reduced the interferon response.

overall_design: Human bronchial airway cells were cultured in air liquid interface for approximately one week. Cells were exposed or not to cigarette smoke for 4 days, then exposed or not to SARS-Covid2 virus for 72 hour. Cultures were then harvested for single cell RNA sequencing.

first: Arunima

last: Purkayastha

first: Chandani

last: Sen

first: Gustavo

last: Garcia Jr

first: Justin

last: Langerman

first: David

middle: W

last: Shia

first: Luisa

middle: K

last: Meneses

first: Preethi

last: Vijayaraj

first: Abdo

last: Durra

first: Caroline

middle: R

last: Koloff

first: Delilah

last: Freund

last: Chi

first: Tammy

last: Rickabaugh

first: A

last: Mulay

first: B

last: Konda

first: Myung

last: Sim

first: Barry

last: Stripp

first: Vaithilingaraja

last: Arumugaswami

first: Brigitte

last: Gomperts


title: Effects of β-glucan Rich Barley Flour on Glucose and Lipid Metabolism in the Ileum, Liver, and Adipose Tissues of High-Fat Diet Induced-Obesity Model Male Mice Analyzed by DNA Microarray

city: Chiyoda-ku

first: Kento

last: Mio

state: Tokyo

address: 12 Sanban-cho

department: Studies in Human Life Sciences

institute: Otsuma Womenʼs University

summary: We evaluated whether intake of β-glucan-rich barley flour affects expression levels of genes related to glucose and lipid metabolism in the ileum, liver, and adipose tissues of mice fed a high-fat diet. C57BL/6J male mice were fed a high-fat diet supplemented with high β-glucan barley, for 92 days. We measured the expression levels of genes involved in glucose and lipid metabolism in the ileum, liver, and adipose tissues using DNA microarray and q-PCR. The concentration of short-chain fatty acids (SCFAs) in the cecum was analyzed by GC/MS. The metabolic syndrome indices were improved by barley flour intake. Microarray analysis showed that the expression of genes related to steroid synthesis was consistently decreased in the liver and adipose tissues. The expression of genes involved in glucose metabolism did not change in these organs. In liver, a negative correlation was showed between some SCFAs and the expression levels of mRNA related to lipid synthesis and degradation. Barley flour affects lipid metabolism at the gene expression levels in both liver and adipose tissues. We suggest that SCFAs are associated with changes in the expression levels of genes related to lipid metabolism in the liver and adipose tissues, which affect lipid accumulation

overall_design: High-fat model mice were fed barley or control diet (cellulose) for 92 days, and ileum, liver, and adipose tissue were collected after dissection. Total RNA in each organs were extracted by using protocol of RNeasy Mini kit. The resultant single-strand cDNA was fragmented and labeled with biotin. cDNA were hybridized to the GeneArray Mouse 2.0ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G according to the manufacturer’s recommendations. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G according to the manufacturer’s recommendations.

first: Seiichiro

last: Aoe


title: MicroRNA profiling in Mesenchymal Stromal Cells: the tissue source as the missing piece in the puzzle of ageing

status: Public on Nov 18 2020

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

institute: University of Verona

summary: We compare miRNA profiling  in two cell populations of mesenchymal stromal cells focusing on senescence-related changes: Human Dental Pulp Stromal Cells (hDPSCs) and human Periosteum-Derived Progenitor Cells (hPDPCs). After these cells were harvested, total RNA extraction and whole genome miRNA profiling was performed, and DIANA-miRPath analysis was applied to find the target/pathways. Our finding is consistent with the idea that the embryological origin influences cell behavior and the ageing process. Moreover, the two populations activate different downstream mechanisms. Our study strengthens the hypothesis that ageing is driven by numerous mediators interacting through an intricate molecular network, which affects adult stem cells self-renewal capability.

overall_design: hDPSCs and hPDPCs miRNA profiling

first: Raffaella

last: Lazzarini

first: Giorgia

last: Cerqueni

first: Andrell

last: Hosein

first: Caterina

last: Licini

first: Concetta

last: De Quattro

first: Monia

last: Orciani

first: Monica

last: Mattioli-Belmonte


title: Transcriptomic Analysis of Nonylphenol Effect on Saccharomyces cerevisiae

status: Public on Nov 12 2020

city: Hatay

first: Ceyhun

last: Bereketoglu

address: Iskenderun Technical University Main Campus, Iskenderun

department: Biomedical Engineering

country: Turkey

institute: Iskenderun Technical University

summary: Nonylphenol (NP), is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the long-term impacts of NP on Saccharomyces cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration exposure for 40 days.  Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated.  GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression and related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the long-term effects of NP at the gene expression level.

overall_design: Yeast cells were exposed to 2 mg/L nonylphenol (NP)  for 40 rounds. The first round of the long-term exposure was initiated by adding NP to the cultures to reach final concentrations of 2 mg/L NP at the beginning of incubation.  At the end of 22 hour of exposure, 1 mL sample was taken from each of the cultures, centrifuged, and supernatants were discarded. The precipitated cells were suspended in 1 mL of liquid YPD medium. This process was repeated three times to remove possible NP residuals. After the washing procedure, suspended cells were transferred to the new 100 mL YPD in 500 mL flasks and NP was added to the cultures to reach the above mentioned final concentrations of NP,  and the second round of the exposure was initiated. The long-term exposure was performed for 40 rounds by repeating the above steps.

first: Gozde

last: Nacar

first: Tugba

last: Sari

first: Ajay

last: Pradhan

first: Bulent

last: Mertoglu


title: Differentially expressed genes in pneumococcus-infected THP-1 monocytes

city: Taipei

first: Yung-Chi

last: Chang

address: Rm 736, No. 1, Sec. 1, Jei-Ai Rd

department: Microbiology

country: Taiwan

institute: National Taiwan University, College of Medicine

summary: To investigate the mechanistic role of NanA and Siglec-5 in this excessive inflammation, we systemically analyzed genes and signaling pathways differentially regulated in macrophages infected with wild type and NanA-deficient pneumococcus.

overall_design: 6 samples are analyzed, including unfected cells as negative control


title: CSF1R defines the Mononuclear Phagocyte System lineage in human blood in health and disease

status: Public on Nov 19 2020

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

summary: Use of  lineage determining receptors as markers for monocytes

overall_design: Blood from three healthy patients were FACS sorted into four CD14/CD16 gates with a CSF1R prior gating. The 4 quadrants of the CD14/CD16 plot were recombined in equal cell numbers for each patient and scRNAseq performed using the 10X genomics platform

first: Theo

last: Combes

first: Federica

last: Orsenigo

first: Alexander

last: Stewart

first: Helena

last: Crowell

first: Deborah

last: Dunn-Walters

first: Simon

last: Draper

first: Ruth

last: Payne

first: Siamon

last: Gordon

last: Martinez


title: KRAS drives immune evasion in a genetic model of pancreatic cancer [bulk RNA-seq]

status: Public on Nov 11 2020

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: Immune evasion is a hallmark of KRAS-driven cancers, but underlying mechanism and clinical implications remain unclear.

overall_design: We used a mouse model of pancreatic carcinogenesis to completely inactivate KRAS by CRISPR-mediated genome editing.

first: Oleksi

last: Petrenko

first: Nancy

last: Reich


title: Gtf2i and Gtf2ird1 E13.5 whole brain ChIP-seq and RNA-seq

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: HetxHet breeding pairs for the Gtf2i/Gtf2ird1 double mutants and Gtf2ird1 were set up for timed breedings. E13.5 embyros of WT, HET, and HOM mutants (n=3 for each genotype and each cross), were used for RNA-seq. Similar breedings were done for ChIP-seq. The ChIP-seq WT controls were E13.5 embyros from WT FVB/ANTJ x FVB/ANTJ and compared to HOM Gtf2i/Gtf2ird1 double mutatns and HOM Gtf2ird1 single mutants. There were n=3 WT and n=3 hom Gtf2ird1 single mutants for Gtf2ird1 ChIP-seq. There were n=4 WT and n=4 hom Gtf2i/Gtf2ird1 double mutants for Gtf2i ChIP-seq. Each genotype had the sample matched input control along with ChIP sample.

overall_design: Gtf2i and Gtf2ird1 E13.5 ChIP-seq and RNA-seq

first: Nathan

last: Kopp


title: Chromatin topology and the timing of enhancer function at the HoxD locus [ChIP-seq]

status: Public on Nov 10 2020

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

summary: The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate separately from two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory sub-modules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrates the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts is eventually resumed, showing that the presence of enhancers sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavourable orientation of CTCF sites.

overall_design: ChIPmentation analysis of H3K27ac, CTCF, RAD21 in embryonic limb tissues of wild-type and mutant mice.

first: Lucille

last: Lopez-Delisle

first: Denis

last: Duboule


title: Chromatin topology and the timing of enhancer function at the HoxD locus

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

overall_design: Refer to individual Series


title: TbSAP is a novel chromatin protein repressing metacyclic Variant Surface Glycoprotein expression sites in bloodstream form Trypanosoma brucei

status: Public on Nov 04 2020

city: London

first: James

last: Budzak

address: Exhibition Road

institute: Imperial College London

summary: The African trypanosome Trypanosoma brucei is a unicellular eukaryote, which relies on a protective Variant Surface Glycoprotein (VSG) coat for survival in the mammalian host. A single trypanosome has >2000 VSG genes and pseudogenes of which only one is expressed from one of ~15 telomeric bloodstream form expression sites (BESs). Infectious metacyclic trypanosomes present within the tsetse fly vector also express VSG from a separate set of telomeric metacyclic ESs (MESs). All MESs are silenced in bloodstream form T. brucei. As very little is known about how this is mediated, we performed a whole genome RNAi library screen to identify MES repressors. This allowed us to identify a novel SAP domain containing DNA binding protein which we called TbSAP. TbSAP is enriched at the nuclear periphery and binds both MESs and BESs. Knockdown of TbSAP in bloodstream form trypanosomes did not result in cells becoming more ‘metacyclic’-like. Instead, there was extensive global upregulation of transcripts including MES VSGs, VSGs within the silent VSG arrays as well as genes immediately downstream of BES promoters. TbSAP therefore appears to be a novel architectural chromatin protein playing an important role in silencing the extensive VSG repertoire of bloodstream form T. brucei.

overall_design: Comparative RNAseq for T. brucei cells subjected to TbSAP (Tb927.10.4440) and tubulin RNAi. Comparison was against 0 h and 72 h RNAi for TbSAP and 0 h and 16 h for tubulin. Parental T. brucei cell line (prior to inclusion of RNAi machinary) was included for TbSAP RNAi analysis. All RNAseq was carried out in biological triplicate.

first: Carys

last: Davies

first: Cher-Pheng

last: Ooi

first: Georgios

last: Sioutas

first: Belinda

last: Hall

first: Haneesh

last: Sidhu

first: Falk

last: Butter

first: Sam

last: Alsford

first: Bill

last: Wickstead

first: Gloria

last: Rudenko


title: Differential expression profiles and functional prediction of circular RNAs in pediatric dilated cardiomyopathy

status: Public on Nov 07 2020

city: jinan

first: sun

last: wei

address: HuaiYin District Jingwuweiqi Road

institute: Provincial Hospital affiliated to Shandong University

summary: Circular RNAs (circRNAs) have emerged as essential regulators and biomarkers of various disease. To assess differential expression levels of circRNAs in pediatric dilated cardiomyopathy (PDCM) and explore their biological and mechanistic significance.

overall_design: RNA microarrays were used to identify differentially expressed circRNAs between three children diagnosed PDCM and three healthy age-matched volunteers. Biological function of circRNAs was assessed with a circRNA-microRNA (miRNA)-mRNA interaction network constructed from Gene Ontology (GO) and the Kyoto encyclopedia of genes and genomes (KEGG). Differentially expressed circRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in 25 children with PDCM and 25 healthy volunteers

first: Bo

last: Han

first: Wei

last: Sun


title: Genome-wide H3K4me3 profile in in vitro produced bovine blastocysts

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

institute: Kyoto University

summary: We aimed to obtain genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3), a representative marker of active chromatin, in bovine blastocysts.

overall_design: In vitro produced bovine blastocysts were processed to ChIP-Seq using H3K4me3 antibody with corresponding Input control. The experiments were triplicated using three biological replicates.

first: Mao

last: Ishibashi

first: Naojiro

last: Minami


title: Single cell RNAseq of Rbp4cre+ neurons from prefrontal cortex

city: Stanford

first: Justus

last: Kebschull

state: CA

address: 327 Campus Drive

institute: Stanford University

summary:
Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks
We perform single nucleus RNAsequencing using a smartseq2 protocol on mouse prefrontal cortex neurons labeled by tdTomato in an Rbp4-cre;Ai14 mouse. Some cells were retrolabeled from various brain regions.

overall_design: Dataset consists from single cell RNAseq data collected from >10 animals

first: Jan

last: Lui


title: Identification of regulatory circRNAs involved in pathogenesis of acute myocardial infarction

city: Shanghai

first: Yangyang

last: Zhang

state: Shanghai

address: 150 Jimo Road

department: Department of Cardiovascular Surgery

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: The circRNA array was applied to investigate the expression level of circRNAs in the blood samples of coronary arteries of AMI patients and normal persons. Differentially-expressed circRNAs and potential circRNA-miRNA networks were identified in AMI patients.

overall_design: Arraystar human circRNA array was applied to detect and quantify circRNAs in the six samples of three acute myocardial infarction (AMI) patients and three normal controls. Blood samples were collected from the coronary arteries of six participants (three with ST-elevation myocardial infarction (STEMI) and three without AMI) undergoing percutaneous coronary intervention (PCI) due to undiagnosed chest pain. The miRNA expression profiles of AMI patients were identified from a public dataset from Gene Expression Omnibus (GEO) database (GSE31568). The miRNA binding sites on the circRNAs were predicted by miRanda. The miRNA enrichment analysis and annotation tool were used to explore the pathways that the dysregulated circRNAs may participate in.

first: Ban

last: Liu

first: Xuebo

first: Cuimei

last: Zhao

first: Jingjing

first: Wen

last: Ge

first: Zhi

last: Li

first: Mengwei

last: Lv

first: Yipeng

last: Feng


title: The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk Sac Mesodermal Progenitors [scRNA-Seq]

status: Public on Nov 01 2020

city: Oxford

first: Luke

middle: Thomas Gilbert

last: Harland

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: Oxford University

summary: Extra-embryonic mesoderm (ExM), the earliest cells that traverse through the primitive streak, give rise to the endothelium as well as hematopoietic progenitors in the developing yolk-sac (YS). How a specific subset of ExM becomes committed to a hematopoietic fate remains unclear. Here we report that Eomesodermin (Eomes), a T-box transcription factor, is transiently expressed in ExM progenitors that generate virtually all YS hematopoietic and endothelial cells. Using an embryonic stem cell (ESC) differentiation system, we find that Eomes activity is essential for the production of primitive erythrocytes and for the normal development of Runx1+ HE that generates the definitive hematopoietic progenitors. RNA-Seq and ATAC-Seq experiments reveal that Eomes governs the accessibility of numerous hematopoietic enhancers that SCL normally utilizes to specify primitive erythrocytes and HE in Flk-1hi/PdgfRa- hematovascular mesoderm. ChIP-seq experiments suggest that Eomes coordinates the development of hemogenic competent mesoderm in the context of Activin/Nodal and Tead-Yap signaling. Finally, single-cell- RNA-seq (scRNAseq) shows that in the absence of Eomes function diversion towards an endothelial rather than hematopoietic fate occurs after the initial specification of Flk-1+/SCL+ hematovascular mesoderm. Collectively, these experiments demonstrate that Eomes sits at the top of the transcriptional hierarchy, functioning upstream of Runx1 expression and SCL functional activity, and promotes hemogenic competence of the entire YS mesodermal lineage.

overall_design: scRNA-seq profiles of wild type and Eomes-null day 4 and day 5 Flk-1hi/PdfgRa- EB cells  generated by deep sequencing using Illumina Nextseq.

middle: T

first: Claire

last: Simon

first: Anna

last: Senft

first: Ita

last: Costello

first: Lucas

last: Greder

first: Elizabeth

last: Bikoff

first: Catherine

last: Porcher

first: Marella

last: de Bruijn

last: Robertson


title: RNA-sequencing analysis of cerebral cortex in Down syndrome and controls

status: Public on Nov 03 2020

city: Zhengzhou

first: Weili

last: Shi

state: Henan

address: 7 Weiwu Road

department: Medical Genetics Institute of Henan Province

institute: Henan Provincial People's Hospital

summary: To determine the relationship between m6A modification and gene expression, we analyzed the RNA-Seq data of the same cortex tissues as MeRIP-Seq analyzed

overall_design: Three of cortex tissues from Down syndrome fetus and two of cortex tissues from controls were analyzed to identify differential expressed genes

first: Shixiu

last: Liao

first: Bingtao

last: Hao


title: MeRIP-sequencing analysis of cerebral cortex in Down syndrome and controls

summary: To explore the characteristics of m6A RNA modification in the Down syndrome brain, we collected cerebral cortex tissues of the fetuses diagnosed with Down syndrome and controls respectively, and performed an optimized methylated RNA immunoprecipitation combined with deep sequencing (MeRIP-seq).

overall_design: Three of cortex tissues from Down syndrome fetus and two of cortex tissues from controls were used to identify the characteristics of m6A RNA modification in the Down syndrome brain and differential expressed m6A related genes in Down syndrome


title: The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk Sac Mesodermal Progenitors [RNA-Seq]

overall_design: mRNA profiles of wild type and Eomes-null day 4 Flk-1hi/PdfgRa- EB cells were generated by deep sequencing in biological triplicate using Illumina HiSeq4000.


title: The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk Sac Mesodermal Progenitors [ChIP-Seq]

overall_design: EoV5 ChIP-Seq occupancy profiles for one wild type and two Eo-V5 clones (A&B) from day 4 EBs, generated by deep sequencing using Illumina HiSeq4000.


title: METTL3-mediated N6-methyladenosine modification is involved in the dysregulation of NRIP1 expression in Down syndrome


title: The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk Sac Mesodermal Progenitors


title: The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk Sac Mesodermal Progenitors [ATAC-Seq]

overall_design: Tn5-accessible chromatin profiles of wild type and Eomes-null day 4 Flk-1hi/PdfgRa- EB cells were generated by deep sequencing in biological triplicate using Illumina HiSeq4000.


title: Heterotrophic growth on formate is dependent on the maintenance of intracellular pH for the thermoacidophilic methanotroph Methylacidiphilum sp RTK17.1.

status: Public on Oct 31 2020

city: Christchurch

first: Carlo

middle: Robert

last: Carere

address: University of Canterbury, Private Bag 4800,, Deliver to Carlo Carere, Link Building, room A311

department: Chemical and Process Engineering

country: New Zealand

institute: University of Canterbury

summary: In this work, we investigated intracellular pH homeostasis within the thermoacidophilc methanotroph Methylacidiphilum sp. RTK17.1.  Our findings show the proton motive force for this species is primarily generated by a pH gradient across the cellular membrane. In batch experiments, the addition of formate resulted in no observable cell growth and, correspondingly, acidification of the cytosol, decreased formate dehydrogenase activity and (presumably) cell-death. Nevertheless, we were able to demonstrable growth on formate as the sole source of metabolizable energy was possible in steady-state (continuous) cultures following the transition from methanol to formate. Under these conditions, biomass productivity yields on formate were 63% less than for growth on methanol. Transcriptome analysis revealed key genes associated with pH homeostasis, methane, methanol and formate metabolism were significantly regulated in response to growth on formate. Collectively, these results suggest environmental formate represents a utilisable source of energy/carbon to the acidophilic methanotrophs during periods of methane starvations and highlights potential short-comings of traditional batch-culture physiological characterisation studies in acidophilic species.

overall_design: Chemostat cell samples (3 total) of Methylacidiphilum sp. RTK17,1 were grown methylotrophically (pH 2.5, 45C) under oxygen limiting conditions in the presence of NH4+. Following the establishment of a steady state condition, methanol was replaced with an equimolar concentration of formate

first: Kiel

last: Hards

first: Kathryn

last: Wigley

last: Carman

first: Karen

last: Houghton

first: Greg

last: Cook

first: Matthew

middle: B

last: Stott


title: Single nucleus RNAseq of cerebellar nucleus neurons in three species

status: Public on Oct 30 2020

first: Justus

middle: M

last: Kebschull

summary: We perform single nucleus RNAsequencing using a smartseq2 protocol on mouse, chicken, and human cerbellar nuclei. Nuclei were released and FACS sorted for NeuN

sample_organism:
Gallus gallus
Homo sapiens
Mus musculus

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus


title: RNA sequencing of cardiac endothelial cells from the cardiovascular disease risk factor mouse models

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

summary: Purpose: Our objective is to profile and compare the cardiac endothelial cell transcriptome, identify and validate the candidate gene from the indicated experimental groups

overall_design:
Four different studies were conducted in C57Bl/6J mice: exercise trained vs. sedentary mice, high-fat diet (HFD) -induced obese vs. lean mice, aged (18 mo) vs. young (2 mo) mice and transverse aortic constriction (TAC) vs. sham -operated mice. Cardiac endothelial cells  were isolated and sorted by FACS, and analyzed by RNA sequencing.
cDNA library was synthesized using SMARTer Stranded Total RNA-Seq Kit V2 – Pico Input Mammalian (Takara Bio, USA) kit, The library quality was determined using bioanalyzer and sequenced using illumina NextSeq 550 System with the following specifications: 1 X 75bp, 50M single end reads.

last: Kivela

first: Karthik

last: Hemanthakumar


title: GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis

status: Public on Oct 26 2020

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of an individual tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant translational GTPases function in the same pathway to mitigate ribosome pausing. Ribosome stalling in the mutant brain led to activation of the integrated stress response (ISR) mediated by GCN2 and decreased mTORC1 signaling. However, in contrast to the ISR, which enhanced neuron survival, reduced mTORC1 signaling increased neuronal death. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective translation elongation.

overall_design: 18 samples are in analyzed in this study in the context of 3 week old C57BL/6J (B6J) mouse cerebellum. These include 3 replicates of the following genotypes Gtpbp1 -/-, Gtpbp2 -/- (mediated through a previously characterized nmf205 point mutation), and wildtype mice. RNA-seq and ribosome footprint profiling datasets were generated for each sample.

first: Markus

last: Terrey

first: Alana

last: Gibson

first: Tianda

last: Deng

first: Ryuta

last: Ishimura

first: Jeffrey

middle: H

last: Chuang

first: Susan

last: Ackerman


title: Transcriptome analysis reveals downregulation of urocortin expression in the hypothalamo-neurohypophysial system of Spontaneously Hypertensive rats

status: Public on Oct 22 2020

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary: Tissue extracted from the Supraoptic nucleus (SON), paraventricular nucleus (PVN) to determine gene expression differences as a consequence of hypertension within these structures

overall_design: SHR and WKY animals at 12-weeks were sacrificed and the PVN and SON were fine dissected.

first: David

last: Murphy

first: Charles

last: Hindmarch

first: Andrew

last: Martin

first: Andre

middle: S

last: Mecawi

first: Vagner

last: Antunes

first: Jose

last: Antunes-Rodrigues

first: Julian

last: Paton

first: Alex

last: Paterson

first: Michael

last: Greenwood

first: Olivera

last: Šarenac

first: Bojana

last: Savić

first: Nina

last: Žigon


title: Development of a comprehensive toxicity pathway model for 17α-ethinylestradiol (EE2) in early life stage fathead minnows (Pimephales promelas)

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

institute: University of Saskatchewan

summary: The goal of this study is to characterize molecular toxicity pathways associated with ethinylestradiol-induced toxicity and link these molecular perturbations to apical outcomes of regulatory relevance.

overall_design: mRNA profiles of whole fathead minnows (Pimephales promelas) exposed to 0.01% DMSO, 20 ng/L EE2, and 100 ng/L EE2 (nominal concentrations)  from < 6 hours post-fertilization to 4 days post-hatch

first: Alper James

last: Alcaraz

last: Potěšil

first: Kamil

last: Mikulášek

first: Derek

last: Green

first: Bradley

last: Park

first: Connor

last: Burbridge

first: Kerstin

last: Bluhm

first: Othman

last: Soufan

first: Taylor

last: Lane

first: Marek

last: Pipal

last: Brinkmann

first: Jianguo

last: Xia

first: Zbyněk

last: Zdráhal

last: Schneider

first: Doug

last: Crump

first: Niladri

last: Basu

first: Natacha

last: Hogan


title: Tracking immune cells from brain metastasis microenvironment to the cerebrospinal fluid

status: Public on Oct 13 2020

city: Barcelona

first: Joan

last: Seoane

address: Vall d'Hebron 119-129

country: Spain

institute: VHIO

summary: PanCancer Immune Panel profiling of 50 brain metastases

overall_design: PanCancer Immune Panel profiling of 50 fresh/frozen brain metastases, 7 duplicated samples have been included, being the Sample name Px_2


title: next generation sequencing of migratory Innate lymphoid cells, T cells and dendritic cells in mesenteric lymph

status: Public on Oct 27 2020

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

summary: This study was designed to identify NGS-derived trascriptomes (RNA-sequencing) of different cell populations (ILCs, T cells and DCs) isolated from the lamina propria of the intestine and from the thoracic duct.

overall_design: Trasncriptomic profile of migratory cells isolated from the thoracic duct and comparison to their tissue resident counterparts

first: Simon

middle: F

last: Milling

first: Verena

last: Kaestele

first: David

last: Withers

first: Tom

last: Cupedo

first: Vuk

last: Cerovik

first: Carl

last: Goodyear


title: Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

first: Ameen

last: Salahudeen

address: 265 Campus Drive

department: Medicine/Hematology

institute: Stanford University School of Medicine

summary: The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange.  Three-dimensional in vitro human distal lung culture systems would strongly facilitate investigation of pathologies including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia.  We generated long-term feeder-free, chemically-defined culture of distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells.  AT2 organoids exhibited AT1 transdifferentiation potential while basal cell organoids developed lumens lined by differentiated club and ciliated cells.  Single cell analysis of basal organoid KRT5+ cells revealed a distinct ITGA6+ITGB4+ mitotic population whose proliferation further segregated to a TNFRSF12Ahi subfraction comprising ~10% of KRT5+ basal cells, residing in clusters within terminal bronchioles and exhibiting enriched clonogenic organoid growth activity.  Distal lung organoids were created with apical-out polarity to display ACE2 on the exposed external surface, facilitating SARS-CoV-2 infection of AT2 and basal cultures and identifying club cells as a novel target population.  This long-term, feeder-free organoid culture of human distal lung, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and establishes a facile in vitro organoid model for human distal lung infections including COVID-19-associated pneumonia.

overall_design: Deep single cell RNA-sequencing analysis of >15,000 organoid cells from distal lung cultures from 3 individuals and purified AT2 cells from a fourth individual. 3-4 technical captures are included for each distal lung culture.

first: Shannon

last: Choi

first: Arjun

last: Rustagi

first: Junjie

last: Zhu

first: Vincent

last: van Unen

first: Sean

last: De la O

first: Ryan

last: Flynn

first: Mar

last: Margalef-Catala

first: Antonio

last: Santos

first: Jihang

last: Ju

first: Arpit

last: Batish

first: Tatsuya

last: Usui

first: Gracy

middle: X

last: Zheng

first: Caitlin

middle: E

last: Edwards

first: Lisa

last: Wagar

last: Luca

first: Benedict

last: Anchang

first: Monica

last: Nagendran

first: Khanh

last: Nguyen

first: Daniel

last: Hart

first: Jessica

last: Terry

first: Phillip

last: Belgrader

first: Solongo

last: Ziraldo

first: Tarjei

last: Mikkelsen

first: Pehr

last: Harbury

first: Jeffrey

last: Glenn

first: K

middle: C

last: Garcia

first: Mark

last: Davis

first: Ralph

last: Baric

first: Chiara

last: Sabatti

first: Manuel

last: Amieva

first: Catherine

last: Blish

first: Tushar

last: Desai

first: Calvin

last: Kuo


title: Comparative transcriptome analysis in adipose and muscle between Chinese buffalo and cattle.

status: Public on Oct 20 2020

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

summary: Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in  the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.

sample_organism:
Bos taurus
Bubalus bubalis

platform_organism:
Bos taurus
Bubalus bubalis

overall_design:
Examination of muscle (the longissimus dorsi muscle) and adipose (the back subcutaneous fat) of 3 Xinyang buffalo and 3 Nanyang cattle, with 30 month of age.
Study includes buffalo adipose samples from GSE112744.

first: Jieping

last: Huang

first: Yun

last: Ma


title: The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity

city: bethesda

first: Elissa

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of porcine blastocyst form cumulus oocyte complexes matured in coculture with porcine luteal cells

city: Buenos Aires

first: Gabriela

middle: Maia

last: Teplitz

address: Chorroarin 280

department: Histology and Embriology

country: Argentina

institute: Universidad de Buenos Aires

summary: The transcriptome pattern in blastocyst that developed from cumulus oocyte complexes matured in coculture with porcine luteal cells was investigated.

overall_design: Two condition experiment,  4 pools of 10 blastocysts, collected on Day 7 and Day 8

first: Marc-André

last: Sirard

first: Daniel

last: Lomabrdo


title: AK-192_pmel-BO112

status: Public on Oct 14 2020

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

summary: Bulk Tumor RNAseq of B16-JAK1KO tumor cells after exposure to vehicle or BO112

overall_design: B16-JAK1KO tumor cell line treated in vitro with vehicle or BO112

last: Kalllbasi


title: AK-098_pmel-BO112

summary: Bulk Tumor RNAseq after Adoptive T cell Therapy and Intratumoral BO112

overall_design: C57BL/6 mice bearing B16-JAK1KO tumors treated with adoptive T cell therapy (non-specific mock T cells versus tumor-specific pmel T cellls) and intratumoral injection (vehicle vs BO112).


title: Effects of restriction on mammary gland transcriptome

status: Public on Oct 10 2020

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

country: France

institute: INRAE

summary: The effects of a negative energy balance induced by a nutritional restriction on mammary gland were evaluated using the 4x44K bovine microarray from Agilent

overall_design: one-color experiment, 50 ng of total RNA from mammary gland of 5 holstein cows before  and after restriction (d6).

first: Pierre-Alexis

last: BILLA

first: Céline

last: BOBY

first: Yannick

last: FAULCONNIER


title: Temporal analysis of mRNA from leaf tissue in field grown rice

status: Public on Oct 07 2020

city: RALEIGH

first: Montana

last: Knight

state: NC

address: Campus Box 7566

department: Genomic Sciences Graduate Program

country: USA

institute: North Carolina State University

summary: Rice (IR64) was grown in a field plot at the International Rice Research Institute in the Phillipines. This data shows transcriptional changes happening throughout the day in leaf tissue and how warm nighttime temperature may influence those transcriptional changes.

overall_design: Leaf tissue was harvested every three hours from dawn to 23 hours past dawn. There are 8 timepoints total with four replicates each. There is a control set and a set grown in warm nighttime temperature,

first: Jigar

first: Lovely

last: Lawas

first: Ashlee

last: Valente

first: Adam

last: Leman

first: Krishna

last: Jagadish SV

first: Colleen

middle: J

last: Doherty


title: Profiling the DNA methylation pattern in B3GALT5 knockout hESCs cultured in basal and 2iLAF media

status: Public on Oct 06 2020

city: Taoyuan

first: Ruey-Jen

last: Lin

address: No.5, Fuxing St., Guishan Dist.

department: Institute of Stem Cell & Translational Cancer Research

institute: Chang Gung Memorial hospital

type: Methylation profiling by high throughput sequencing

summary: We analyzed the DNA methylation pattern in B3GALT5-Knockout H9 cells (B3GALT5-KO) relative to wild type H9 cells (WT) by whole-genome bisulfite sequencing. Collectively, our results reveal that B3GALT5-Knockout cells cultured in 2iLAF condition represent naïve-specific characteristics as well as WT cells convert to naïve state in 5iLAF condition. These findings support that loss of B3GALT5 which result in depletion of primed-specific GSLs not only do not have influence on maintain pluripotency and ability to specific lineage differentiation but also could promotes naive pluripotency generation in hESCs.

overall_design: This data includes four Bisulfite-seq datasets. Two primed and two naïve hESCs were profiled in experiments. Primed samples consist of H9 hESCs with or without knockout of B3GALT5 where indicated, in standard primed hESC conditions. Naïve samples consist of H9 hESCs with or without knockout of B3GALT5 that were profiled after conversion to the naïve state (5iLAF or 2iLAF medium where indicated).

first: Bei-Chia

last: Yang

first: Ming-Wei

last: Kuo

first: Yun-Shien

last: Lee

first: John

last: Yu


title: Profiling the mRNA pattern in B3GALT5 knockout hESCs cultured in basal and 2iLAF media

summary: We analyzed the RNA expression pattern in B3GALT5-Knockout H9 cells (B3GALT5-KO) relative to wild type H9 cells (WT) by RNA-seq. Collectively, our results reveal that B3GALT5-Knockout cells cultured in 2iLAF condition represent naïve-specific characteristics as well as WT cells convert to naïve state in 5iLAF condition. These findings support that loss of B3GALT5 which result in depletion of primed-specific GSLs not only do not have influence on maintain pluripotency and ability to specific lineage differentiation but also could promotes naive pluripotency generation in hESCs.

overall_design: This data includes five RNA-seq datasets. Two primed, two naïve hESCs and 1 control hESC samples were profiled in experiments. Primed samples consist of H9 hESCs with or without knockout of B3GALT5 where indicated, in standard primed hESC conditions. Naïve samples consist of H9 hESCs with or without knockout of B3GALT5 that were profiled after conversion to the naïve state (5iLAF or 2iLAF medium where indicated). A control sample is WT of H9 cultured in 2iLAF medium.

first: Alice


title: Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle

city: madrid

first: Paulina

middle: G.

last: Eusebi

state: madrid

address: Ave. Puerta del hierro

department: Animal Production

institute: Universidad Complutense de Madrid

summary: This study compared gene expression profiles of 16 prefrontal cortex (PFC) samples from aggressive and non-aggressive cattle breeds: Lidia, selected for agonistic responses, and Wagyu, specialized on meat production and selected for tameness. RNA sequencing was used to identify and classify 918 up and 278 down-regulated differentiated expressed genes (DEG). The functional interpretation of the up-regulated genes in the aggressive cohort revealed enrichment of pathways such as the Alzheimer disease-presenilin, integrins or the ERK/MAPK signaling cascade, all implicated in the development of abnormal aggressive behaviors and neurophysiological disorders. Moreover, gonadotropins, leading to testosterone release, are also up-regulated as a natural mechanisms enhancing aggression. Concomitantly, heterotrimeric G-protein pathways, associated with low reactivity mental states, and the GAD2 gene, a repressor of agonistic reactions at the PFC, are down-regulated, guaranteeing the development of the adequate responses required by the aggressive Lidia cattle.  We also identified six upstream regulators, whose functional activity fits with the etiology of abnormal behavioral responses associated with aggression.

overall_design: 16 non-castrated male bovines  8 belonging to the Lidia breed and 8 from the Wagyu breed, for the aggressive and non-aggressive cohorts respectively

middle: G

first: Natalia

last: Sevane

first: Manuel

last: Pizarro

first: Javier

last: Cañón

first: Susana

last: Dunner


title: Spatio-temporal transcriptional profiling of leaf development in rice

city: Tokyo

first: Masayuki

last: Miya

address: Bunkyo, Yayoi 1-1-1

country: Japan

institute: The University of Tokyo

summary: Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages.

overall_design: To obtain a comprehensive transcriptome of leaf development in rice, we sampled 12 leaf parts representing various stages and components along the longitudinal axis. Rice seedlings at the four-leaf stage were dissected into 12 parts: shoot apex containing the SAM and P1 and P2 leaf primordia; entire P3 leaf primordium; apical, middle, and proximal parts of P4 leaf blade; P4 leaf sheath; and the leaf blade, sheath, and boundary region of P5 and P6 leaves. Three biological replicates were prepared for each part, and their RNA was hybridized to a 44K rice microarray.

first: Takanori

last: Yoshikawa

first: Yutaka

last: Sato

first: Jun-Ichi

last: Itoh


title: The acute host-response of turkeys colonized with Campylobacter coli

status: Public on Oct 01 2020

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Consumption of contaminated poultry products is one of the main sources of human campylobacteriosis, of which Campylobacter jejuni subsp. jejuni (C. jejuni) and C. coli are responsible for approximately 98% of the cases. The ceca of commercial turkeys are the main anatomical site where Campylobacter asymptomatically colonizes. We have previously colonized the ceca of commercial turkey poults with C. jejuni, and demonstrated acute changes in cytokine gene expression in cecal tissue and histologically scored intestinal lesions at 2 days post-inoculation (dpi). The host-response of turkeys to C. coli colonization is unknown. Cecal tonsils (CT) are an important part of the gastrointestinal-associated lymphoid tissue that function to sample material passing in and out of the ceca and generating immune responses against intestinal pathogens. The CT immune response towards Campylobacter is unknown. In this study, we generated a C. coli kanamycin-resistant construct (CcK) for enumeration from cecal contents after experimental challenge. In vitro analysis of CcK demonstrated no changes in motility when compared to the parent isolate, but in vitro growth rates were significantly different than the parent strain. Poults were inoculated by oral gavage with CcK (5x10^7 cfu) or sterile-media (mock-colonized), and euthanized at 1 and 3 dpi. At both time points, CcK was recovered from cecal contents, but not from the mock-colonized group. As a marker of acute inflammation, serum alpha-1 acid glycoprotein was significantly elevated at 3 dpi in CcK inoculated poults compared to mock-infected samples. Significant histological lesions were detected in cecal and CT tissues of CcK colonized poults at 1 and 3 dpi, respectively. RNAseq analysis identified 250 differentially expressed genes (DEG) in CT from CcK colonized poults at 3 dpi, of which 194 were upregulated and 56 were downregulated. From the DEG, 9 significantly enriched biological pathways were identified, including platelet aggregation, response to oxidative stress and negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway. These data suggest that C. coli induced an acute inflammatory response in the intestinal tract of poults, and that platelet aggregation and oxidative stress in the CT may affect the turkey’s ability to resist Campylobacter colonization. Results from this study provide insight into host-response of the turkey CT to Campylobacter colonization. These findings will help to develop and test Campylobacter mitigation strategies to promote food safety in commercial turkeys.

overall_design: Transcriptomic profile of turkey cecal tonsils colonized with Campylobacter coli, eight biological replicates, using Illumina HiSeq3000.

first: Matthew

last: Sylte

first: Julian

last: Trachsel

first: Yuko

first: Zuowei

last: Wu

first: Torey

last: Looft

first: Timothy

middle: A

last: Johnson

first: Lawrance

last: Chandra

first: Qijing

last: Zhang


title: Non-viral Induction of Transgene-free iPSCs from Somatic Fibroblasts of Multiple Mammalian Species [marmoset]

city: Shinjuku

first: Sho

last: Yoshimatsu

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: Induced pluripotent stem cells (iPSCs) are capable of providing an unlimited source of cells from all three germ layers as well as germ cells. The derivation and usage of iPSCs from various animal models may facilitate stem-cell-based therapy, generation of gene-modified animals, and evolutionary studies assessing interspecies differences. However, there is a lack of species-wide methods for deriving iPSCs, in particular by means of non-viral and non-transgene-integrating (NTI) approaches. Here, we demonstrated the derivation of iPSCs from somatic fibroblasts of multiple mammalian species from three different taxonomic orders, including the common marmoset (Callithrix jacchus) in Primates, the dog (Canis lupus familiaris) in Carnivora, and the pig (Sus scrofa) in Cetartiodactyla, by combinatorial usage of chemical compounds and NTI episomal vectors. Interestingly, the somatic fibroblasts temporarily acquired a neural stem cell (NSC)-like state during the reprogramming procedure. Collectively, our method, robustly applicable to various species, holds a great potential for facilitating stem-cell-based research using various animals in Mammalia.

overall_design: RNA seq of marmoset fibroblasts, iNSLCs, in vivo neurospheres and iPSCs

first: Mayutaka

last: Nakajima

first: Hideyuki

last: Okano


title: DNA methylation analysis of cloned HCT116 cells treated with a DNA demethylating drug.

status: Public on Oct 02 2020

city: Shinagawa-ku

last: Takeshima

department: Institute for Advanced Life Sciences

institute: Hoshi University

type: Methylation profiling by genome tiling array

summary: Epigenetic reprogramming using demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen.  Low-dose treatment for a prolonged period shows a high therapeutic efficacy, despite its small demethylating effect.  Here, we aimed to reveal the mechanisms of how such low-dose treatment shows high efficacy by focusing on epigenetic reprograming at the single-cell level.  Single-cell RNA-sequencing of HCT116 cells treated with decitabine (DAC) revealed that up-regulated genes were highly variable at the single-cell level.  To analyze functional consequences at the single-cell level, DAC-treated HCT116 cells were cloned.  While only partial reduction of methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes was observed, depending upon clones.  For example, p16 was completely demethylated in the H3-32 clone out of 9 clones, and this clone showed slower proliferation than other clones without demethylation.  In addition, in this clone, the fraction of cells with tetraploid became much larger, indicating that cellular senescence was induced.  These results showed that epigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the high efficacy of low-dose DNA demethylating therapy.

overall_design: DNA methylation statuses of cloned HCT116 cells were analyzed using Infinium HumanMethylation450.

first: Yukie

last: Yoda

first: Naoko

last: Watanabe

first: Toshikazu

last: Ushijima