title: Tissue transcriptome atlas across DIO and lean mouse tissues

status: Public on Oct 13 2021

city: Seattle

first: Sara

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

institute: Novo Nordisk Research Center Seattle, Inc.

summary: RNA sequencing was performed on several tissues extracted from 5 lean and 5 diet-induced obese (DIO) mice.

first: Burak

last: Kutlu

first: Leandro

middle: Z

last: Agudelo


title: Regulation of hepatocellular carcinoma growth by UPF1 variants not through nonsense-mediated mRNA decay

city: Seoul

first: Suman

last: Lee

address: FTC, 222 Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang university

type: Expression profiling by high throughput sequencing

summary: Multiple studies showed that overexpression of UPF1 reduced the growth of HCC. However, it remains unanswered how UPF1 expression retarded HCC proliferation. Thus, this study employed UPF1 variants to evaluate the UPF1 function in HCC growth inhibition. Transcriptome analysis indicated that the level of DUSP1, dual specificity phosphatase 1, was upregulated by UPF1 variants by posttranscriptional regulation. The increase of DUPS1 by UPF1 overexpression repressed the downstream signaling, inhibiting cell growth.

overall_design: Examination of transcriptome difference between UPF1 variants overexpression Huh7 cells and control Huh7 cells.

first: Yukyung

last: Hwang

first: TaeHun

last: Kim

first: Jaemin

last: Jeong

first: Dongho

last: Choi

first: Jungwook


title: Unrestricted SUMOylation drives lymphomagenesis

status: Public on Oct 11 2021

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

type: Genome binding/occupancy profiling by high throughput sequencing


title: C2C12 expressing desmin: WT vs Mutations R406W and I451M

status: Public on Oct 09 2021

city: Paris

first: Onnik

last: Agbulut

address: 7 quai st-bernard

country: France

institute: Sorbonne Université

summary: C2C12 cell lines were genetically engineered to stably express WT human Desmin or the Desmin mutant R406W or I451M. Non-modified C2C12 cells were used as control. The goal was to determine the effect of different desmin mutation on the gene expression in a myoblast cell line.

overall_design: Three experimental conditions: WT vs control (1 biological sample), R406W vs Control (1 biological sample), I451M vs control (2 biological samples)

first: O


title: Genome-wide analysis of iPSC-derived neurons with EGFP or TERT transduction

status: Public on Oct 12 2021

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

country: USA

institute: University of Texas, MD Anderson Cancer Center

summary: Analysis of TERT-dependent global gene expression changes in iPSC-derived human AD neurons. The hypothesis tested in the present study was that TERT influences the regulation of gene expressions in the iPSC-derived human neurons. Results provide important information of the response of iPSC-derived neurons in presence and absence of TERT induction.

overall_design: Total RNA obtained from EGFP- or TERT-transduced iPSC-derived neurons

first: Ronald

middle: A

last: DePinho

first: Hong

middle: S

last: Shim


title: Genome-wide analysis of wildtype and mTERT KO (G1) mouse brain

summary: Analysis of TERT-dependent global gene expression changes in mouse brain. The hypothesis tested in the present study was that TERT influences the regulation of gene expressions in the mouse brains. Results provide important information of the response of in vivo mouse brains in presence and absence of Tert expression.

overall_design: Total RNA obtained from wildtype and mTERT KO (G1) mouse brains


title: Transcriptomic analysis of the hippocampus in Alzheimer’s disease

status: Public on Oct 05 2021

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: Purpose: The goal of this study is to compare NGS-derived transcriptome profiling (RNA-seq) in AD patients’ hippocampus. Methods: mRNA profiles of human hippocampus from AD patients and healthy controls were generated by deep sequencing, using Illumina GAIIx. Results: Using an optimized data analysis workflow, more than 20000 transcripts in hippocampus were detected. Top 6 genes were selected and related to “ion transport”. Correlation analysis demonstrated negative relationship of gene expression level with the neuropathologic changes.

overall_design: mRNA profiles of hippocampus in AD patients and healthy controls.

first: Xia

last: Wang


title: Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits (RNA-Seq)

status: Public on Oct 01 2021

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

summary: To investigate the role of the hypothalamus in influencing complex traits, we generated ATAC-seq, RNA-seq, and Promoter Focused Capture C to gain insight into the gene regulatory arcitecture contacting promoters in an embryonic stem cell dervived model of hypothalamic neuron differentiation

overall_design: We performed ATAC-seq, RNA-seq, and Promoter Focused Capture C on stages of ESC dervived hypothalamic like neuron differentiation (ESC: day 0; HP: day 12; HN: day 27).

first: Struan

last: . Grant


title: Excess S-Adenosylmethionine inhibits methylation via catabolism to adenine

status: Public on Sep 23 2021

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

country: United Kingdom

institute: University of Manchester

summary: Mouse embryonic fibroblasts were treated with 1mM SAM, 1mM adenine or 10microM, and transcriptome signatures were compared to untreated cells.

overall_design: Cells were cultivated in 3 replicate 10cm Petri dishes per treatment until confluence. Medium was replaced with medium containing either 1mM S-adenosylmethionine (SAM) and 3.3 mM HCl, 1mM adenine and 3.3 mM HCl, 10 microM Deazaneplanocin A (DZ) and 3.3 mM HCl, or 3.3 mM HCl. Since the solvent of adenine was HCl, the same amount of HCl was added to all other dishes.

first: Ben

last: Saer

first: Peter

last: Briggs

first: Andrew

last: Hayes


title: RdsA is a global regulator that controls cell shape and division in Rhizobium etli

status: Public on Sep 22 2021

city: Cuernavaca

first: David

last: Romero

state: Morelos

address: Ave. Universidad 2001. Col. Chamilpa

department: Center for Genomic Sciences

country: Mexico

institute: National Autonomous University of Mexico

summary: Unlike other bacteria, cell growth in rhizobiales is unipolar and asymmetric. The regulation of cell division, and its coordination with metabolic processes is an active field of research. In Rhizobium etli, gene RHE_PE00024, located in a secondary chromosome, is essential for growth. This gene encodes a hybrid histidine kinase sensor protein, participating in a, as yet undescribed, two-component signaling system. In this work, we show that a conditional knockdown mutant (cKD24) in RHE_PE00024 (hereby referred as rdsA, after rhizobium division and shape) generates a striking phenotype, characterized by cells with a round shape, with stochastic and uncoordinated cell division. A fraction of the cells showed also multiple ectopic polar growths, sometimes leading to growth from the old pole, a sector that is normally inactive for growth in a wild-type cell. Homodimerization of RdsA appears to be required for normal function. RNAseq analysis of mutant cKD24 reveals global changes, with differentially expressed genes in at least five biological processes: cell division, wall biogenesis, respiration, translation, and motility. These modifications may affect proper structuring of the divisome, as well as peptidoglycan synthesis. Together, these results indicate that the hybrid histidine kinase RdsA is an essential global regulator influencing cell division and cell shape in R. etli.

overall_design: Differential expression profiling of genes associated with RdsA depletion (strain cKD24). Control strain: R etli CE3 wild-type. Strains were grown in Y minimal medium for 9 h at 30°C. Three biological replicates for each strain.

first: Sofía

last: Martínez-Absalón

first: Carmen

last: Guadarrama

first: Araceli

last: Dávalos


title: Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits

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

overall_design: Refer to individual Series


title: A male-derived non-ribosomal peptide pheromone controls female schistosome development

status: Public on Oct 04 2021

city: Dallas

first: James

middle: J.

last: Collins

address: 5323 Harry Hines Blvd.

department: Pharmacology

institute: UT Southwestern

summary: gli1 is a gene in the male S. mansoni required  for female sexual development. As a putative transcription factor, RNAseq comparing pairs with gli1 knocked-down or control males was performed to look for the genes which are trancriptionally regulated by gli1. sm-nrps was one of the essential candidate discovered in this analysis that has been characterized in the same publication, revealing a pheromone directed novel mechanism of female schistosome sexual development.

overall_design: RNA sequencing of virgin  male/female schistosome parasites after 3 days of pairing or no-contact co-culture under the condtion of pairing with gli RNAi males or control RNAi males.

first: Jipeng

middle: J


title: Transcriptomic analysis of DENV-specific CD8+T cell responses in acute disease does not support qualitative differences as drivers of disease severity

status: Public on Sep 21 2021

city: La Jolla

first: Alba

last: Grifoni

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: In this study, we assessed the contribution of dengue-specific CD8+T cells in hospitalized samples with mild (dengue fever; DF) and severe (dengue hemorrhagic fever; DHF) forms of the disease. Our in-depth transcriptomic analysis provides no evidence for qualitative differences in terms of CD8+T cell response against dengue, therefore, concluding that CD8+T cell response is not a contributing factor in the development of severe dengue disease.

overall_design: 40 individuals that required hospitalization due to DENV infection (based on clinical diagnosis and being positive either with PCR or IgM serology assay), have been enrolled and the corresponding blood samples were collected during hospitalization and during a follow up visit in convalescent phase. The 40 individuals are classified based on diseases severity in 20 with the mild form of the disease (Dengue Fever; DF) and 20 with the most severe form of the disease (Dengue Hemorragic Fever; DHF). For each donor, PBMCs purified from the blood samples have been stimulated with DENV-specific pool of class I peptides for 6 hours followed by IFNg capture assay.  After stimulation, the CD8+CD3+ cells have been sorted based on being IFNg positive or IFNg negative and both conditions were sequenced using a microscaled  approach.

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette


title: whole-gene transcriptome profiling of Panc-1 which were treated with conditinal meida (CM) from CAFS or CAFR

status: Public on Sep 16 2021

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Tumor stroma of pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant and heterogeneous cancer-associated fibroblasts (CAFs) that are critically involved in chemoresistance. However, the underlying mechanism of CAFs in chemoresistance is unclear. Here, we show that CAFR, a CAFs subset derived from oxaliplatin-resistant PDAC patients, produces more IL8 than CAFS isolated form oxaliplatin-sensitive PDAC patients. CAFR derived IL8 promotes PDAC oxaliplatin chemoresistance. Base on long non-coding RNA (lncRNA) profiling in tumor cells incubated with CAF, we identify that UPK1A-AS, which is directly induced by IL8/NF-kappa B signaling, functions as a pro-chemoresistant lncRNA and is critical for active IL8-induced oxaliplatin resistance. Impressively, blocking UPK1A-AS1 activation increases sensitivity of tumor cell response to oxaliplatin chemotherapy in vivo. Mechanically, UPK1A-AS1 strengths the interaction of Ku70 and Ku80 to enhance double-strand DNA break (DSB) repair, thereby coordinating the NHEJ pathway. Clinically, UPK1A-AS1 expression is positively correlated with IL8 expression, poor chemotherapeutic response and shorter PFS of PDAC patients. Collectively, our study discovers a lncRNA-mediated mechanism for CAF derived IL8 paracrine-dependent oxaliplatin resistance and highlights UPK1A-AS1 as potential therapeutic targets.

overall_design: whole-gene transcriptome profiling of Panc-1 which were treated with CAFS-CM or CAFR-CM respectively. It is conducted in triplicate.

first: Xiang

last: Zhang

first: Chonghui

last: Hu

first: Shangyou

last: Zheng


title: ELK3 controls gastric cancer cell migration and invasion by regulating ECM remodeling-related genes

status: Public on Sep 14 2021

city: Seongnam-si

first: Minwook

last: Lee

state: Gyeonggi

address: 335 Pangyo-ro, Bundang-gu

institute: CHA University

summary: Current therapeutic strategies, including surgery and chemotherapy, for gastric cancer improve survival; however, the survival rate for those with metastatic gastric cancer is very low. The molecular mechanisms underlying dissemination of gastric cancer cells to distant organs are unknown. Here, we show that the ELK3 gene is necessary for migration and invasion of gastric cancer cells. The ELK3 gene modulates expression of extracellular matrix (ECM) remodeling-related genes such as LOXL2, SERPINF1, COL16A1, NID1, and SNAI1 to facilitate cancer cell dissemination. Our in silico analysis indicated that ELK3 expression was positively correlated with these ECM remodeling-related genes in gastric cancer cells and human gastric cancer patients. High expression of ELK3 and other ECM remodeling-related genes was also closely associated with a worse prognosis of gastric cancer patients. These findings suggested that ELK3 acts as an important regulator of gastric cancer dissemination by regulating ECM remodeling.

overall_design: Gene expression comparison with or without ELK3; between SNU638 wild type and ELK3 knockdown.

first: Hyeon-Ju

last: Cho

first: Kyung-Soon

last: Park

first: Hae-Yun

last: Jung


title: Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes

status: Public on Sep 17 2021

city: CHENGDU

first: CHENGCHENG

last: LIU

state: SICHUAN

address: No. 14, Section 3, Renminnan Road

institute: Sichuan University

summary:
Purpose: This study provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.
Methods: HUVECs were seeded in 6-well plates and cultured to 80% confluence. After washing with phosphate-buffered saline (PBS), cell were infected with P. gingivalis at a multiplicity of infection (MOI) of 100 for 2 h at 37 °C in 5% CO2, unless otherwise stated. Non-adherent bacteria were removed by washing with PBS, and the cell-adherent bacteria were killed using gentamicin (300 μg/mL) and metronidazole (200 μg/mL) for 1 h at 37 °C in 5% CO2.Total RNA was isolated from the samples using TRIzol® reagent.cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA).
Results: Using an optimized data analysis workflow,  intracellular P. gingivalis showed a total of 573 DEGs compared with the control bacteria, and of these DEGs, 304 and 269 were upregulated and downregulated, respectively. A total of 838 DEGs were detected in P. gingivalis-infected HUVECs compared with their uninfected counterparts, and of these, 297 and 541 genes were upregulated and downregulated, respectively.
Conclusions: This study firstly provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.

sample_organism:
Homo sapiens
Porphyromonas gingivalis ATCC 33277

overall_design: P. gingivalis cultured in the miedum;  intracellular P. gingivlais; HUVEC cultured in the medium; HUVEC infected with P. gingivalis

first: Chengcheng

last: Liu


title: Multi-omics profiling of mouse myocardial infarction

city: Shanghai

first: Wenju

address: 1239  siping road

institute: University of Tongji

summary: Myocardial infarction (MI),  the most severe manifestation of coronary artery disease, is a multifactorial pathophysiologic process. Here, we constructed a MI mouse model through ligation of the proximal left anterior descending coronary artery. Then we detected and analysed  multi-omics (transcriptome and proteome) at different time points (Control, 10 mininte, 1 hour, 6 hour, 24 hour and 72 hour) after MI. Immune-related pathway, pyroptosis pathway, and autophagy pathway r were significantly increased after MI.

overall_design: RNA-seq analysis of mouse myocardial infarction at different time points (Control, 10 mininte, 1 hour, 6 hour, 24 hour and 72 hour) after MI.

first: Junwei

last: Shen


title: Differential gene expression in M. tuberculosis infected-murine bone marrow-derived macrophages upon colchicine treatment

status: Public on Sep 11 2021

first: Sung Jae

last: Shin

address: 50-1 Yonsei-ro

department: Department of Microbiology

institute: Yonsei University College of Medicine

summary: We investigated the molecular mechanisms by which colchicine regulates host defense in macrophages against M. tuberculosis infection. To elucidate this, we performed global gene expression analysis of M. tuberculosis infected-bone marrow-derived macrophages after colchicine treatment.

overall_design: Bone marrow-derived macrophages (BMDMs) were differentiated from 6~7 weeks old female C57BL/6 mice and then divided into 9 groups 1) Naïve BMDMs 2) M. tuberculosis infected BMDMs 3) M. tuberculosis infected BMDMs followed by colchicine treatment for 4 h 4) Naive BMDMs 5) M. tuberculosis infected BMDMs 6) M. tuberculosis infected BMDMs followed by colchicine treatment for 4 h 7) Naïve BMDMs 8) M. tuberculosis infected BMDMs 9) M. tuberculosis infected BMDMs followed by colchicine treatment for 4 h

first: Kee Woong

last: Kwon

first: Lee-Han

last: Kim


title: Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Cancer cells interact with a wide variety of other cell types, but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single-cell RNA-seq (scRNA-seq) has helped define these TME cell types, it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here, we integrate spatial transcriptomics with scRNA-seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well-defined transgenic zebrafish model of BRAFV600E-driven melanoma, we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased, data-driven approach, we identify spatially-patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA-seq, we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes, and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress their expression outside of this region. This unique ETS-driven interface transcriptional state is conserved across ten different human patient samples, suggesting this is a conserved feature of human melanoma. Taken together, our results demonstrate the power of spatial and single-cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues.

overall_design: Spatial transcriptomics (Visium platform) of zebrafish bearing BRAF-V600E driven melanomas. Single-cell RNA-seq (10X Genomics v3) of two such zebrafish. Single-nucleus RNA-seq (10X Genomics v3) of three such zebrafish (pooled into one reaction).

first: Reuben

last: Moncada

middle: V


title: Tuber-omics in potato with the T and D types of cytoplasm showed differentially expressed genes and proteins in response to cold storage

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

summary: For the first time, we report differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in potato (Solanum tuberosum L.) tubers characterized by light and dark chip color after cold storage. Two potato diploid progenies derived from reciprocal crosses of parental clones possessing the T- and D-type cytoplasm were used. We recognized 48 and 15 DEGs as compared to RNA-seq data of contrasting segregants. We identified DEPs in potato tuber amyloplast and mitochondrial fractions. Seven and five DEPs were identified in the amyloplast fractions of the T – and D – type cytoplasm, respectively. Higher number of DEPs were selected from the mitochondrial fraction. The corresponding values were 97 and 105, including 39 common DEPs in the T – and D – type cytoplasm. These findings suggest that mitochondria may play a more important role than amyloplasts in response of potato tubers to cold treatment and that this influence can be different for the T – and D – type cytoplasm. However, we showed that the mt/nucDNA and pt/nucDNA ratios tend to increase for tubers characterized by dark chip color when compared with light chip color samples. Therefore, a protective effect of reducing sugars on both amyloplasts and mitochondria during low temperature treatment should be considered.

overall_design: Tuber-omics approach to find differences in T- and D- potato cytoplasm in response to cold sweetening

first: Katarzyna

last: Szajko

first: Małgorzata

last: Heidorn-Czarna

first: Paulina

last: Smyda-Dajmund

first: Iwona

last: Wasilewicz-Flis

first: Hanna

last: Jańska

first: Waldemar

last: MarczewskI


title: the myoblast differentiation difference in normal and DM1 murine cell models

status: Public on Sep 08 2021

city: Wuhu

first: Xiaopeng

address: 1 East Beijing Rd.

institute: Anhui Normal University

summary: To study the gene expression profile difference in the myoblast differentiation of normal and DM1 groups, we performed RNA-seq on the total RNA samples collected from the in vitro myoblast differentiation day 4 of normal and DM1 C2C12 cell models. Normal and DM1 cell models were bulit by stably transfecting C2C12 cells with GFP-CUG5 and GFP-CUG200 plasmids. Each group contained three biological replicates. The expression matrix was obtained by Hisat2 followed by Stringtie.

overall_design: RNA-seq of normal and DM1 C2C12 cell differentiated for 4 days


title: Gene expression profiles of the prostates of prostate-specific Pten-/- mice

status: Public on Sep 10 2021

city: Piscataway

first: Hong

last: Wang

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

institute: Rutgers the State Univesrity of New Jersey

summary: We reported the gene expression profiles of prostate dorsal-lateral-ventral glands of prostate-specific Pten-/- mice on AIN93M diet, 60%Kcal high-fat diet, and AIN93M diet containing 0.05% delta-tocotrienol at 20 weeks of age.

overall_design: To study the effects of metabolic syndrome and delta-tocotrienol on the development of prostate cancer, we investigated the transcriptomes of the prostate of prostate-specific Pten-/- mice on AIN93M diet (control), 60% Kcal high-fat diet, and AIN93M diet containing 0.05% delta-tocotrienol starting at 6 weeks of age. Total RNA samples were extracted from prostate dorsal-lateral-ventral glands, separated under dissection microscope, collected from the mice at 20 weeks of age. RNA-sequencing was completed by BGI (US).

first: Chung

last: Yang


title: Transcriptomics approach to understand the role of vitamin A in Citrobacter rodentium infection in the mouse small intestine and colon

status: Public on Sep 09 2021

city: New York city

first: Zhi

last: Chai

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary:
Overall hypothesis: RNAseq can be used to examine and compare the vitamin A (VA) effect, Infection effect caused by Citrobacter rodentium (C. rodentium), and the Interaction effect (VA status × C. rodentium infection) in mouse small intestine (SI) and colon, on the scale of global transcriptome.
Methods: Vitamin A deficient (VAD) mice were generated by feeding VAD diet to the pregnant C57/BL6 dams and their post-weaning offspring. Vitamin A sufficient (VAS) mice were fed with purified diet containing normal amount of VA. At weaning, mice were maintained on their respective diets and assigned to one of the four treatment groups (non-infected VAD, infected VAD, non-infected VAS and infected VAS) until the end of the experiments. For the infected groups, age-matched VAD or VAS mice were orally inoculated with C. rodentium. Mice during early (SI study) or peak (colon study) C. rodentium infection were euthanized in two separate studies. The SI study focused on SI and analyses were performed on samples collected 5 days post-infection. The colon study analyzed samples on post-infection day 10, the peak of C. rodentium infection. Total mRNA extracted from SI and colon were sequenced using Illumina HiSeq 2500 platform. Three to six biological replicates were sequenced in each group. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression patterns and co-expression patterns.
Results: a) differentially expression genes (DEGs) corresponding to VA effect were present in both the SI and colon. In SI, DEGs altered by VA were mainly involved in the retinoid metabolic pathway and immunity-related pathways. Novel target genes (e.g. Mbl2, Mmp9, Cxcl14, and Nr0b2) and cell types (based on Tuft cell and mast cell markers) under the regulation of VA were suggested by differential expression analysis coupled with the co-expression network analysis. In regard to the colon, VA demonstrated an overall suppressive effect on the cell division pathway. Finally, the comparison of co-expression modules between SI and colon indicated distinct regulatory networks in these two organs. b) In the SI, no Infection effect was detected during early infection, whereas in the colon, during peak of C. rodentium infection: 1) It has been shown that infection upregulated innate and adaptive immune functions, epithelial proliferation, apoptosis, endoplasmic reticulum stress, and reactive oxygen species production, as well as downregulated ion and water absorption. This helped to confirm the findings in previous studies, consolidating the knowledge-base about the host response to C. rodentium, 2) Pathways (e.g. neuron activity, smooth muscle contraction, vascular constriction, and developmental regulation) and additional ion transporters previously not known to be influenced by C. rodentium were suggested as potential mechanisms responsible for the diarrhea pathology and host response. 3) Retinoic acid receptor (RAR) and vitamin D receptor (VDR) signaling pathways appeared to be downregulated by infection, indicating that the malabsorption of micronutrients might be a danger signal for the host to switch from homeostasis to an anti-infection mode. c) In the SI, no Interaction (VA status × C. rodentium infection) effect was detected during early infection. In colon, 1329 genes corresponded to the Interaction effect. During the peak of C. rodentium infection, the sufficient stimulation of cell division, protein catabolism, apoptosis, transcription regulation, MHC class I, interferons, and cytokine signaling might be of key importance for the resistance of VAS mice. In addition, the proper maintenance of the proliferation, differentiation, migration, and activation of T cells and leukocytes during peak infection may also confer the VAS hosts with higher survival and clearance rate. On the other hand, our data suggested that the higher rate of lethal dehydration observed in infected VAD mice, may be attributed to the disrupted of HCO3- metabolism and an improperly high level of Cl- secretion.
Conclusions: VA alters the gene expression profile in both SI and colon, whereas the Infection effect and the Interaction effect were only observed in colon during peak of C. rodentium infection, but not in the SI during early infection. Our studies suggest novel target genes and cell types under the regulation of VA in the SI, and indicate that the resistance of the VAS hosts may be attributed to the concordant control over ion/water absorption, immune functions, as well as the balance between epithelial hyperplasia and apoptosis.

overall_design:
mRNA profiles of small intestine (SI) and colon from four treatment groups (non-infected VAD, infected VAD, non-infected VAS and infected VAS) were generated by RNAseq, with n=3~6, using Illumina HiSeq 2500 platform. The SI study focused on SI and analyses were performed on samples collected 5 days post-infection. The colon study analyzed samples on post-infection day 10, the peak of C. rodentium infection. Those time points were chosen to ensure the presence of C. rodentium pathogen in the target organs. With respect to vitamin A status, the deficient and adequate states should remain the same, whether on day 5 or day 10 relative to infection, as the mice had been on their designated diets for at least 9 weeks.
In the validation study, the VAD mice in the RA treatment group received a daily oral dose of 37.5 ug of RA in 10 ul corn oil for four consecutive days prior to the day of sample collection, whereas the VAD mice without repletion served as the control group which received 10 ul corn oil as placebo. Each of the experimental groups contained three mice (9 to 11 weeks, young adult) when tissue samples were collected.

first: A

last: Ross


title: The endometrial response to pregnancy is altered in cows after uterine infection.

status: Public on Sep 07 2021

city: Gainesville

first: Mackenzie

last: Dickson

state: Florida

address: 2250 Shealy Drive

department: Animal Science

institute: University of Florida

summary: Pregnancy induces changes in the transcriptome of the bovine endometrium from 15 days after insemination. However, pregnancy is less likely to occur if cows had a postpartum bacterial infection of the uterus. We hypothesized that uterine bacterial infection alters the endometrial transcriptomic signature of pregnancy. To examine the endometrial transcriptomic signature of pregnancy, cows were inseminated 130 days after intrauterine infusion of pathogenic bacteria and endometrium was collected 16 days later for RNA sequencing. We found 171 pregnancy regulated genes in cows 146 days after bacterial infection. When comparing our findings with three previous studies that described the endometrial transcriptomic signature of pregnancy in healthy cows, 24 genes were consistently differentially expressed in pregnancy, including MX1, MX2 and STAT1. However, 12 pregnancy regulated genes were only found in the endometrium of healthy cows, including ISG15 and TRANK1. Furthermore, 28 pregnancy regulated genes were only found in the endometrium of cows following bacterial infection and these were associated with altered iNOS, TLR, and IL-7 canonical signaling pathways. Although 94 predicted upstream regulators were conserved amongst the studies, 14 were found only in the endometrium of pregnant healthy cows, and 5 were found only in cows following bacterial infection, including AIRE, NFKBIA, and DUSP1. In conclusion, there were both consistent and discordant features of the endometrial transcriptomic signature of pregnancy 146 days after intrauterine bacterial infusion. These findings imply that there is an essential transcriptomic signature of pregnancy, but that infection induces long term changes in the endometrium that affect the transcriptomic response to pregnancy.

overall_design: To understand effect of uterine infection on endometrium, seven cows received intrauterine infusion of pathogenic E. coli and T. pyogenes to mimic a uterine infection. Cows were inseminated 130 days after bacteria infusion, and uteri collected and classified as pregnant or non-pregnant at day 16 post-insemination (146 days after bacteria infusion). To analyze the impact of bacteria infusion on the endometrial transcriptomic signature of pregnancy, intercarunular endometrium was collected and processed for RNA sequencing. We hypothesized that uterine bacterial infection alters the endometrial transcriptomic signature of pregnancy.

first: Jeanette

last: Bishop

first: Thomas

middle: R

last: Hansen

first: I

middle: M

last: Sheldon

first: John

last: Bromfield


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung [CUT&RUN]

city: Cambridge

first: Carla

last: Concepcion

state: MA

address: 500 Main Street, 76-431

department: Koch Institute

institute: MIT

summary: SMARCA4 (BRG1) encodes for one of two mutually-exclusive ATPases present in mammalian SWI/SNF chromatin remodeling complexes, and is among the most frequently mutated genes in human lung adenocarcinoma. Despite its prevalence, the functional consequences of SMARCA4 mutation on tumor initiation, progression and chromatin regulation in lung cancer remains poorly understood. Using genetically engineered mouse models, patient-derived xenografts, and single-cell epigenomic profiling, we demonstrate that loss of Smarca4 sensitizes CCSP+ cells within the lung in a cell-type dependent fashion to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence. Consistent with these phenotypes, Smarca4-deficient primary tumors lack lung lineage transcription factor activities and instead show hyper-activation of embryonic stem cell-like programs, resembling a metastatic cell state. Mechanistically, we show that all three classes of SWI/SNF complexes are unable to bind and open chromatin at distinct regulatory regions in the absence of SMARCA4, thereby preventing lineage factors from binding to their targets and maintaining cell identity – ultimately accelerating tumor progression. Thus, the SWI/SNF complex – via Smarca4 – acts as a gatekeeper for lineage-specific cellular transformation and metastasis during lung cancer evolution.

overall_design: Isogenic pairs of murine KrasG12D/+;Trp53-/- lung adenocarcinoma cell lines harboring intact Smarca4 or loss-of-function Smarca4 mutations generated by CRISPR in vitro. Biological replicates were generated from two independent tumor-derived parental cell lines

middle: P

first: Sai

last: Ma

first: Lindsay

last: LaFave

first: Arjun

last: Bhutkar

first: Manyuan

last: Liu

first: Lydia

last: DeAngelo

first: Jonathan

middle: Y

last: Kim

first: Isabella

last: Del Priore

first: Adam

last: Schoenfeld

first: Vinay

middle: K

last: Kartha

first: Peter

last: Westcott

first: Francisco

last: Sánchez-Rivera

first: Kevin

last: Meli

first: Manav

last: Gupta

first: Gregory

last: Riely

first: Natasha

last: Rekhtman

first: Charles

last: Rudin

middle: F

first: Aviv

last: Regev

first: Jason

middle: D

last: Buenrostro

first: Tyler

last: Jacks


title: Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

city: Eilat

first: Eran

last: Yanowski

address: North beach

country: Israel

institute: National Center for Mariculture

summary: We report that delta cells are Sox9 descendants that expand at the periphery of the regenerating islets following partial pancreatectomy. We further characterize regeneration-driven heterogeneity of beta cells at a single-cell resolution, demonstrating sub-populations of ER-stressed, proliferating and highly-functioning beta-cells. We further systematically map sub populations of beta-cells that are paired with other endocrine cell types. Our analysis suggests that the particular cluster of beta-cells that pair with delta-cells benefits from stress protection, implying that the interaction between beta and delta-cells safeguards against regeneration-associated challenges.

overall_design: Single-cell RNA seq on dissociated isolated islets, 4 weeks following partial pancreatectomy. Data of 2300 cells collected from 6 pancreata analyzed by MetaCell

last: Hornstein

first: Nancy-Sarah

last: Yacovzada

first: Eyal

last: David

first: Amir

last: Giladi

first: Diego

last: Jaitin

last: Farack

first: Adi

last: Egozi

first: Danny

last: Ben-Zvi

first: Shalev

last: Itzkovitz

first: Ido

last: Amit


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung

first: Carla

last: Concepcion

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation [ATAC-seq]

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. Morc3 knock-out cells display de-repression, reduced H3K9me3 and increased chromatin accessibility of distinct ERV classes. We found that the GHKL ATPase domain of Morc3 is critical for ERV silencing, since mutants which cannot bind ATP, or which are defective in ATP hydrolysis cannot rescue the Morc3 ko phenotype. Proteomic analysis revealed that Morc3 mutant protein which cannot bind ATP fails to interact with the H3.3 chaperone Daxx. This interaction depends on Morc3 sumoylation, as Daxx lacking the SUMO interaction domain shows reduced association with Morc3. Notably, in Morc3 ko cells, we observed strongly reduced H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as critical regulator of Daxx-mediated H3.3 incorporation into ERV regions.

overall_design: Chromatin accessibility analysis in wild type, Morc3 knock out and different Morc3 rescue mouse embryonic stem cells

first: Sophia

last: Groh


title: Genetic engineering of the first functional human cardiomyocyte lines for building clinically relevant atrial fibrillation models

status: Public on Aug 30 2021

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

summary: Using conditional immortalization, we generated the first lines of human cardiomyocytes with preserved cardiomyogenic differentiation capacity. These human immortalized Atrial Myocytes (hiAMs) display strict control over proliferation and differentiation, allowing massive (quadrillion-fold) expansion followed by differentiation towards fully functional (i.e. excitable and contractile) human atrial cardiomyocytes. Here, we compared the transcriptome of three hiAM monoclones after differentiation (D12) with hESC-derived AMs (D28) using RNA-sequencing.

overall_design: Total RNA of hiAM monoclones 2.38, 2.52 and 2.90 was sequenced after differentiation (D12). Three hiAM monoclones and four hESC-derived AM replicates were used.

first: Niels

last: Harlaar

last: Cofiño Fabrés

first: Gert

last: Veenstra

first: Robert

last: Passier

first: Daniël

last: Pijnappels

first: Antoine

last: de Vries


title: Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing of polarized cystic fibrosis (CF) and non-CF human airway cell cultures following transduction of primary basal cells with lentivirus

status: Public on Aug 31 2021

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to compare cell composition, gene expression, and transduction efficiency of different epithelial cell types following transduction with lentiviruses containing either green fluorescent protein (GFP) or the human CFTR gene.

overall_design: Primary basal cells were collected from CF and non-CF lung donors, transduced with a lentivirus and polarized, prepared for single cell sequencing via 10X Genomics Chromium controller, and sequenced on Illumina HiSeq4000 and NovaSeq6000

first: Ashley

middle: L

last: Cooney

first: Andrew

last: Thurman

first: Paul

middle: B

last: McCray Jr.

first: Patrick

last: Sinn


title: Gene expression profiles of embryonic motor neurons in the SOD1G93A mouse model of amyotrophic lateral sclerosis: insights into earliest pathogenesis

city: Parkville

first: fatemeh

last: zanganeh

state: Victoria

address: 30 royal pde

country: Australia

institute: Florey

summary: Although ALS typically presents in mid to late-life, there is increasing evidence for a protracted preclinical period of motor neuron dysfunction. The goal of this study is to identify the earliest gene expression patterns in lower motor neurons that drive selective neuronal vulnerability in a mouse model of ALS.  We have implemented transgenic SOD1G93A with a lower motor neuron fluorescent reporter (HB9-GFP) mice to unambiguously isolate spinal motor neurons using FACS for gene expression profiling using RNA sequencing at embryonic day (E)12.5. Data from this transcriptomic study allowed the identification of disturbance in MN homeostasis which occur at the day of birth of spinal motor neurons in SOD1G93A mice. Pathway analysis uncovered several remarkably dysregulated pathways including RNA metabolism disturbance and excitotoxicity. Our findings have the potential to reveal insights into the incipient molecular mechanisms that confer motor neuron vulnerability and therefore may highlight relevant gene targets and pathways for effective intervention in ALS.

overall_design: Gene expression profile of mouse spinal motor neurons. Wild-type control with 4 biological replicates compared with mouse  SOD1G93A motor neurons 4 biological replicates at embryonic day 12.5.

first: Fatemeh

last: Zanganeh


title: Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

status: Public on Aug 26 2021

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin.  But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence.  We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories.  Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress.  From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.

overall_design: Hi-C experiments on control, low salt expanded, and recontracted lymphoblast nuclei

first: Jacob

middle: T

last: Sanders

first: Rosela

last: Golloshi

first: Peyton

middle: H

last: Terry

first: Darrian

middle: G

last: Nash

first: Yang

last: Xu

first: Job

last: Dekker


title: ZMYND8 is potential selective therapeutic target for modulating the IRF8/MYC transcriptional networks in AML

status: Public on Sep 06 2021

city: PHILADELPHIA

first: Zhendong

last: Cao

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania


title: Transcriptomic profiling of untreated and oxidative stress treated Wild-type and IPO13-/- mouse embryonic stem cells to study the role of IPO13 in transcriptional response to stress.

city: Melbourne

first: David

middle: A

last: Jans

state: Clayton

address: 23 Innovation Walk

department: Biochemistry and Molecular Biology

institute: Monash University

summary: Purpose: The importin (IPO) superfamily member IPO13 is able to mediate nuclear transport bidirectionally. To better understand IPO13 involvement in cellular signalling, we performed transcriptomic analysis on wild-type and IPO13-knockout mouse embryonic stem cells (mESCs), with gene ontology (GO) annotation results indicating enrichment of differentially expressed genes involved in stress responses and regulation of apoptosis. To examine IPO13's contribtion to the response to cellular stress, we employed RNA sequencing to investigate and compare the transcription profile of wild-type and IPO13-knockout ESCs in the presence and absence of oxidative stress. Methods: Wild-type and IPO13-knock out mESCs were treated with or without 125 µM H2O2 for 1 h, after which the medium was replaced and cells recovered in the absence of H2O2 for 2 h. Total RNA was isolated and used to generate sequencing libraries using Illumina TruSeq Stranded mRNA Library Prep Kit. Sequencing was then performed on an Illumina HiSeq2500 platform. qRT-PCR validation was performed using SYBR Green assays. Results: Results comparing Wild-type and IPO13-knock out cell lines indicated that IPO13 knock out results in the down-regulation of 338 genes and up-regulation of 536 genes. This included genes involved in stress response and apoptotic pathways. Comparison of specific gene subset differentially expressed in response to H2O2 treatment identifiedd 277 IPO13-dependent genes up- or down-regulated exclusively in the Wild-type cell line and not in the IPO13-knock out cell line, highlighting the importance of IPO13 in the transcriptional response to oxidative stress. Conclusion: IPO13 plays a key role in the stress response.

overall_design: Examination of mRNA levels from Wild-type and IPO13-/- mouse embryonic stem cells under untreated and hydrogen peroxide treated conditions to identify genetic targets of IPO13 in cells undergoing oxiative stress.

first: Katarzyna

last: Gajewska

first: Kylie

last: Wagstaff

first: Mirana

last: Ramialison

first: Helen

last: Lescesen


title: Comprehensive Evaluation of Human Brain Gene Expression Deconvolution Methods

status: Public on Aug 28 2021

city: Adelaide

first: Urwah

last: Nawaz

state: SA

address: 4 North Terrace

department: Adelaide Medical Science

institute: UNIVERSITY OF ADELAIDE

summary: We benchmarked deconvolution algorithms on human brain gene expression data. The data deposited here include A) mixtures on which algorithms were benchmarked, as well as B) signatures of pure brain cell-type expression

overall_design: 5 RNA-seq samples generated from mixtures of cultured neuronal and astrocyte RNA (neuronal:astrocyte RNA ratios of 0:100,40:60,45:55,50:50, and 100:0). 10 RNA-seq samples of paired cytoplasmic and nuclear preparations from 5 bulk adult human brain tissue samples.

first: Gavin

middle: J

last: Sutton

first: Daniel

last: Poppe

first: Rebecca

last: Simmons

first: Ryan

last: Lister

first: Johann

last: Gagnon-Bartsch

first: Irina

last: Voineagu


title: Single cell transcriptional profiling reveals signatures of helper, effector, and regulatory MAIT cells during homeostasis and activation

status: Public on Aug 19 2021

first: Christina

last: Leslie

address: 1275 York Ave

summary: Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer.  Although MAIT cells are identified by a semi-invariant T cell receptor, their phenotypic and functional heterogeneity is not well understood.  Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during acute and chronic antigen-specific activation with the MR1 ligand 5-OP-RU and non-specific TCR stimulation.  We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+ or CD8+ co-expression.  During acute activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression of GZMB, IFNG and TNF.  In contrast, chronic stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion.  We further demonstrate a FOXP3 expressing MAIT cell subset that phenotypically resembles conventional regulatory T cells.  Moreover, scRNAseq-defined MAIT cell subpopulations were also detected in individuals recently exposed to Mycobacterium tuberculosis, confirming their presence during human infection.  Our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease.

overall_design: scRNA-seq from 3 donors with two timpoints / multiple stimulation conditions each.  27 samples total.

first: Chirag

last: Krishna

middle: S


title: Glioma associated macrophages are functionally and transcriptionally distinct from tumour microglia in a mouse model of glioblastoma

status: Public on Aug 17 2021

city: Manchester

first: Amir

middle: Saam

last: Youshani

address: Oxford Road

department: Faculty of Biology, Medicine and Health

institute: University of Manchester

summary: We characterised tumour macrophages and tumour microglia using flow cytometry. We subsequently isolated tumour macrophages and tumour microglia, using flow-cell sorting in a mouse glioblastoma model and performed RNA-sequencing to identify: unique cell surface markers, upregulation of pro or anti-inflammatory genes and important functional pathways to overall determine the functional roles of tumour macrophages and tumour microglia.

overall_design: Immunocompetent chimeric mice implanted with syngeneic murine GBM GL-261 cells, flow-cell sorted into 3 tumour populations: tumour differentiated macrophages, tumour undifferentiated macrophages and tumour microglia. A fourth population, normal microglia, was sampled from normal wild-type mice with no tumour.

first: Liisi

last: Laaniste

first: Ian

last: Kamaly-Asl

first: Brian

last: Bigger


title: Epigenome analysis of cord blood DNA from infants born into the SWS study

status: Public on Aug 18 2021

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

summary: Genome wide DNA methylation profiling of umbilical cord blood DNA samples. The Illumina Infinium MethylationEPIC array  was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples included 470 cord blood samples from infants born to women in the Southampton Women's Survery (SWS) cohort, to examine the association between DNA methylation in the infant and aspects of health and disease in early and life and childhood.

overall_design: Bisulphite converted DNA from the 470 samples were hybridised to the Illumina Human Infinium MethylationEPIC array


title: Reprogramming of glucocorticoid receptor function by hypoxia: ChIP-seq in the liver.

status: Public on Aug 11 2021

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Glucocorticoids (GCs) are the most important stress hormones. They act via the GC receptor GR (encoded by the Nr3c1 gene). Their role is to control metabolic pathways, and to limit inflammation. The latter is often compromised, by unknown mechanisms, in severe inflammatory conditions. We here investigated the in vivo impact of hypoxia on GR function in mice, by genome wide analysis in liver and by means of deep hypoxia. Our data reveal that hypoxia leads to profound reductions in transcriptional output of GR, when stimulated with dexamethasone, leading to absent induction of genes with anti-inflammatory functions such as Tsc22d3 and Dusp1 in liver and other organs. Hypoxia also activates the entire HPA axis, by HIF1α and HIF2α activation in hypothalamus, causing long-term corticosterone production by adrenals. The latter leads to lipolysis in adipose tissue, followed by β-oxidation and ketogenesis in liver, but also to the reprogramming of GR, whereby GR limits its anti-inflammatory functions. These genome-wide RNAseq and ChIPSeq data, accompanied with studies using GR inhibitor, GR mutant mice and adrenalectomized animals suggest that hypoxia leads to increased sensitivity for acute inflammation and lack of protection by dexamethasone, due to the chronic HPA axis stimulation. Our data unfold new physiological pathways, that may have consequences for patients suffering from GC resistance or living at high altitudes.

overall_design:
We subjected 6 groups to ChIP-seq with 3 biological replicates each: normoxia +/- DEX, 6h hypoxia +/- DEX and 24h hypoxia +/- DEX. An input sample of the normoxia, 6h hypoxia and 24h of hypoxia were take as controls
Please note that the bigwig file generated from all three replicates is linked to the corresponding 'replicate 1' sample records.

first: Tineke

last: Vanderhaeghen

first: Deepika

last: Watts

first: Ville

last: Paakinaho

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Jolien

last: Vandewalle

first: Charlotte

last: Wallaeys

first: Louise

last: Nuyttens

first: Melanie

last: Eggermont

first: Sylviane

last: Dewaele

first: Joke

middle: V

last: Berghe

first: Joey

last: De Backer

first: Laura

last: Dirkx

first: Sylvia

last: Dewilde

first: Guy

last: Caljon

first: Bart

last: Ghesquière

first: Ben

last: Wielockx

first: Jorma

last: Palvimo

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: Long-term Expansion of Porcine Intestinal Organoids serves as an Ex Vivo Model for Swine Enteric Coronavirus infection

city: Shanghai

first: Changlong

last: Liu

state: Shanghai

address: 518 Ziyue Road, Minhang

institute: Shanghai Veterinary Research Institute

summary: We designed a long-term culture system for porcine intestinal organoids from intestinal crypt or single Lgr5+ stem cells by combining previously defined insights in the growth requirements of intestinal epithelium of human and mouse. We showed that long-term cultured swine intestinal organoids were expanded in vitro more than six months at least and maintained the potential to differentiate into different types of cells. These organoids were successfully infected with porcine enteric coronavirus including porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV). RNA-seq analysis showed that robust induction of transcripts associated with antiviral signaling in response to enteric coronavrius infection, including a number of interferon-stimulated genes and cytokines. Moreover, gene set enrichment analysis indicated that PEDV infection could suppress immune response in organoids. This 3D intestinal organoid model offers a long-term, renewable resource for investigating porcine intestinal infections with a variety of pathogens.

overall_design: To better understanding how porcine intestinal organoids respond to porcine coronavirus infection, we performed RNA sequencing (RNA-seq) experiments using porcine intestinal organoids infected with 0.1 MOI of PEDV, TGEV or MOCK infected and evaluated the transcript landscape of porcine small intestinal organoids at 48 hrs after viral challenges. Total RNAs were isolated and sequencing libraries were prepared. The libraries were sequenced using standard methods for paired-end 150-bp reads, on an Illumina Novaseq 6000 sequencer.

first: Min

last: Zhang

first: Lilei

last: Lv

first: Hongming

last: Cai


title: HSPC scRNA seq

status: Public on Aug 13 2021

city: illkirch

first: giovanni

last: cova

address: 1 Rue Laurent Fries

institute: igbmc

summary: Our understanding of cell fate decisions in hematopoietic stem cells is incomplete. Here, we show that the transcription factor Helios is highly expressed in murine hematopoietic stem and progenitor cells (HSPCs), where it is required to suppress the separation of the platelet/megakaryocyte lineage from the HSPC pool. Helios acts mainly in quiescent cells, where it directly represses the megakaryocyte gene expression program in cells as early as the stem cell stage. Helios binding promotes chromatin compaction, notably at the regulatory regions of platelet-specific genes recognized by the Gata2 and Runx1 transcriptional activators, implicated in megakaryocyte priming. Helios null HSPCs are biased toward the megakaryocyte lineage at the expense of the lymphoid and partially resemble cells of aging animals. We propose that Helios acts as a guardian of HSPC pluripotency by continuously repressing the megakaryocyte fate, which in turn allows downstream lymphoid priming to take place. These results highlight the importance of negative and positive priming events in lineage commitment.

overall_design: We performed scRNA sequencing to understand Helios function in the heterogeneous hematopoietic stem and progenitor (HSPC) cells population. We combined this technology to CITE-sequencing to obtain measurement at the protein and transcriptome level and to HASH-sequencing in order to measure these data simultaneously in WT and Helios deficient HSPC in duplicate.

first: Giovanni

last: Cova

first: Peggy

last: Kirstetter

first: Philippe

last: Kastner

first: Susan

last: Chan


title: Multi-Omics Insights into the Mechanism of Liver Injury in Dextran Sulfate Sodium-Induced Colitis

status: Public on Aug 16 2021

city: Hangzhou

first: Luoyi

last: Zhu

state: Zhejiang

address: 866 Yuhang Tang Road

institute: Zhejiang University

summary: Liver injury is a common complication of inflammatory bowel disease (IBD). However, the mechanisms of liver injury development are not clear in IBD patients. Gut microbiota is thought to be engaged in IBD pathogenesis. Here, by an integrated analysis of host transcriptome and colonic microbiome, we have attempted to reveal the mechanism of liver injury in colitis mice. In this study, dextran sulfate sodium (DSS) -induced mice colitis model was constructed. Liver and colon transcriptome results showed that immune response and lipid metabolism-related pathways were dramatically altered, while DNA damage repair-related pathways were only significantly down-regulated in the colon. The microbiota of DSS-treated mice underwent strong transitions. Correlation analyses identified genes associated with liver and colon injury, whose expression was associated with the abundance of liver and gut health-related bacteria Collectively, the results indicate that the liver injury in colitis mice may be related to the intestinal dysbiosis and host-microbiota interactions. These findings may provide new insights for identifying potential targets for the treatment of IBD and its induced liver injury.

overall_design: Twelve 6-week-old C57BL/6 mice were weighed on day 0 of the experiment and randomly divided into control (CON group) and DSS groups (6 per group). The mice in the DSS group drank sterilized water containing 3% DSS (36- 50 kDa; MP Biomedicals, California, USA) ad libitum for 7 consecutive days, and the control group drank sterilized distilled water.

first: Xiao

last: Xiao

first: Jie

last: Fu

first: Yizhen

last: Wang

first: Xin

last: Zong


title: Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells


title: The RNA-seq result of GC cells which were treated with chrysin

city: Changchun

first: Dongxu

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

institute: Jilin University

summary: Chrysin has been reported to have anticancer effect. We used 40μM chrysin to treat SGC7901 cells for 48h, then sequenced their RNA, analyzed the differentially expressed genes before and after treatment, screened out the anticancer target of chrysin, and then carried on the next analysis

overall_design: RNA-seq of SGC7901 cells untreated or treated with 40μM chrysin for 48h.

first: Xiaowei

last: Zhong

first: Lin

last: Chen

first: Chengshun

last: Li


title: Identification of nucleolar associated domains (NADS)

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

summary: This study aims to identify genomic contacts with the nucleolus (nucleolar associated domains, NADs). We established a novel methodology that we applied to identify NADs in embryonic stem cells (ESCs). The results revealed unprecedented distinct layers of genome compartmentalization that are distinguished according to gene expression and chromatin states thereby providing novel insights into basic principles of genome organization and its role in gene expression and cell function.

overall_design: Nucleolar-DamID, ChIP seq, RNA seq in mouse ESC

first: Cristiana

last: Bersaglieri

first: Jelena

last: Kresoja-Rakic

first: Shivani

last: Gupta

first: Dominik

last: Bär

first: Rostyslav

last: Kuzyakiv


title: Antibiotics exposure impacts the gut microbiota and influences energy and metabolic homeostasis in Spodoptera frugiperda

status: Public on Aug 06 2021

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Insect gut microbiota plays important roles in acquiring nutrition, preventing pathogens infection, immune responses, and communicating with the environment. Gut microbiota can be affected by some external factors such as foods, temperature, and antibiotics. Spodoptera frugiperda (Lepidoptera: Noctuidae) is an important destructive pest of grain crops all over the world. The function of gut microbiota in S. frugiperda remains to be investigated. In this study, we fed the S. frugiperda with the antibiotic mixture (penicillin, gentamicin, rifampicin, and streptomycin) to perturb the gut microbiota, and further examined the effect of dysbiosis in gut microbiota on the gene expression of S. frugiperda by RNA sequencing. We found the composition and diversity of the gut bacterial community were changed in S. frugiperda after antibiotics treatmen, and the expression of genes related to energy and metabolic process were affected after antibiotics exposure in S. frugiperda. Our work will help understand the role of gut microbiota in insects.

sample_organism:
Spodoptera frugiperda
insect gut metagenome

overall_design: Spodoptera frugiperda were reared with the artificial diet with or without antibiotics, respectively from the newly hatched larvae to the 3-day-old sixth instar larvae. RNA-seq and 16S rDNA of midguts were performed to study the effects of gut microflora on host transcription.

first: Yaqing

first: Huanchan

last: Zhou

first: Yushan

last: Lai


title: RNA-sequencing analysis of mouse liver with a global ERK1, hepatocyte-specific ERK2 or double ERK1/2 knockout

city: Atlanta

first: Mark

last: Czaja

state: GA

address: 615 Michael Street, Suite 201

department: Medicine

institute: Emory University School of Medicine

summary: The analysis examined the effects of a global ERK1 and/or tamoxifen-inducible, hepatocyte-specific ERK2 knockout on the liver transcriptome. Transcriptomes from the livers with a ERK1/2 double knockout were compared to the livers of mice with an ERK1 or ERK2 knockout.

overall_design: ERK1, ERK2 and ERK1/2 knockout mice were injected with tamoxifen and the livers harvested after 3 weeks for transcriptome analysis.

first: Francesca

last: Cingolani


title: A Single-Cell Atlas of Murine Liver Non-parenchymal Cells in Typical Disease Models

status: Public on Aug 01 2021

city: HangZhou

first: jingyang

last: qian

address: No. 886, Yuhangtang Road

summary: We provided a comprehensive single-cell transcriptomic atlas of murine liver non-parenchymal cells (NPCs) in different diseases and analyzed the heterogeneity of inter- and intra-group NPCs. Our study offers a valuable resource for better understanding liver physiology and pathology, and bring new directions for the development of clinical diagnostic markers and effective therapeutic targets.

overall_design: We performed unbiased scRNA-seq analysis of 171,814 NPCs from 18 mice liver (3 mice per group) from a healthy group and 5 typical disease models including alcoholic liver disease, nonalcoholic steatohepatitis, drug-induced liver injury, cholestatic liver injury, and liver ischemia-reperfusion injury. Immunofluorescence and immunohistochemical staining were used for validation experiments.

first: Zheng

first: Jingyang

last: Qian


title: PAX9 determines epigenetic state transition and cell fate in small cell lung cancer

status: Public on Aug 03 2021

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Small cell lung cancer (SCLC) is a more aggressive and deadlier form of lung cancer with limited effective therapies currently available. By utilizing a genome-wide CRISPR-Cas9 dropout screen, we have identified the Paired box protein 9 (PAX9) as an essential factor for the cell viability of SCLC-A type, which accounts for approximately 70% of all SCLC. PAX9 is transcriptionally driven by the BAP1/ASXL3/BRD4 epigenetic axis and is overexpressed in human malignant SCLC tumor samples. Genome-wide studies have revealed that PAX9 occupies distal enhancer elements and represses gene expression by restricting enhancer activity. Genetic depletion of PAX9 leads to a dramatic induction of a primed-active enhancer transition, resulting in an increased expression of a large number of neural differentiation and tumor-suppressive genes in multiple SCLC cell lines. Mechanistically, PAX9 interacts and co-functions with the Nucleosome Remodeling and Deacetylase (NuRD) complex at enhancers and they repress the nearby gene expression, which could be rescued by pharmacological HDAC inhibition. Overall, this study provides mechanistic insight into the oncogenic function of the PAX9/NuRD complex epigenetic axis in human SCLC and suggests that re-activation of the primed enhancers may have therapeutic efficacy in treating SCLC-A type cancers expressing high levels of PAX9.

overall_design: To examine changes in histone modification and gene expression after depletion of PAX9 in SCLC cells

first: Zibo

last: Zhao


title: RNA-seq of WNT16-treated and Wild Type Human Limbal Epithelial Stem Cells

status: Public on Jul 30 2021

first: Qihua

last: Le

address: No. 83 Fen Yang Rd

department: Department of Ophthalmology

institute: Eye, Ear, Nose & Throat Hospital of Fudan University

summary: We first reported that WNT16 has the advanced effect on the proliferation and stemness maintenance of human limbal epithelial stem cells. To investigte the potential mechanism of WNT16 regulation, RNA-seq was used to analyze the differential expressed genes and relative cellular pathways between WNT16-treated and wild type human limbal  epithelial stem cells.

overall_design: RNA profiles of WNT16-treated and Wild Type Human Limbal Epithelial Stem Cells（3 biological replicate，respectively）

first: Songjiao


title: Single-cell RNA sequencing reveals the diversity of the immunological landscape in response to murine coronavirus infection of the central nervous system

status: Public on Aug 09 2021

city: Irvine

first: Thomas

last: Lane

state: CA

address: Ring Rd.

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Intracranial (i.c.) infection of susceptible C57BL/6 mice with a neurotropic JHM strain mouse hepatitis virus (a member of the Coronaviridae family) results in acute encephalomyelitis and viral persistence associated with an immune-mediated demyelinating disease. The present study was undertaken to better understand the molecular pathways evoked during innate and adaptive immune responses as well as the chronic demyelinating stage of disease in response to JHMV infection of the central nervous system (CNS). Using single cell RNA sequencing analysis (scRNAseq) on flow-sorted CD45-positive cells (CD45+) enriched from brains and spinal cords of experimental mice, we demonstrate the heterogeneity of the immune response as determined by unique molecular signatures and pathways involved in effective anti-viral host defense. Furthermore, we identify potential genes involved in contributing to demyelination as well as remyelination being expressed by both microglia and macrophages. Collectively, these findings emphasize the diversity of the immune response and molecular networks at defined stages following viral infection of the CNS.

overall_design: Adult (5-6 week old) C57BL/6 mice were intracranially (i.c.) infected with 1,500 plaque forming units (PFU) of JHMV and CD45-positive (CD45+) cells were flow sorted from the brains of JHMV-infected mice at days 3 and 7 post-infection (p.i.) and spinal cords at day 21 p.i. as well as the brains of infected mice. FACS sorted CD45+ cells then underwent single-cell RNA-sequencing analysis

first: Amber

middle: R

last: Syage

first: H

last: Ekiz

middle: E


title: Amplicon-seq of SVA methylation in human sperm

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

type: Methylation profiling by high throughput sequencing

summary: DNA methylation, repressive histone modifications, and PIWI-interacting RNA are essential for controlling retroelement silencing in the mammalian germ line. Dysregulation of retroelement silencing is associated with male sterility. Although DNA methylation mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are associated with DNA methylation of retroelements in human primordial germ cells (hPGCs), and hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. Furthermore, we show that the degree of de novo DNA methylation in SVAs varies among human individuals, which confers a major inter-individual epigenetic variation in sperm. Collectively, our results provide potential molecular mechanisms of how retroelements are regulated during human male germ cells

overall_design: Examination of DNA methylation of SVA transposons from five sperm donors

first: Yoichi

last: Shinkai


title: Gene expression profiling of FFPE kidney cancer samples

status: Public on Jul 28 2021

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: We used Illumina microarrays to profile RNA expression in formalin-fixed paraffin-embedded (FFPE) samples of 22 metastatic or advanced RCC cases.

overall_design: 22 kidney cancer samples were profiled using Illumina HumanHT-12 WG-DASL V4.0 R2 gene expression bead arrays

first: Maxim

last: Sorokin

first: Anton

last: Buzdin


title: Longitudinal Transcriptomic response to SARS-CoV-2 infection

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

summary: Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-PCR cycle threshold (Ct) of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.

overall_design:
Shotgun RNAseq of SARS-CoV-2-positive NP swabs at different timepoints after infection, including both paired and unpaired samples
*** Submitter declares that the raw data have not been submitted due to patient privacy concerns and the University of Washington IRB's strict prohibitions. ***

first: Michelle

last: Lin

first: Pavitra

last: Roychoudhury


title: Nox4-IGF2 axis promotes differentiation of embryoid body cells into derivatives of the three embryonic germ layers

city: Seoul

first: Jaewon

last: Kim

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

summary: Reactive oxygen species (ROS) play important roles as second messengers in a wide array of cellular processes including differentiation of stem cells. We identified Nox4 as the major ROS generating enzyme whose expression is induced during differentiation of embryoid body (EB) into cells of all three germ layers. The role of Nox4 was examined using iPS cells generated from Nox4 -/- mouse. Differentiation markers showed significantly reduced expression levels consistent with the importance of Nox4-generated ROS during this process. From transcriptomic analyses, we found insulin-like growth factor 2 (IGF2), a member of a gene family extensively involved in embryonic development, as one of the most down-regulated genes. Indeed, addition of IGF2 to culture partly restored the differentiation efficiency of Nox4-/- iPS cells. Our results reveal an important signaling axis mediated by ROS in control of crucial events during differentiation of pluripotent stem cells.

overall_design: Time-series mRNA profiles of wild type (WT) and Nox4 knockout iPSC

first: Jaesang

first: Yun

last: Bae

first: Sanghyuk

last: Lee

first: Jusong

first: Hee

last: Lim


title: Unique nascent transcriptomes define naïve, primed and paused embryonic pluripotent states.

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Unique transcriptomes define naïve, primed and paused embryonic pluripotent states.  Here we perform calibrated transient transcription sequencing (TT-seq) to de novo define and quantify coding and non-coding transcription units (TUs) in different pluripotent states. We observe a global reduction of RNA synthesis, total RNA amount and turnover rates in ground state (2i) and paused pluripotency (mTORi). We demonstrate that elongation speed can be reliably estimated from TT-seq nascent RNA and RNA Polymerase II occupancy levels, and observe a transcriptome-wide attenuation of elongation speeds in these two inhibitor-induced states. Comparing closely related transcriptional states with different elongation speeds, we also discover a relationship between elongation speed and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ESC cells are controlled predominantly on the level of RNA synthesis and signaling pathways governing different pluripotent states directly control key parameters of transcription.

overall_design: TT-seq on mESC pluripotent states: SL, 2i, and mTORi. With both label RNA (LRNA) and fragmented total RNA (FRNA).

first: Rui

last: Shao


title: Differential expression profiles of RNAs in mouse melanoma cells treated with ATRA and PB-4

status: Public on Jul 24 2021

city: Yantai

first: Defang

last: Li

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We extracted the total RNA of B16 cells treated with ATRA or PB-4 for 48 h and used RNA-seq technology to detect differentially expressed RNAs such as lncRNAs, miRNAs, and mRNAs in B16 cells. The results showed that compared with the normal control group, 102 lncRNAs, 24 miRNAs, and 761 mRNAs showed differential expression in the ATRA-treated group, and 306 lncRNAs, 105 miRNAs, and 2567 mRNAs showed differential expression in the PB-4-treated group.

overall_design: Detection of RNAs expression profile after B16 cell differentiation induced by ATRA and PB-4.

first: Dan

last: Wang


title: Immune-related transcriptomic landscape of primary tumors and lymph node metastasis of chemotherapy-naïve breast cancer patients

status: Public on Jul 21 2021

city: Gdansk

first: Anna

middle: J.

last: Zaczek

address: Debinki 1

institute: Medical University of Gdansk

summary:
Immune system plays a dual role in cancer by either targeting or supporting neoplastic cells at various stages of disease, including metastasis. Yet, the exact immune-related transcriptome profiles of breast cancer cells and their evolution during dissemination remain undiscovered.
This study aimed at exploring immune-related transcriptomic landscape of primary tumors and lymph node metastasis of chemotherapy-naïve breast cancer patients.

overall_design: This data set consists of immune-related gene expression profiles of 35 primary tumors and 11 matched lymph node metastases, derived from 35 breast cancer patients treated at Medical University of Gdańsk, Poland, between 2010 and 2013.  Total RNA was extracted from FFPE material, pre-amplified using nCounter Low RNA Input Kit and subsequently analyzed using NanoString nCounter System (NanoString Technologies) and dedicated PanCancer Immune Profiling Panel.

first: Marta

last: Popeda

first: Natalia

last: Bednarz-Knoll

first: Aleksandra

last: Markiewicz

first: Tomasz

last: Stokowy

first: Jolanta

last: Szade

first: Magdalena

last: Niemira

first: Agnieszka

last: Bielska

first: Adam

last: Kretowski


title: Transcriptome data for HEK293T cells depleted of one subunit of DNA-PK complex: Ku70, Ku80 or DNA-PKcs.

status: Public on Jul 23 2021

first: Andrey

last: Anisenko

address: Leninskye Gory, 1/40

department: Chemistry department

institute: Lomonosov Moscow State University

summary: DNA-PK is a heterotrimeric complex that consists of Ku70 (XRCC6), Ku80 (XRCC5) and DNA-PKcs (PRKDC) subunits. DNA-PK complex is a major player in DNA double strand break (DSB) repair via non-homologous end joining pathway. This process requires all of DNA-PK subunits. Ku70/Ku80 heterodimers firstly bind to DNA-ends at DSB, that increase affinity of DNA-PKcs to DNA-ends. Recruitment of DNA-PKcs subunit to DSB leads to phosphorylation events near DSB, recruitment of another NHEJ-related genes that restore DNA integrity. However, today a lot of evidence demonstrate participation of DNA-PK components in other cellular process, e.g. cytosolic DNA sensing, apoptosis regulation, cellular movement and adhesion. It is important to note that not all subunits of DNA-PK complex are necessary for these process. This demonstrate the independent functions of DNA-PK subunits. Here we for the first time using NGS-sequencing analyzed the transcriptional changes in HEK293T cells under depletion of Ku70, Ku80 or DNA-PKcs to characterize the independent functions of each subunit.

overall_design: Transcriptome examination of HEK293T cells with Ku70, Ku80 or DNA-PKcs monoallelic knock-out treated with siControl, siKu70, siKu80, siDNA-PKcs to additionally reduce proteins level.

first: Olga

last: Shadrina

first: Irina

last: Garanina

first: Marina

last: Gottikh


title: Genome-wide CRISPR screen to identfy immune evasion genes in pancreatic cancer

status: Public on Jul 27 2021

first: Gerald

last: Schwank

department: Institute of Pharmacology and Toxicology

summary: Here we systematically dissected PDA intrinsic mechanisms of immune evasion by in vitro and in vivo CRISPR screening. Beyond the conserved set of genes regulating anti-cancer immunity we identified Rnf31 and Vps4b as essential factors required for escaping CD8+ T cell-killing. While the absence of Rnf31 induced sensitivity to T cell killing through TNF-mediated apoptosis in murine cancer cells and human PDA organoids, loss of Vps4b abrogated functional autophagy, resulting in accumulation of CD8+ T cell-derived granzyme B and subsequent tumor cell lysis.

overall_design: Genome-wide CRISPR screen in pancreatic cancer cells using the Brie sgRNA library. Cancer cells were co-cultured with CD8 T cells and resistors/sensitizer (genes) were identified after T cell selection. Candidates Rnf31 and Vps4b were chosen for further analysis and RNA-Seq was performed on WT-KPC cells or KPC cells with Rnf31/Vps4b knockout with and without T cell co-culture. The same as done for Stat1-KO KPC cells as a resistor to T cell killing.

first: Nina

last: Frey

first: Sharan

last: Janjuha


title: RNA-seq in osteoblast differentiation

status: Public on Jul 14 2021

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Transitions between cell fates commonly occur in development and disease. The vascular  endothelium is an essential contributor of osteoprogenitors to vascular calcification through  endothelial-mesenchymal transitions, in which endothelial cells (ECs) gain plasticity and  differentiate into osteoblast-like cells. Transcriptome profiling reveals transcriptional regulation in osteoblastic fate to endothelial differentiation.

overall_design: Transcriptional regulation in osteoblast differentiation

first: X

first: J

last: Yao


title: Androgen Receptor splice variant V7 (AR-V7) mediates AR signalling in castration resistant prostate cancer (CRPC) [ChIP-exo]

status: Public on Jul 07 2021

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: CRPC remains AR dependent. There are multiple mechanisms for reactivation of AR including expression of constitutively active AR splices variant AR-V7 (AR3). Earlier studies suggest that though the variants regulate many of the same genes as AR, they also have unique targets. Another argument is that the variant is a “weak” AR. We have used an LNCaP cell line that expresses AR-V7 in response to doxycycline to compare DNA interactions of the two isoforms and to identify differential regulation of target genes. ChIP-exo method was used to map AR and AR-V7 interaction with DNA in LNCaP engineered cell line (LNCaP AR-V7) at single base resolution.

overall_design: AR and AR-V7 DNA binding by ChIP-exo

first: Paul

last: Basil

first: Nancy

last: Weigel


title: Sci-Space E14 Mouse Embryo Data

status: Public on Jul 01 2021

first: Sanjay

last: Srivatsan

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

summary: Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.

overall_design: Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.

first: Mary

last: Regier


title: Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells [scRNA-Seq]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We reported the scRNA-seq of hESC-derived SHOX2+mCherry+ cells and SHOX2-mCherry+ cells

overall_design: Chen, Shuibing

last: Zumbo

first: Friederike

last: Dündar


title: Transcriptome of Xoo BXO43 and XopQ-

status: Public on Jun 29 2021

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

country: India

institute: Centre for cellular and molecular biology (CCMB)

summary: The aim of the study was to understand the differences in the transcriptome of Xanthomonas oryzae pv. oryzae BXO43 vs it's XopQ mutatnt that is virulence deficient. Our study indicates a key role of XopQ in regulating biofilm to planktonic lifestyle switch in Xoo.

overall_design: Global RNA profiling of laboratory grown Xoo strains - WT and XopQ-.

first: Hitendra

middle: K

last: Patel

first: Sohini

last: Deb


title: Recurrent application of dietary restriction reduces tumor load and increases lifespan in an intestinal cancer model

status: Public on Jul 05 2021

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

summary: Intestinal cancers are highly responsive to their nutrient environment. However, previous studies integrating nutrition into the network of cancer progression are largely inconsistent. We therefore investigated the effects of dietary restriction, which is the most consistently found beneficial nutritional intervention, on the development of intestinal stem cell tumors in a Drosophila melanogaster model. Submission to dietary restriction led to a decline in tumor mass and a morphological as well as functional rehabilitation of the intestine. Nevertheless, flies submitted to dietary restriction exhibited a drastically reduced lifespan due to substantial loss of body mass. To circumvent these destructive consequences, we applied a nutritional regimen consisting of alternating phases of dietary restriction and a fully nutritious diet. Strikingly, the recurrent diet reduced tumor mass and reinstated gut functionality to the same extend as continuous dietary restriction, while restoring the lifespan of tumor-bearing flies back to the level of healthy controls.

sample_organism:
Drosophila melanogaster
insect gut metagenome

overall_design: 16S rRNA and transcriptome sequencing were performed to investigate the effects of dietary restriction on the development of intestinal stem cell tumors in a Drosophila melanogaster model.

first: Roxana

middle: M

last: Pfefferkorn

first: Benedikt

last: Mortzfeld

first: Jakob

last: von Frieling

first: Christoph

last: Kaleta

first: Philip

last: Rosenstiel

first: John

last: Baines

first: Holger

last: Heine

first: Thomas

last: Roeder


title: High Throghput sequencing analysis of NVEGF and NLS-NVEGF with and without Dox treatment Transcriptomes

status: Public on Jun 17 2021

city: Haifa

first: Marina

last: Katsman

address: Technion City

department: Biotechnology and Food Engineering

institute: Technion

summary: The aim of this experiment is to find differential expression of genes following expression of VEGF isoform in the nucleus.

overall_design: Two cell types, expressing N-VEGF or NLS-N-VEGF, were grown in the presence or absence of the Tet-on promoter inducer, doxycycline (dox).

first: Aviva

last: Azriel

first: Ben-Zion

last: Levi

first: Guy

last: Horev


title: Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells

first: Shuibing

last: Chen

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

overall_design: Refer to individual Series


title: Exposure to copper compromises the maturational competency of porcine oocytes via oxidative stress-induced DNA damage

status: Public on Jun 28 2021

city: Nan Jing

first: Qian

last: Gao

address: No 1, Weigang

institute: Nanjing Agricultural University

summary: Copper (Cu) is not only one of the essential trace elements for animal body, but also an important nutrient component for normal physiology and metabolism of animal reproductive system. Lack or excess of copper will directly or indirectly affect animal reproductive activities. However, the effect of copper on reproductive performance of boars and sows has not been studied and the effect of excessive Copper addition on reproductive performance of sows is even less, and the molecular mechanism is poorly understood. Here, we document that copper has the negative effects on the oocyte maturation and Organelle function. We show that copper exposure perturbs the porcine oocyte meiotic maturation and impair the spindle/chromosome structure, displaying an obviously defective spindle assembly, and abnormal distribution of actin dynamics and cortical granules. In addition, single-cell transcriptome analysis identifies target effectors of copper in porcine oocytes, which was further demonstrated that copper exposure affects the distribution and function of mitochondria, and high ROS levels, DNA damage, and early apoptosis in porcine oocytes. Collectively, we demonstrate that copper exposure causes abnormalities in mitochondrial function and distribution, resulting in increased oxidative stress ROS levels, DNA damage and apoptosis, ultimately leading to decreased quality of porcine oocytes.

overall_design: Transcriptomic analysis of oocytes at M II stage was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Illumina platform.


title: Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells [RNA-seq]

summary: The sinoatrial node (SAN) is the primary pacemaker of the heart. The human SAN is poorly understood due to limited primary tissue access and lack of robust in vitro derivation methods. We developed an efficient strategy, using a dual SHOX2:GFP; MYH6:mCherry knock-in reporter line, to generate and purify human pluripotent stem cell-derived SAN cells (hPSC-SAN), displaying molecular and electrophysiological characteristics of bona-fide nodal cells. We modeled cell type specific toxicity upon treatment with doxorubicin (DOXO) using hPSC-SAN generated from a library of induced pluripotent stem cells (iPSCs).  We discovered 3 new genetic loci associated with increased sensitivity to DOXO-induced hPSC-SAN death. Genetic variants in these loci were associated with significantly higher early arrhythmia risk in patients receiving DOXO, confirmed by an unbiased PheWAS analysis. Finally, the in vitro DOXO assay enabled an unbiased drug screening platform and identification of physcion as a candidate therapeutic that can partially block DOXO-mediated cardiac toxicity.

overall_design: We reported the RNA-seq of hESC-derived SHOX2+mCherry+ cells and SHOX2-mCherry+ cells

first: Chen

last: Shuibing


title: To identify GCM1 novel target genes by chromatin immunoprecipitation-on-chip (ChIP-chip) analysis

status: Public on Jun 11 2021

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

type: Genome binding/occupancy profiling by genome tiling array

summary: In this study, we performed chromatin immunoprecipitation-on-chip (ChIP-chip) analysis and identified the gene for high-temperature requirement protein A4 (HtrA4) as a GCM1 target gene, which encodes a serine protease facilitating cleavage of fibronectin and invasion of placental cells. Importantly, HtrA4 is immunolocalized in EVTs at the maternal-fetal interface, and its expression is decreased by hypoxia and in preeclampsia, a pregnancy complication associated with placental hypoxia and shallow trophoblast invasion.

overall_design: Analysis of GCM1-binding sequences by ChIP-chip.

first: Liang

last: Wang

first: Yun

first: Hungwen


title: Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures

status: Public on Jun 14 2021

city: La Jolla

first: Rekha

last: Dhanwani

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Parkinson’s disease (PD) is a multi-stage neurodegenerative disorder with largely unknown etiology. To further characterize the role of T cells in PD associated autoimmunity, we performed RNA sequencing on PBMC and peripheral CD4 and CD8 memory T cell subsets derived from PD patients and age-matched healthy controls. Considering T cell reactivity to -syn, the study revealed a broad differential gene expression profile in memory T cell subsets and a specific PD associated gene signature. This study found a significant enrichment of transcriptomic signatures previously associated with PD, such as oxidative stress and phosphorylation, autophagy of mitochondria, cholesterol metabolism, and inflammation. We also identified novel genes associated with PD, including xx. Altogether, the findings in this study suggest that the study of circulating T cells from PD subjects with an ongoing -syn-specific T cell response may provide new insights to understand the complexity of the disease and suggest potential intervention targets.

overall_design:
PBMCs (PD n=32; HC= n=14), CD4 memory (PD n=34; HC= n=19) and CD8 memory (PD n=36; HC n=20) T cells from PD  and HC subjects were sorted and RNA was extracted.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Alessandro

last: Sette

first: Cecilia

last: Lindestam Arlehamn


title: High throughput sequencing analysis of dNVEGF under hypoxia or normoxia conditions compered to willd type.

summary: The aim of this experiment is to find the effect of the NVEGF remmoval in hypoxia or normoxia conditions in NIH3T3 cells, by examining the differential gene expression between the groups.

overall_design: mRNA profiles of 3T3 (WT) and dNVEGF