title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding   transcripts in adult mouse somatic (non-reproductive) cells (nucRNA-Seq)

overall_design: Frozen left ventricles were obtained from either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th intron of the Uty gene) or their wild-type counterparts from the isogenic strain C57BL/6.Y<129P2> adult mice.  For each strain, the procedure was repeated on three different days in order to obtain triplicate samples.


title: The role of CDK7 in cutaneous melanoma

status: Public on Sep 18 2020

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

country: USA

institute: NYU Langone Health

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding   transcripts in adult mouse somatic (non-reproductive) cells (ChIP-Seq)

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

summary: In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class   of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes,   which include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes.  However, the impact   of targeted mutations of these genes on the functions of adult non-reproductive somatic cells   is still unknown due to lack of experimental evidence.  We thus compared adult male mice   carrying a gene trap within their Uty gene (UtyGT) to wild-type (WT) isogenic controls, and   performed deep sequencing of RNA and genome-wide profiling of chromatin in extracts   from either cardiac tissue, cardiomyocyte-specific nuclei and purified cardiomyocytes.    The impact of UtyGT on gene transcription was mostly limited to its effects on genes   surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs)   contained within their introns, Eif2s3y, as well as on the autosomal Malat1 lncRNA.    Notwithstanding, UtyGT also caused coordinate changes in the abundance of   hundreds of mRNA transcripts related to particular cell functions, including   RNA processing and translation.  The results altogether indicated that tightly   co-regulated chrY genes had nonetheless more widespread effects on the   autosomal transcriptome in adult somatic cells, most likely due to mechanisms   other than just transcriptional regulation of protein-coding genes.

overall_design: The two mouse strains were either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th  intron of the Uty gene) and its wild-type counterpart from the isogenic strain C57BL/6.Y<129P2>.  Duplicate samples (ech_1 and ech_2) were generated for each strain.  Each sample comprised left ventricular tissue obtained from 40 day-old  male mice.


title: Metabolic adaptation of white adipose tissue to acute, short-term environmental oxygen restriction in mice

status: Public on Sep 21 2020

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: White adipose tissue (WAT) expansion during e.g. obesity reduces oxygen availability in WAT in mice. Little is known on the adaptation of WAT to mild environmental oxygen restriction (OxR). Therefore, we studied metabolic adaptation to acute OxR in fasted, diet-induced moderately obese mice that were exposed to mild hypoxic (12% O2) or normoxic (20.9% O2) conditions for only 6 hours. Adaptation was assessed by determination of amino acids and (acyl)carnitines levels in serum and WAT, and by whole genome expression analysis in WAT. Adaptation was also assessed during the exposure using indirect calorimetry. We found that OxR reduced mitochondrial oxidation at whole-body level, as shown by a reduction in whole-body oxygen consumption and an increase in serum long-chain acylcarnitine levels. WAT did not seem to contribute to this serum profile since only short-chain acylcarnitines were increased in WAT and gene expression analysis indicated an increase in mitochondrial oxidation, based on coordinate down-regulation of Sirt4, Gpam and Chchd3/Minos3. In addition, OxR did not induce oxidative stress in obese WAT, but increased molecular pathways involved in cell growth and proliferation. OxR increased levels of tyrosine, lysine and ornithine in serum and of leucine/isoleucine in WAT. This study shows that OxR limits oxidative phosphorylation at whole-body level, but in WAT compensatory mechanisms seem to operate. The down-regulation of the mitochondria-related genes Sirt4, Gpam, and Chchd3 may be considered as a biomarker profile for WAT mitochondrial reprogramming in response to acute exposure to limited oxygen availability.

overall_design: Two-condition experiment, normoxia (20.9% oxygen) vs. hypoxia (12% oxygen) treated mice. Biological replicates: 12 control (normoxia) replicates, 10 hypoxia replicates.

first: L

middle: P

last: Duivenvoorde

first: E

middle: M

first: I

last: van der Stelt

last: Hoek-van den Hil

first: J

last: Keijer


title: miRNA expression profiling and identification of a miRNA regulator for axon guidance in the olfactory bulb of adult mice

city: Zhengzhou

first: Ao

last: Shen

address: No. 1 Jianshe East Road

country: China

institute: First Affiliated Hospital of Zhengzhou University

summary: Using the highly sensitive miRNA array, we screened 40 microRNAs abundant in the olfactory bulb and we explored the functions of these miRNAs in the olfactory bulb by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the axon guidance process. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry and dual luciferase reporter assay results showed that miR-30c is a specific regulator of semaphorin-3A, which will give new insights in disclosing the mechanism of functional maintenance and sexual-specific differentiation of the olfactory bulb.

overall_design: In this study, three samples from steady-state mice were used to acquire the miRNA expression profiling and the function of the abundant miRNAs in the olfactory bulb were analyzed by bioinformatic methods,finally, miR-30c was experimentally validated to be a regulator of semaphorin-3A, an important axon guidance cue in the nervous system.

first: Ting

middle: T

last: Sun

first: Shu

middle: C

last: Ling


title: RNAseq of U87/over-expressed DPF3 U87 treated with bulk control/0.5mM 8-cpt-cAMP combination with 1nM MS275 for 48hrs

status: Public on Sep 17 2020

city: GuangZhou

first: liu

last: xincheng

address: zhongshan Road 74

institute: sysu

summary: Transcriptomics revealed that the combination of 8-cpt-cAMP and MS275 could maximize the glioma differentation compared to control or use either drug alone

overall_design: U87/DPF3-over-expressed U87 cells were treated with bulk control or a combination 0.5mM 8-cpt-cAMP and 1nM MS275 for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

first: Xincheng

last: Liu


title: Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells (hPSCs)

city: Calgary

first: Leili

last: Rohani

state: Alberta

address: 405J, 1919 University Drive, NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Although cell therapies require large numbers of quality-controlled hPSCs, existing technologies are limited in their ability to efficiently grow and scale stem cells. We report here that cell-state conversion from primed-to-naïve pluripotency enhances the biomanufacturing of hPSCs. Naïve hPSCs exhibit superior growth kinetics and aggregate formation characteristics in stirred suspension bioreactors compared to their primed counterparts. Moreover, we demonstrate the role of the bioreactor mechanical environment in the maintenance of naïve pluripotency, through transcriptomic enrichment of mechano-sensing signaling for cells in the bioreactor along with a decrease in expression of lineage-specific and primed pluripotency hallmarks. Bioreactor-cultured, naïve hPSCs maintain epigenetic hallmarks of naïve pluripotency, exhibit robust production of naïve pluripotency metabolites, and display reduced expression of primed pluripotency cell surface markers. We also show that these cells retain the ability to undergo targeted differentiation into beating cardiomyocytes, hepatocytes and neural rosettes. They additionally display faster kinetics of teratoma formation compared to their primed counterparts. Naïve bioreactor hPSCs also retain structurally stable chromosomes. Our research corroborates that converting hPSCs to the naïve state enhances hPSC manufacturing and indicates a potentially important role for the bioreactor’s mechanical environment in maintaining naïve pluripotency.

overall_design: RNA-seq experiment was performed on naïve human pluripotent stem cells cultured under three different conditions: 1) static, 2) static suspension, 3) stirred suspension culture. We performed three pairwise transcriptomic comparisons: 1) Transcriptomic comparison of naïve hPSCs cultured under static suspension and static culture, 2) Transcriptomic comparison of naïve hPSCs cultured under stirred suspension and static culture, 3) Transcriptomic comparison of naïve hPSCs cultured under stirred suspension and static suspension culture.

first: Derrick

middle: E

last: Rancourt


title: Vascular transcription factors control epidermal responses to limiting phosphate conditions

city: Zwijnaarde

first: Kevin

last: Verstaen

address: Technologiepark-Zwijnaarde 71

department: VIB Single Cell Core

country: Belgium

institute: VIB

summary: Optimal plant growth is hampered by limiting amounts of the essential macronutrient phosphate in most soils. As a response, plant roots produce root hairs to capture this immobile nutrient. Although vital to high-yielding crops, this response remains poorly understood. By generating and exploiting a high spatial and temporal resolution single cell atlas of the Arabidopsis root, we show a remarkable enrichment of TMO5/LHW target genes in root hair epidermal cells. Moreover, these vascular bHLH factors are sufficient to induce a root hair formation response in the epidermal cells, similar as observed during low phosphate conditions, via the downstream cytokinin signaling. We further show that root hair formation under low phosphate conditions is almost absent when TMO5 function or cytokinin signaling is perturbed. In conclusion, cytokinin signaling links the adaptation of roots under low phosphate conditions in the epidermis to perception in vascular cells.

overall_design: Single-cell RNA-seq experiments were performed in triplicate on protoplast cells extracted from the root-tips of 6 day old Arabidopsis thaliana seedlings.

first: Jos

middle: R

last: Wendrich

first: BaoJun

last: Yang

first: Niels

last: Vandamme

first: Wouter

last: Smet

first: Celien

last: Van de Velde

first: Max

last: Minne

first: Brecht

last: Wybouw

first: Eliana

last: Mor

first: Helena

last: Arents

first: Jonah

last: Nolf

first: Julie

last: Van Duyse

first: Gert

last: Van Isterdael

first: Steven

last: Maere

first: Yvan

last: Saeys

first: Bert

last: De Rybel


title: miRNA profile regulated by SOX2 in glioma stem-like cell

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

summary: Patient-derived glioma stem-like cell (GSC-11), a kind gift of Dr. Lang at UT MD Anderson Cancer Center, was subjected to a transient transfection to down-regulate SOX2 expression. Specific human SOX2 siRNA and a non-targeting control siRNA (si-Scramble) were used in four independent experiments. The cells were then cultured for 72 h after transfection and subjected to the miRNA array analysis.

overall_design: miRNA array profile of 2 conditions and 1 replicate per condition. Patient derived glioma stem-like cell were used and treated as indicated in the summary: GSC11 cells were transfected with a siRNA against SOX2 or a non-targeting control siRNA (si-Scramble). Equal amount of total RNA from each sample was pooled prior to miRNA expression analysis.

last: Alonso

first: Elizabeth

last: Guruceaga


title: METTL5, an 18S rRNA-specific m6A methyltransferase, regulates the Integrated Stress Response [eCLIP]

city: Boston

first: Yang

last: Shi

state: Massachusetts

address: 320 LONGWOOD AVE

department: NEWBORN MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

summary: RNA N6-methyladenosine (m6A) modification is present in different RNA molecules, including protein-coding mRNAs and non-coding RNAs such as ribosomal RNAs (rRNAs).Here, we report that mammalian METTL5, a member of a highly conserved methyltransferase family, specifically methylates adenosine 1832 (A1832) in the 18S rRNA in vivo and in vitro.

overall_design: We used eCLIP-seq to identify the binding targets of METTL5 in human 293T cells.

first: Hao

last: Chen


title: To study the effect of moss extract as anthelmintic on cestodes and nematodes of chick and sheep

city: CHENNAI

first: Florida

last: Tilton

state: Tamil Nadu

address: 7, Leo Muthu Street, Kalaimagal Nagar, Ekkaduthangal

country: India

institute: Biozone Research Technologies

summary: The bryophyte was collected and dried. Aqueous extract was prepared and different concentration of the extracts were treat against Ascardia galli, chicken nematode and Trichostrongylus, sheep nematode. Control was maintained for both. The control and treated samples were further processed to study the gene expression by isolating and sequencing mRNA using Illumina next-gen sequencing.

sample_organism:
Trichostrongylus colubriformis
Ascaridia galli

overall_design: Examination of gene expression between control and treated samples.

first: Sunila

last: Yennamaneni

first: Padmavathi

last: Sriram


title: Single cell sequencing of mice brain after stereotactic injection treatment

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

institute: Southern Medical University

summary: We report the application of single cell sequencing technology for high-throughput profiling in mice brain cells.In order to search for SCZ-related molecular pathways in different brain cell types affected by immune activation, we first activated the peripheral immune system by intraperitoneal injection (IPI) of lipopolysaccharide (LPS) into adolescent mice twice on post-natal day 45 and 46, and collected the serum from the mice on the third day. Then we performed intracerebroventricular injection (ICVI) of 15 ul of serum from the immune-activated mice. After ICVI of immune-activated serum for one week, we carried out single-cell transcriptome sequencing on the brains from the mice. This study provides characterization of diverse cell populations towards different treatments.

overall_design: Examination of 2 treatment effects on brain cells in mice.

first: Yue

last: Gao

first: Xiaozhen

last: Liang

first: Yanjun

last: Li

first: Shuangyan

first: Bing

last: Zhang


title: Possible role of environmental microbiome on B-cell bronchiolitis-alveolar ductitis and emphysema in metal machining workers

first: Leopoldo

middle: Nicolas

last: Segal

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

institute: NYU School of Medicine

summary: Here we report 16s rRNA data from environmental samples that include metal working fluid and air from a machine facility and lung tissue samples.  Microbiota composition of environmental and lung tissue samples showed greater similarity between case samples than between control samples.

overall_design: 16S rRNA was quantified and sequenced (MiSeq)

middle: N


title: RNA-seq of scallop mantle tissue

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

summary: We produced RNA-seq data from mantle tissue of the King Scallop, Pecten maximus, and identified expression of pathways involved in pigmentation of the shell.

overall_design: Sequencing of total RNA prepared from mantle tissue

first: Suzanne

last: Williams

first: Nathan

last: Kenny


title: Yap/Taz promote the scavenging of extracellular nutrients through macropinocytosis [ATAC-Seq]

first: Bryan

last: King

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: The uptake of macromolecules and cellular debris through macropinocytosis has emerged as an important nutrient acquisition strategy of cancer cells. Genetic alterations commonly found in human cancers (e.g. mutations in KRAS or loss of PTEN) have been shown to increase macropinocytosis. To identify additional effectors that enable cell growth dependent on the uptake of extracellular proteins, pancreatic ductal adenocarcinoma (PDA) cells were selected for growth in medium where extracellular albumin was the obligate source of the essential amino acid leucine. Analysis of global changes in chromatin availability and gene expression revealed that PDA cells selected under these conditions exhibited elevated activity of the transcriptional activators Yap/Taz. Knockout of Yap/Taz prevented growth of PDA cells in leucine-deficient medium, but not in complete medium. Furthermore, constitutively active forms of Yap or Taz were sufficient to stimulate macropinocytosis of extracellular protein. Together, these studies suggest that the Hippo pathway effectors Yap and Taz are important transcriptional regulators of endocytic nutrient uptake.

overall_design: Murine pancreatic adenocarcinoma cells (KRPC) were cultured short-term (16h) or long-term (21d) in leucine-deficient media supplemented with 3% bovine serum albumin and subjected to ATAC-seq analysis.

first: Craig

middle: B

last: Thompson


title: Yap/Taz promote the scavenging of extracellular nutrients through macropinocytosis


title: YAP and AP-1 cooperate to initiate rapid pancreatic cancer development from the ductal cell population in mice

city: Daejeon

first: David

last: Eisenbarth

address: 335 Gwahak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

summary:
Purpose: We aimed to elucidate the unique consequences of YAP/TAZ activation in pancreatic ductal cells.

Methods: We isolated RNA from Lats1 and Lats2 double knockout ductal cells from Lats1fl/fl; Lats2fl/fl; Sox9-CreER mice.

Results: Oncogenic activation of YAP in ductal cells lead to the rapid development of carcinoma in situ with microinvasion.

overall_design: mRNA profiles of pancreatic duct cells from control and Lats1/2 knockout mice were created by mRNA-sequencing.

first: Dae-Sik

last: Lim

first: Jaeoh

last: Park


title: Targeting myostatin/activin A protects against skeletal muscle and bone loss during spaceflight

status: Public on Sep 16 2020

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: Among the physiological consequences of extended space flight are loss of skeletal muscle and bone mass. One signaling pathway that plays an important role in maintaining muscle and bone  homeostasis is that regulated by the secreted signaling proteins, myostatin and activin A. Here, we used both pharmacological and genetic approaches to investigate the effect of targeting myostatin/activin A signaling in mice that were sent to the International Space Station. We show that inhibition of myostatin/activin A signaling has a significant protective effect against microgravity-induced muscle and bone loss. These findings have implications for therapeutic strategies to combat the concomitant muscle and bone loss occurring in people afflicted with disuse atrophy on Earth as well as in astronauts in space, especially during prolonged missions.

overall_design:
To study the effects of blocking MSTN/activin signaling in microgravity proteomic analysis of plasma using the SomaScan® Assay was carried out, which uses aptamers to measure relative levels of over 5000 secreted proteins.
Protein profiling of mouse samples extracted from plasma.

first: Se-jin

last: Lee


title: Yap/Taz promote the scavenging of extracellular nutrients through macropinocytosis [RNA-Seq]

overall_design: Murine pancreatic adenocarcinoma cells (KRPC) were cultured short-term (16h) or long-term (21d) in leucine-deficient media +/- 3% bovine serum albumin and subjected to RNA-seq analysis.

first: Wilhelm

last: Palm

first: Jingwen

last: Araki


title: RNAseq from human islets treated with brefeldin A as a model of Golgi stress

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: Type 1 diabetes (T1D) is characterized by immune mediated destruction of insulin producing β cells. Biomarkers capable of identifying T1D risk and dissecting disease-related heterogeneity represent an unmet clinical need. Aims: Towards the goal of informing T1D biomarker strategies, we profiled different classes of RNAs in human islet-derived exosomes and identified RNAs that were differentially expressed under cytokine stress conditions. Human pancreatic islets were obtained from cadaveric donors and treated with/without IL-1β and IFN-γ to mimic the pro-inflammatory T1D milieu. Total RNA and small RNA sequencing were performed to identify long (mRNA and long non-coding RNAs) and different classes of small non-coding RNAs. RNAs with fold change ≥ 1.3 and p-value < 0.05 were considered as differentially expressed. mRNAs and miRNAs species represented the most abundant long and small RNA species, respectively. Expression patterns of each class of RNA were changed with cytokine treatment. Differentially expressed long RNAs and targets of small non-coding RNAs were predicted to be involved in insulin secretion, calcium signaling, necrosis and apoptosis. Our data provides the first comprehensive catalog of protein coding and non-coding RNAs in human islet-derived exosomes and identifies RNAs that are dysregulated under cytokine stress.

overall_design: Identification of differentially expressed mRNA from Brefeldin A treated vs. control human pancreatic islets.

first: Robert

last: Bone

first: Farooq

last: Syed

first: Huanmei

last: Wu

first: Preethi

last: Krishnan

first: Sharmila

last: Selvaraj

first: Sayali

last: Talware


title: Tumour-associated microglia/macrophages in Glioblastoma are heterogenous and display higher immunological reactivity under aconitate decarboxylase 1 deficiency

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

summary: In Glioblastoma (GBM), tumour-associated microglia/macrophages (TAMs) represent the most abundant cells of the stromal compartment contributing to tumour immune escape mechanisms. Thus, strategies targeting TAMs are emerging as promising objectives for immunotherapy. However, TAMs heterogeneity is only starting to emerge and little is known about their contribution to GBM progression. Here, we comprehensively study the  molecular changes of TAMs in the GL261 GBM mouse model by single-cell RNA-sequencing across GBM progression and in the absence of Acod1/Irg1, a key gene involved in macrophage metabolic reprogramming. We identify distinct TAM profiles, mainly based on their ontogeny, which recapitulate microglia- versus macrophage-like features showing key transcriptional differences and rapidly adapting along GBM stages. Notably, we uncover a decreased antigen-presenting cell signature in TAMs along tumour progression that is less prominent in Acod1/Irg1-deficient mice. Overall, our results provide insights into TAMs heterogeneity and highlight a potential role for Acod1/Irg1 in TAMs polarization along GBM progression.

overall_design: Single-cell RNA-Sequencing experiments were performed on a total of 8 samples.

first: Yolanda

last: Pires Afonso

first: Arnaud

last: Muller

first: Carole

last: Sousa

first: Anaïs

last: Oudin

first: Antonio

last: Cosma

first: Rashi

last: Halder

first: Anna

last: Golebiewska

first: Djalil

last: Coowar

first: Simone

last: Niclou

first: Alexander

last: Skupin

first: Alessandro

last: Michelucci


title: The effects of liraglutide and dapagliflozin on cardiac function and structure in a multi-hit mouse model of Heart Failure with Preserved Ejection Fraction

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

institute: Hubrecht Institute

summary: Aims: Heart failure with preserved ejection fraction (HFpEF) is a multifactorial disease that constitutes several distinct phenotypes, including a common cardiometabolic phenotype with obesity and type 2 diabetes mellitus. Treatment options for HFpEF are limited, and development of novel therapeutics is hindered by the paucity of suitable preclinical HFpEF models that recapitulate the complexity of human HFpEF. Metabolic drugs, like Glucagon Like Peptide Receptor Agonist (GLP-1RA) and Sodium Glucose Transporter 2 inhibitors (SGLT2i), have emerged as promising drugs to restore metabolic perturbations and may have value in the treatment of the cardiometabolic HFpEF phenotype. We aimed to develop a multifactorial HFpEF mouse model that closely resembles the cardiometabolic HFpEF phenotype, and evaluated the GLP-1 RA liraglutide and a SGLT2i dapagliflozin. Methods&Results: Aged (18-22 months old) female C57BL/6J mice were fed a standardized chow (CTRL) or high fat diet (HFD) for 12 weeks. After 8 weeks HFD, Angiotensin-II (ANGII), was administered for 4 weeks via osmotic mini-pumps. HFD+ANGII resulted in a cardiometabolic HFpEF phenotype, including obesity, impaired glucose handling and metabolic dysregulation with inflammation. The multiple-hit resulted in typical clinical HFpEF features, including cardiac hypertrophy and fibrosis with preserved fractional shortening but with impaired myocardial deformation, atrial enlargement lung congestion, and elevated blood pressures. Treatment with liraglutide attenuated the cardiometabolic dysregulation and improved cardiac function, with reduced cardiac hypertrophy, less myocardial fibrosis, and attenuation of atrial weight, natriuretic peptide levels, and lung congestion. Dapagliflozin treatment improved glucose handling, but had mild effects on the HFpEF phenotype. Conclusions: We developed a mouse model that recapitulates the human HFpEF disease, providing a novel opportunity to study disease pathogenesis and development of enhanced therapeutic approaches. We furthermore show that attenuation of cardiometabolic dysregulation may represent a novel therapeutic target for treatment of HFpEF.

overall_design: 4 samples per condition, Female, 18-22 months old C57BL6/J, high fat diet (HFD) + angiotensin-II (ANGII) versus Control (LFD)

first: Coenraad

last: Withaar

first: Laura

last: Meems

first: George

last: Markousis-Mavrogenis

middle: J

first: Herman

middle: H

last: Silljé

first: Marloes

last: Schouten

first: Martin

last: Dokter

first: Adriaan

middle: A

last: Voors

first: B

middle: D

last: Westenbrink

first: Carolyn

middle: S

last: Lam

first: Rudolf

last: de Boer


title: Metabolite Patterns in Human Myeloid Hematopoiesis Result from Lineage-Dependent Active Metabolic Pathways

city: Villingen-Schwenningen

first: Lars

last: Kaiser

address: Jakob-Kienzle-Str. 17

department: Medical and Life Sciences

country: Germany

institute: University Furtwangen

summary: Assessment of hematotoxicity from environmental or xenobiotic compounds is of notable interest and is frequently assessed via the colony forming unit (CFU) assay. Identification of the mode of action of single compounds is of further interest, as this often enables transfer of results across different tissues and compounds. Metabolomics displays one promising approach for such identification, nevertheless, suitability with current protocols is restricted. Here, we combined a hematopoietic stem and progenitor cell (HSPC) expansion approach with distinct lineage differentiations, resulting in formation of erythrocytes, dendritic cells and neutrophils. We examined the unique combination of pathway activity in glycolysis, glutaminolysis, polyamine synthesis, fatty acid oxidation and synthesis, as well as glycerophospholipid and sphingolipid metabolism. We further assessed their interconnections and essentialness for each lineage formation. By this, we provide further insights into active metabolic pathways during the differentiation of HSPC into different lineages, enabling profound understanding of possible metabolic changes in each lineage caused by exogenous compounds.

overall_design: Expressional profiling during myeloid hematopoiesis, generated from one progenitor population, 4 samples analysed, one from progenitor population, one from each differentiated population

first: Helga

last: Weinschrott

first: Isabel

last: Quint

first: Markus

last: Blaess

first: René

last: Csuk

first: Manfred

last: Jung

first: Matthias

last: Kohl

first: Hans-Peter

last: Deigner


title: RNA-seq analysis of different sub-regions of developing grains in rice

city: Zurich

first: Weihong

last: Qi

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETHZ

summary: Popular rice mega varieties lack sufficient key micronutrients (e.g., Fe, Zn), vitamins and a balanced amino acid composition that are essential for a healthy diet. The major bottleneck for improving the nutritional quality of popular rice varieties through conventional breeding or gene technology is our lack of an integrated understanding of the biochemical and molecular processes that occur during rice grain filling (and their determining genes or loci). In this project, we will perform molecular expression profiling on specific tissue layers of the rice grain. To perform this experiment, the material will be developing rice seeds from plants grown hydroponically under controlled greenhouse conditions. Then, the laser microdissection approach will be applied to dissect different parts of the grain (i.e, vascular trace, aleurone, nucellar epidermis, etc). Total RNA will be extracted from these dissected parts and RNA sequencing will be performed. In this project, we will learn how the synthesis and deposition of grain nutrients is regulated, particularly, during grain filling.

overall_design: 47 samples were collected and 39 samples passed QC. Biological replicates of poor quality (i.e., with low correlation coefficients) were excluded, therefore, 28 samples in total were used for detailed analysis [NE_4DAF(3), OVT_4DAF(3), CC_4DAF(2), EN_4DAF(1), NE_8DAF(3), OVT_8DAF(2), CC_8DAF(1), EN_8DAF(2), NE_16DAF(3), OVT_16DAF(1), CC_16DAF(2), EN_16DAF(2), AL_16DAF(3)]

first: Ting-Ying

last: Wu

first: Navreet

last: Bhullar

first: Wilhelm

last: Gruissem


title: CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation

city: Stanford

first: Christopher

middle: Michael

last: Weber

state: CA

address: B209 Beckman Center

institute: Stanford University

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

overall_design: Refer to individual Series


title: CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation [ChIP-seq]

summary: The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder (ASD). CHD8 has a dosage-sensitive role in ASD but when and how it becomes critical to human social function is unclear. Here, we conducted genomic analyses of heterozygous and homozygous Chd8 mouse embryonic stem cells and differentiated neural progenitors. We identify dosage-sensitive CHD8 transcriptional targets, sites of regulated accessibility, and an unexpected cooperation with SOX transcription factors. Collectively, our findings reveal that CHD8 negatively regulates expression of neuronal genes to maintain pluripotency and also during differentiation. Thus, CHD8 is essential for both the maintenance of pluripotency and neural differentiation, providing mechanistic insight into its function with potential implications for ASD.

overall_design: We conducted CHD8 ChIPseq in mouse ES cells (2i growth conditions), containing a homozygous C-term 3xFLAG tag inserted into the endogenous locus.


title: CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation [RNA-seq]

overall_design: We conducted RNAseq on WT, CHD8+/-, CHD8-/- mouse embryonic stem cells (mESCs) cultured in 2i and differentiated neural progenitor cells (NPCs).


title: Anti-lymphoma activities of different compounds

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: 4 lymphoma cell lines (DOHH2, OCILy10, TMD8 and Toledo) have been treated with DMSO, CB103, NEO02734 or OTX015. The transcriptome has been sequenced after 6hrs from the treatment. The gene expression levels have been compared in order to elucidate the differencies and similarities for the different drugs compare to DMSO (control group).

overall_design: Transcriptome profiles of 6hrs and 14days for 6 lymphoma cell lines treated with DMSO, Vorinostat and Pracinostat.

first: Francesco

last: Bertoni


title: Single-cell RNA-seq analysis of mouse and human prostate

city: New York

first: Luis

last: Aparicio

address: 390 Fort Washington Avenue  9E

institute: Columbia University

summary: Single-cell RNA-seq analysis of wild-type mouse and benign human prostate

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For mouse studies, 8-10 weeks C57BL6/N mice were euthanized, and the full proximal-distal extent of each prostate lobe (Anterior (AP), Dorsal (DP), Ventral (VP) and Lateral (LP)) was microdissected down to its junction with the urethral epithelium. Dissected prostate lobes, either individually or combined, were processed for single-cell RNA-seq. For human studies, specimens were obtained from patients undergoing prostatectomy at the Department of Urology of the Columbia University Irving Medical Center. All patients gave informed consent under the auspices of an Institutional Review Board-approved protocol. Upon surgery, prostate tissues were submitted to the Department of Pathology for standard gross pathological examination and sectioning. Specimens not required for diagnostic testing were de-identified and transferred to the research facility for single-cell RNA-seq.
***Please note that  raw data files are currently unavailable and will be provided later.

first: Michael

last: Shen

last: Cambuli

first: Laura

last: Crowley

first: Maho

last: Shibata


title: Plasticity of ether lipids promotes ferroptosis susceptibility and evasion

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

summary: Ferroptosis, an iron-dependent, non-apoptotic cell death program, is involved in a variety of degenerative diseases and represents a targetable vulnerability in certain cancers. The ferroptosis-susceptible cell-state can either preexist in cells arising from certain lineages or be acquired during cell-state transitions. Precisely how ferroptosis susceptibility is dynamically regulated remains poorly understood. Using genome-wide CRISPR/Cas9 suppressor screens, we identify a key role for peroxisome–ether phospholipid genes in driving ferroptosis susceptibility and evasion in ovarian cancer.

overall_design: Ovcar8 CRISPR library infected cells treated with escalating doses of RSL3 (Selleckchem) for 4 days each: 0.5 μM, 1 μM, and 2μM. 1×10^7 cells each were collected from the surviving population of RSL3-treated cells and an endpoint-matched untreated population for downstream sequencing analysis.

first: Whitney

last: Henry

first: Heather

last: Keys


title: RNA stability measurements in RBMS1 knockdown cells and control cells

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: In order to identify RBMS1-dependent changes in RNA stability, RBMS1 levels in SW480 breast cancer cells were stably knocked-down using short-hairpin RNAs. The cells were then treated with alpha-amanitin to inhibit transcription, RNA was isolated at 0 and 9 hours post-alpha-amanitin treatment, and the samples were transcriptomically profiled.

overall_design: shRNAs targeting either RBMS1 (TRCN0000074936 and TRCN0000291051, Sigma) or a control shRNA were stably expressed in SW480 breast cancer cells. These cells were treated with 10ug/mL alpha-amanitin to inhibit transcription, and total RNA was isolated at 0 and 9 hours post-alpha-amanitin treatment.

first: J

last: Yu

first: A

last: Navickas

first: H


title: Total RNA sequencing of RBMS1 knockdown cells

summary: We compared gene expression in RBMS1 knockdown and control cells in the SW480 background.

overall_design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina NextSeq 500.


title: RNA-sequencing and Exome-sequencing analysis of ferroptosis-resistant 786-O GPX4-null carcinoma cells following in vivo selection

summary: We have used in vivo selection to isolate GPX4 knockout 786-O cells that have evaded ferroptosis in vivo in mouse xenograft experiments. RNA-seq and Exome-seq profiling were performed to characterize the mechanisms underlying ferroptosis evasion in these in vivo-derived ferroptosis resistant cells.

overall_design:
Two tumor cell lines were isolated from GPX4 wildtype 786-O tumors. Four GPX4-null 786-O cell lines were isolated from overt GPX4-knockout tumors growing on two mice. Two replicates of each cell line were performed in the RNA-Seq experiment. One replicate of each cell line was performed in the Exome-seq experiment.

WTL: (GPX4) wildtype, left tumor
WTR: (GPX4) wildtype, right tumor
FR2aL: Secondary ferroptosis-resistant line from mouse1 (a), left tumor
FR2aR: Secondary ferroptosis-resistant line from mouse1 (a), right tumor
FR2dL: Secondary ferroptosis-resistant line from mouse2 (or "d"), left tumor
FR2dR: Secondary ferroptosis-resistant line from mouse2 (or "d"), right tumor

first: Stuart

last: Schreiber


title: CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation [ATAC-seq]

department: Pathology

overall_design: We conducted ATACseq on WT, CHD8+/-, CHD8-/- mouse embryonic stem cells (mESCs) and differentiated neural progenitor cells (NPCs).


title: RNA sequencing of cells


title: Total RNA sequencing of AKAP12 knockdown cells

summary: We compared gene expression in AKAP12 knockdown and control cells in the SW480 background.

overall_design: Libraries were generated using QuantSeq 3-end RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 4000.


title: Sirt2 Inhibition Reprograms T Cell Metabolism to Confer Superior Anti-Tumor Immunity

city: Tampa

first: Sungjune

last: Kim

address: 12902 USF Magnolia Driv

institute: RADIATION ONCOLOGY

summary: Metabolism is a key driver of T cell functions, and the switch from oxidative-phosphorylation to aerobic glycolysis is a hallmark of T cell activation. However, the mechanisms underlying the metabolic switch remain unclear. Here, we report that the Sirtuin-2 (Sirt2) deacetylase protein functions as a metabolic checkpoint that harnesses T cell effector functions and impairs anti-tumor immunity. Specifically, upregulation of Sirt2 expression in human tumor-infiltrating T lymphocytes (TILs) negatively correlates with response to Nivolumab and TIL therapy in non-small cell lung cancer. Mechanistically, Sirt2 suppresses aerobic glycolysis by deacetylating key glycolytic enzymes. Accordingly, Sirt2-deficient T cells manifest increased glycolysis, display enhanced proliferation and effector functions, and have superior anti-tumor activity. Importantly, pharmacologic inhibition of Sirt2 endows human TILs with these superior metabolic fitness and enhanced effector functions. These findings indicate Sirt2 as an actionable target for reprogramming T cell metabolism to augment a broad spectrum of cancer immunotherapies.

overall_design: Spleens were collected from C57BL/6J and Sirt2-/- mice and were processed into single-cell suspensions. CD4+ T cells were negatively enriched and were either followed directly by RNA extraction (naïve = 0 hour) or stimulated for 24 hours. WT and Sirt2-/- CD4+ T cells were activated with plate-bound anti-CD3 antibody (5 μg/ml, 145-2C11, BioXCell) for 24 hours.

first: Imene

last: Hamaidi

first: Lin

last: Zhang

first: Nayoung

first: Min-Hsuan

last: Wang

first: Cristina

last: Iclozan

first: Bin

last: Fang

first: Min

last: Liu

first: John

last: Koomen

first: Anders

last: Berglund

first: Sean

last: Yoder

first: Jiqiang

last: Yao

first: Ben

last: Creelan

first: Scott

last: Antonia


title: RNA-seq analysis of the central nervous systems from Drosophila larvae with reprogrammed glia

city: Philadelphia

first: Feng

last: Li

state: PA

address: 3501 civic center blvd

institute: Children's hospital of philadelphia

summary: In our study, we found that reprogrammed glia by activating PI3K and EGFR pathways promotes axon regeneration in the central nervous systems of Drosophila larvae. Thus, we analysized the transcriptome of the CNS collected from flies with or without repromgrammed glia by RNA-seq.

overall_design: collected 70-100 larvae central nervous systems for each sample, and two samples for either control group or treatment group

first: Yuanquan

last: Song


title: Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

summary: We report the ChIP-seq analysis of Sox17 genome-wide binding and its loss-of-function transcriptomic analysis of both Sox17 and Ctnnb1 (beta-catenin) by RNA-seq.

overall_design: ChIP-seq was performed to detect endogenous Sox17 binding (N&F stage 10.5) and RNA-seq was used to assess gene expression changes in Sox17 (N&F stages 9, 9.5, 10, 10.5, 11, 12) or Ctnnb1 (N&F stages 7, 8, 9, 9.5, 10, 10.5, 11, 12) in morpholino antisense oligo injected versus uninjected control embryos

first: Aaron

last: Zorn

first: Shreyasi

last: Mukherjee


title: RNAseq Analysis for pBABE versus caMNK D4m.3a Melanoma cells

city: Montreal

first: Sonia

middle: V

last: del Rincon

state: Quebec

address: 3755 cote Sainte Catherine Road

institute: Lady Davis Institute

summary: We want to investigate the transcriptional differences between pBABE D4m.3a melanoma cells (cancer cell control) and caMNK D4m.3a melanoma cells (cancer cells with constitutive activation of MNK) to find the transcriptional changes in melanoma cells upon MNK overexpression. This study allows us to examine the role MNK has in regulating key oncogenic factors involved in melanoma metastasis, proliferation and tumor development.

overall_design: 2 biological replicates of pBABE D4m.3a melanoma cells and 3 biological replicates of caMNK D4m.3a cells were analyzed. pBABE cells were used as reference control

first: Christophe

last: Goncalves

first: William

last: Yang

first: Audrey

last: Emond

first: Wilson

last: Miller.

last: Del Rincon


title: Development of gene expression signatures for phytochrome mediated  lifestyle decision and pathogenesis regulation

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: To further development of our gene expression approach to establish that XooBphP acts as the major determinant of pathogenic circadian clock, we have employed whole genome microarray expression profiling as a discovery plateform to identify genes with the potential to synchronize the diurnal cycle by XooBphP to circumvent the host circadian defence response.

overall_design:
gene expression after grown overnight in peptone-sucrose medium
Agilent Whole Genome Xanthomonas oryzae 8x15k Gene Expression  (AMADID: 74281) designed by Genotypic Technology privatted Limited, Bangalore

first: Raj

middle: K

last: Verma

first: Subhadeep

last: Chatterjee


title: Gene expression in matched primary and liver metastases

first: Hani

last: Goodarzi

summary: We profiled primary colon cancer and liver metastatic tumours from two patients.

overall_design: We performed RNA-sequencing to measure gene expression changes between matched primary and metastatic foci.

first: J

last: Yu

first: A

last: Navickas

first: RW

last: Warren

first: H


title: A novel FACS-based method to isolate enriched populations of neurons, astrocytes, and microglia

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: We developed a novel FACS-based method to isolate enriched populations of neurons, astrocytes, and microglia. Whole mouse brains were digested, and populations of neurons, astrocytes, and microglia were subsequently enriched by FACS using a combination of positive gating on cell-type specific markers and stringent negative selection against markers of oligodendrocytes and endothelial cells. We confirmed a strong enrichment of corresponding cell-type specific genes in isolated populations and a reduction in gene markers of endothelial cells and oligodendrocytes, demonstrating that highly pure populations of neurons, astrocytes, and microglia were obtained.

overall_design: CNS cells from untreated wildtype mice were isolated using fluorescent activated cell sorting.

first: Julie

middle: C

last: Ullman

first: Anastasia

middle: G

last: Henry


title: Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

summary: Glutathione S-transferase omega 1 (GSTO1) is an atypical GST isoform that is overexpressed in several cancers and has been implicated in drug resistance. Currently, no small-molecule drug targeting GSTO1 is under clinical development. Using genetic tools, including extensive bioinformatics analysis coupled with CRISPR/Cas9 technologies, we have validated GSTO1 as an impactful target in oncology. Through transcriptional profiling using Bru-seq and RNA-seq coupled with proteomics, we uncovered novel pharmacodynamic markers and cellular pathways regulated by GSTO1. Our CRISPR/Cas9 GSTO1 knockout (KO) cell lines do not form tumors or display growth delay in vivo and form smaller 3D spheroids in vitro. Through multi-omics studies in GSTO1 KO cells, we found a strong positive correlation with cell adhesion molecules and interferon response pathways, and a strong negative correlation with Myc transcriptional signature. Importantly, we also identified several clinically used drugs showing significant synthetic lethality with loss or inhibition of GSTO1. We discovered that tissue factor (gene name, F3) transcription and protein expression are downregulated in response to GSTO1 KO.  Associated with poor patient survival and promotion of tumor progression in multiple cancers, F3 is a known risk factor for metastasis. F3 transcription is under the regulation of IL-1β, whose secretion is decreased upon GSTO1 inhibition, suggesting that IL-1β links GSTO1 expression and F3 transcription. In summary, our results implicate GSTO1 as a therapeutic target in cancer and offer new mechanistic insights into its significant role in cancer progression.

overall_design: Cells were lysed with TRIzol® Reagent (ThermoFisher Scientific, Waltham, MA) at room temperature. RNA was further purified with DirectZol kit (Zymo Research, Irvine, CA). RNA quality was assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared with TruSeq Stranded mRNA Library Prep (Illumina) per the supplier’s protocol with 1μg of RNA and 12 cycles of PCR amplification. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (Illumina). The libraries were barcoded, pooled and sequenced using 50bp paired-end 50bp (U-87 MG, University of Michigan DNA Sequencing Core, MI) and single-end 50bp (HCT116, University of Michgian DNA Sequencing Core, MI) sequencing. Reads were mapped to GRCh38 using STAR v2.5.2 and gene quantifications were calculated using Cufflinks v2.2.1 to quantify refGene annotations. Gene read counts calculated using featureCounts v1.6.1 were used to evaluate differential expression using DESeq2 v1.18.1. Protein coding genes were considered significantly differentially expressed with a mean FPKM > 0.5 and absolute fold change > 1.5 and FDR adjusted p-value < 0.05. All gene readouts where required to be mappable to both an HGNC and Entrez identifier to be considered for gene set enrichment analyses.

first: Nouri

last: Neamati

first: Yibin

last: Xu


title: Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance (Hereford vs Holstein-Friesian)

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: The goal was to examine and compare the transcriptomic profiles of fully differentiated 15 month old muscle derived from bulls belonging to different breeds and showing different performance.

overall_design: Comparison of transcriptomic profiles of mature tissue (15 month old) of semitendinosus muscle from beef breeds Hereford (HER) vs. dairy breed Holstein-Friesian (HF) - used as a control. Each comaprison was performed in four biological repetitions.

first: Anna

last: Ciecierska


title: SIRT7 safeguards genome stability and suppresses colorectal tumorigenesis

city: Shanghai

first: Xiyang

last: Liu

state: Shanghai

address: 320 Yueyang Road, Shanghai, 20025 P.R. China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: SIRT7 is a member of the mammalian sirtuin family and functions as a NAD+-dependent deacylase. Studies in culture cells and human clinical data have implicated the role of SIRT7 in tumorigenesis. However, controversies were raised as to whether SIRT7 is oncogenic or tumor suppressive. Here we show that SIRT7 deficiency led to aneuploidy and aging-phenotypes, including senescence and nucleolin expansion. SIRT7 knockout mice were susceptible to DSS-induced colitis and alcohol-derived DNA damage, in advance led to intestinal epithelial barrier disruption. Devoid of SIRT7 aggravated the susceptibility of colorectal cancer incidence in APCMin/+ mouse model with further dysregulated Wnt signaling. Our findings indicated a tumor suppressive role of SIRT7 in vivo, novel strategies design for activating SIRT7 in treating colon cancer may be reappraised.

overall_design: Intestinal mRNA profiles of three 5-month old Apc min/+ (Apc min/+) versus APC min/+ ; Sirt7 -/- (Apc min/+;Sirt7KO) mice.

first: Yun-Chi

last: Tang

first: Hung-Chun

last: Chang


title: Gene expression profiling of neutrophils derived from K14HPV16/H2b and FVBN/H2b mice.

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Cancers induced by human papillomaviruses should, in principle, be responsive to immunotherapy by virtue of expressing the immunogenic oncoproteins E6/E7 that drive malignancy. Rather, advanced forms of cervical cancer are poorly responsive to immune response-enhancing treatments involving therapeutic vaccination against these viral neo-antigens. Leveraging a transgenic mouse model for HPV-derived cancers, termed K14HPV16/H2b, we demonstrate that therapeutic vaccination with a nanoparticle-based vaccine alone or in combination with anti-PD-1/anti-CTLA4 does not elicit tumor regression nor increase the minimal CD8+ T cell infiltrates in the tumor microenvironment (TME), suggesting the presence of immunosuppressive barriers. We demonstrated that myeloid cells in lymphoid organs of K14HPV16/H2b mice possess potent immunosuppressive activity for both antigen presenting cells and CD8+ T cells that dampens the anti-tumor immune responsiveness. Our data highlight a link between HPV-induced cancers, systemic amplification of myeloid cells, and the detrimental effects of these cells on the generation of anti-tumor immune responses in the periphery, resulting in poor CD8 T cell activation and limited migration to the tumor site.

overall_design: Comparison of K14HPV16/H2b-derived with FVBN/H2b-derived neutrophils.

first: Gabriele

last: Galliverti

first: Stephan

last: Wullschleger

last: Zangger

first: Douglas

last: Hanahan


title: Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance (Limusine vs Holstein-Friesian)

overall_design: Comparison of transcriptomic profiles of mature tissue (15 month old) of semitendinosus muscle from beef breeds Limousin and (LIM) vs. dairy breed Holstein-Friesian (HF) - used as a control. Each comaprison was performed in four bilogical repetitions.


title: Brain delivery and efficacy of a lysosomal enzyme using a blood-brain barrier transport vehicle [RNA-seq]

summary: The enzyme transport vehicle (ETV:IDS) is a lysosomal enzyme fused to iduronate 2-sulfatase (ETV:IDS), the lysosomal enzyme deficient in mucopolysaccharidosis type II (MPS II). ETV:IDS treatment significantly improved brain delivery of IDS in a preclinical model of disease, enabling enhanced distribution to neurons, astrocytes, and microglia throughout the brain. Improved brain exposure for ETV:IDS translated to a significant reduction in accumulated substrates in these CNS cell types and peripheral tissues, and in a complete correction of downstream disease-relevant pathologies in the brain, including secondary accumulation of lysosomal lipids, perturbed gene expression, neuroinflammation, and neuronal injury. These results highlight the therapeutic potential of the ETV approach as a new treatment paradigm for MPS II and for other CNS diseases more broadly.

overall_design: Cells from mice of two genotypes (TfR KI, IDS KO/TfR KO), treated with either vehicle of ETV:IDS were isolated using fluorescent activated cell sorting.


title: Brain delivery and efficacy of a lysosomal enzyme using a blood-brain barrier transport vehicle

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

overall_design: Refer to individual Series


title: RNA-seq analysis of mammary tissue reveals persistent changes in gene expression profiles dependent upon the level of folic acid intake in C56BL/6 mice.

status: Public on Sep 15 2020

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:
Purpose: To identify, using RNA-sequencing, differentially expressed genes in the mammary gland of mice supplemented with FA. We aimed to ascertain whether gene expression is persistently altered after increased FA supplementation, whether such alterations are related to genes implicated in epigenetic regulation and disease risk.
Methods: Mammary gland mRNA profiles of mice 4 weeks after folic acid supplementation (5mg/kg vs 1mg/kg) during adulthood were generated by deep sequencing using RNA sequencing. The sequence reads that passed quality filters were aligned to the mouse genome using TopHat and analyzed at the gene level using DESeq2. qRT–PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (build mm10) and identified 222 genes differentially expressed between the two group (adjsuted p value <0.05). 191 of these were upregulated and 31 were downregulated. Geneset enrichment analysis identified several enriched pathways, including epithelial mesenchymal transition and myogenesis.
Conclusions: Our study provides novel insights into the persistent effects of FA intake on the C57BL/6 mammary transcriptome and identifies putative gene targets and molecular pathways that help to understand how increasing FA intake may modulate the long term expression of gene networks and disease pathways.

overall_design: C57BL/6 Mammary gland RNA transcriptomes 4 weeks after a follic acid supplemntation (5mg/kg or 1mg/kg).


title: Expression data from cardiac-specific miR-100 overexpressing mice

city: Freiburg

first: Christian

last: Smolka

state: Baden Württemberg

address: Breisacher Strasse 33

department: Department of Cardiology and Angiology I

institute: Heart Center Freiburg University

summary:
During heart failure development, cardiac tissue undergoes diverse adaptions, for example on a structural and/or metabolic basis, to fulfill the requirements needed to provide a proper circulation to the whole body.
We used microarray analysis to identify possible new targets of microRNA-100 in heart tissue.

overall_design: Left ventricular heart tissue samples from 8 weeks old, male, untreated wildtype (4x) and cardiac-specific microRNA-100 overexpressing mice (4x) was used for RNA extraction and hybridization on Affymetrix microarrays.


title: Generation of Escherichia coli Enhanced Acetate Utilization through Compensatory ATP Consumption via Adaptive Laboratory Evolution

city: Daejeon

first: Wonjae

last: Seong

address: Gwahak-ro 125

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. The transcriptomes according to the medium status (M9 aceate, M9 glucose) of the evolved strain (SBA01) and its parent strain (DSM01) were compared using RNA-seq.

overall_design: mRNA sequencing of E.coli strain SBA01 growing under the M9 glucose and M9 acetate and DSM01 growing under the M9 glucose, triplicated.

first: Gui

last: Han

first: Hyun

last: Lim

first: Ji

last: Baek

first: Soo-Jung

last: Kim

first: Donghyuk

first: Seong

first: Haseong

first: Seung-Goo

last: Lee

first: Dae-Hee


title: Regulation of acupuncture on genes in brain stem

city: Tianjin

first: Ru

middle: Si

last: Qin

address: No.10 Poyang Lake Road, Tuanbo new town, Jinghai District, Tianjin

institute: Tianjin University of Traditional Chinese Medicine

summary:
Recent clinical trials have shown that hand acupuncture improves cognition and other clinical outcomes of central nerve injuries including TBI,and we would like to observe that the effects  of acupuncture on key signaling pathways and neuronal networks of the brainstem in TBI rats to promote the recovery of consciousness.
We used microarray to detail the expression of wake-up related genes in brainstem

overall_design: The 1h brainstem samples (n=5) were mixed, extracted, purified, whose qualities were tested for total RNA with a standard Affymetrix protocol according to Shanghai Biotechnology Corporation (Shanghai, China) as reported previously.

first: Siru

first: Zhifang

last: Xu


title: GM-CSF-producing T helper cells: a distinct subset  of T helper cells that acquire Th1 phenotype during the CNS inflammation.

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Using scRNA-seq and CyTOF, we identified eight populations of antigen-experienced CD45RA-CD4+ T cells in blood of healthy donors, including a population of GM-CSF-producing Th cells (ThGM) that lacked expression of signature transcription factors and cytokines of established Th lineages. In addition to GM-CSF, human and mouse ThGM cells also expressed IL-2, TNF, IL-3 and CCL20. ThGM cells maintained their phenotype through several cycles of activation, but upregulated expression of T-bet and IFN-g upon exposure to IL-12 in vitro, and in the CNS of mice with autoimmune neuroinflammation. ThGM cells were encephalitogenic; T-bet was not required for their development, but it was required for their encephalitogenicity. These findings demonstrate that ThGM cells constitute a distinct population of Th cells with lineage characteristics.

overall_design: 5 scRNAseq datasets were analyzed.

first: Javad

last: Rasouli

first: Giacomo

last: Casella

first: Satoshi

last: Yoshimura

first: Weifeng

last: Zhang

first: Dan

last: Xiao

first: Michael

last: Gonzalez

first: Alice

last: Wiedeman

first: Elisabeth

middle: R

last: Mari

first: Hakon

last: Hakonarson

first: S

last: Long

first: Guang-Xian

first: Bogoljub

last: Ciric

first: Abdolmohamad

last: Rostami


title: YAP orchestrates heterotypic endothelial cell communication via HGF/c-MET signaling in liver tumorigenesis

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Disturbance of heterologous cell communication is associated with a structural reorganization of the vascular niche, a process called capillarization, which is already initiated in early stages of liver tumor development. In this study, the molecular characterization of endothelial cell (EC) subpopulations from healthy livers and yes-associated protein (Yap)-induced liver tumors revealed a dynamic crosstalk between liver sinusoidal endothelial cells (LSECs) and capillary endothelial cells (CECs). Initial paracrine stimuli from parenchymal cells include the Yap/Tead4 target gene osteopontin (Opn), which promotes CECs expansion through the induction of c-Met and sensitization towards LSEC-derived hepatocyte growth factor (Hgf). In addition, Yap/Tead4-induced C-C motif chemokine ligand 2 (Ccl2) recruits bone-marrow-derived macrophages (BMDMs) with an unpolarized phenotype (M0) to the perivascular space of expanding CECs.

overall_design: 10 samples in total: 3 unstimulated, 4 samples 3 hours after HGF stimulation, 3 samples 6 h after HGF stimulation.

first: Stefan

last: Thomann

first: Kai

last: Breuhahn


title: Liver macrophages in YapS127A and wildtype livers

overall_design: 8 samples: 4 macrophage samples derived from wildtype livers and 4 macrophage samples derived from YapS127A tumor bearing livers.


overall_design: 6 samples in total: 3 samples  capillary endothelial cells (CECs) and 3 samples liver sinusoidal endothelial cells (LSECs), both groups isolated from C57Bl/6N  mice


title: Cortical RORb is required for layer 4 transcriptional identity and barrel integrity

city: Waltham

first: Erin

middle: Amelia

last: Clark

state: MA

address: 415 South St

department: Biology

institute: Brandeis University

summary: RNA-seq and ATAC-seq from layer 4 cortical neurons expressing RORb-gfp or GFP in an RORb KO.

overall_design: RNA-seq and ATAC-seq from FACS isolated neruons. RNA-seq was carried out on ~1000 L4 S1 neurons from mice of different ages (P2, P7, and P30). ATAC-seq was carred out on ~40,000 L4 neurons from P28-P30 mice. All samples were collected from a pool of cells taken from at least 1 male and 1 female.

first: Sacha

last: Nelson

first: Emma

last: Myers

first: Anton

last: Schulmann


overall_design: 3-4 biological samples per disease stage and cell type were analyzed. Wt determines ECs from non-tumor bearing mice; early determines ECs derived from preneoplastic livers below a liver weight of 5g. Late determines ECs derived from tumor-bearing livers above 5g liver weight.  Preneoplastic and tumor-bearing livers are from Yap-transgenic (TG) animals.


title: Effect of Idelalisib in follicular lymphoma monocultures and cocultured with follicular dendritic cells (FDC)

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

institute: IDIBAPS

summary:
Follicular Lymphoma primary cells (FL)  were treated with the PI3K delta inhibitor idelalisib (500nM, 48h) in the presence or absence of follicular dendritic cells
We used microarrays to uncover the mechanisms underlying mechanism of resistance and sensitivity of FL to idelalisib

overall_design: Global RNA expression was done in five primary FL biopsies  treated  in vitro  with idelalisib in monoculture or cocultured with follicular dendritic cells

first: Neus

last: Aymerich

first: Martina

last: Guerrero-Hernández

first: Alba

last: Matas-Céspedes


title: Transcriptomic regulation of human mesenchymal stem cells in delivering anti-tumorigenic effects on leukaemic cell lines

city: SERI KEMBANGAN

first: VAHID

last: HOSSEINPOUR SARMADI

state: SELANGOR

address: C-12-06, THE HERITAGE RESIDENCY, JALAN DAGANG

country: Malaysia

institute: University Putra Malaysia

summary: The present study was designed to investigate the effect of human umbilical cord-derived MSCs (UC-MSCs) on the proliferation of leukaemic cells and gauged the transcriptomic modulation and the signalling pathways that potentially inflicted by UC-MSCs.

overall_design: Level of genes expression in BV173 (Leukemic origin cell line) in co-culture with UC-MSCs after 72 hours as a experiment and BV173 alone as a control were evaluated by using microarray in 3 independent biological replication.

first: Vahid

last: Sarmadi

first: Rajesh

last: Ramasay


title: Expression data of different hormone treatments from a staygreen mutant of citrus and its wild type

city: Wuhan

first: Feng

last: Zhu

address: No.1,Shizishan Street

department: College of Horticulture & Forestry Sciences

institute: Huazhong Agricultural University

summary: The fruits color is one of the most important appearance qualities of citrus fruits. To illuminate the potential regulation of the color formation process of citrus fruits, the present study compared the different genes expression pattern between a spontaneous stay-green mutant and its wild type under different hormones treatments

overall_design: The flavode of the citrus were collected at 170 days after flowering after different hormones treatment for RNA extraction and hybridization on Affymetrix microarrays.

first: Yunjiang

last: Cheng


title: Profiling the repo>+ (control) and repo>AmaRNAi knockdown third instar Drosophila brains using Drop-seq (single cell RNA-seq)

status: Public on Sep 14 2020

city: Chicago

first: Elizaveta

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: We characterized the glial cells in the Drosophila third instar brain using single cell RNA-seq and compared a Ama knockdown glia to the control. The results identified defects in surface glia, an increase in infiltrating hemocytes, and a novel Ama knockdown cluster defined by sty.

overall_design: Examining control and repo>AmaRNAi glia using single cell RNA-seq.

first: Majd

middle: M

last: Ariss

first: Maxim

last: Frolov

first: Abul

last: Islam


title: p53 activation during ribosome biogenesis regulates normal erythroid differentiation. [expression]

city: Paris

first: Ismael

last: Boussaid

address: 22 Rue Mechain

country: France

institute: Inserm

summary: The role of ribosome biogenesis in erythroid development is supported by the recognition of erythroid defects in ribosomopathies in both Diamond-Blackfan anemia and 5q- syndrome. Whether ribosome biogenesis exerts a regulatory function on normal erythroid development is still unknown. In the present study, a detailed characterization of ribosome biogenesis dynamics during human and murine erythropoiesis shows that ribosome biogenesis is abruptly interrupted by the drop of rDNA transcription and the collapse of ribosomal protein neo-synthesis. Its premature arrest by RNA polI inhibitor, CX-5461 targets the proliferation of immature erythroblasts. We also show that p53 is activated spontaneously or in response to CX-5461 concomitantly to ribosome biogenesis arrest, and drives a transcriptional program in which genes involved in cell cycle arrest, negative regulation of apoptosis and DNA damage response were upregulated. RNA polI transcriptional stress results in nucleolar disruption and activation of ATR-CHK1-p53 pathway. Our results imply that the timing of ribosome biogenesis extinction and p53 activation are crucial for erythroid development. In ribosomopathies in which ribosome availability is altered by unbalanced production of ribosomal proteins, the threshold of ribosome biogenesis down-regulation could be prematurely reached and together with pathological p53 activation prevents a normal expansion of erythroid progenitors.

overall_design: The purpose of the dataset is to profile  analyze the effect of ribosome biogenesis in erythroblast cells

first: Michaela

last: Fontenay


title: Expression data from FACS-purified Lgr5-EGFP+ intestinal cells from Ubc9+/+ and Ubc9+/- mice

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

summary:
The Lgr5+ intestinal stem cell, Paneth and transit-amplifying cell compartment constitute the intestinal crypt which is the constant source of differentiated epithelial cells that replenish the intestinal villi ensuring organ maintenance and regeneration. The Lgr5+ crypt-based columnar (CBC) cells have been identified as the intestinal stem cells (ISCs) and, importantly, as cells-of-origin of intestinal cancer.
We used microarrays to detail the global program of gene expression in normal ISCs describing a mild downregulation of the sumoylation (post-translational modification (PTM) of proteins by SUMO) imposed by the loss of one allele of the unique E2-conjugating enzyme (Ubc9) of the pathway.

overall_design: Lgr5-EGFPhigh, CD24middle, EpCampositive and PInegative intestinal stem cells from normal Lgr5-EGFP mice either wt for Ubc9 or heterozygous (Ubc9+/-) were sorted into RNA later solution and kept at -80ºC until further processing. 5 8-12 weeks-old mice from each group were used. 3 males and 2 females per group were used and were analysed together. RNA from more than 5000 cells was extracted using trizol and high-quality RNA was used for hybridization.

first: Ignacio

last: López

first: Juan

middle: P

first: Jacob

last: Seeler

first: Anne

last: Dejean


title: Affymetrix SNP array data of a TRNT1 positive MDS adult patient

city: Perugia

first: Cristina

last: Mecucci

address: piazzale Menghini n.9

department: Medicine

country: Italy

institute: University of Perugia

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

summary: SIFD (Congenital sideroblastic anemia, B-cell immunodeficiency, Periodic fevers and Developmental delay) Syndrome is caused by biallelic mutations in tRNA nucleotidyltransferase CCA-adding, 1 (TRNT1) gene. The onset of the disease is usually neonatal or in early infancy and the clinical presentation is widely heterogeneous. Myelodysplastic syndromes (MDS) with ring sideroblasts, which is characterised by somatic mutations in SF3B1 gene in more than 80% of cases, have never been reported as associated with SIFD Syndrome.   Here we report a case of an adult male patient with a novel non-sense heterozygous mutation in TRNT1 gene, which developed MDS with somatic K700E SF3B1 mutation and trisomy 8. WES revealed additional somatic variations affecting genes implicated in cell proliferation, apoptosis and DNA mismatch repair: ARID1A, HERC1, IL4R, TMEM260 and CDKL3. Besides the typical recurrent aseptic pneumonias and sinopulmonary bacterial infections, he developed lymphohistiocytic subcutaneous panniculitis and subsequently a subcutaneous panniculitis-like T-cell lymphoma (SPTCL), suggesting that predisposition in the TRNT1 positive syndrome extends to both lymphoid and myeloid neoplasms.  This report is particularly relevant to provide insights on the hematological impact of TRNT1 positive syndrome in adults and to improve early diagnosis and management of this rare disease.

overall_design: Copy number analysis of TRNT1 mutated MDS case

first: Gianluca

last: Barba

first: Valeria

last: Di Battista


title: Expression data of intestinal polyps and intestinal normal tissue from Ubc9+/+ and Ubc9+/- Villin-CreERT2;Apcf/+ mice 12 weeks after 4-OHT treatment

summary:
Most human cancers present hyperactivated sumoylation, and cancer cell lines are usually highly sensitive to the lack of it, supporting potential application of sumoylation chemical inhibitors in cancer therapy. Here, we explored the impact of hyposumoylation (Ubc9 haploinsufficiency) on cancer development in mice using Apc loss-driven intestinal tumorigenesis model.
We used microarrays to compare the global program of gene expression in intestinal polyps and normal tissue from mice homozygous (+/+) and heterozygous (+/-) for Ubc9, which encodes the unique SUMO E2-conjugating enzyme. This analysis was performed in the context of a conditional ablation of tumor suppressor Apc all along the crypt-villus axis through expresion of Cre recombinase driven by the intestinal specific promoter Villin

overall_design: Instestinal adenomatous polyps (≥0.5 mm in diameter) and intestinal normal tisues were harvested from washed and londitudinally openned intestines obtained 12 weeks after 4-OHT treatment of 8-12 weeks-old mice. RNA was extracted using Trizol protocol  and high-quality RNA was used for hybridizationand to obtain the trasncriptome by using GeneChip MoGene 2.0 ST arrays. 2 polyps and 2 normal samples were analysed per mice. 3 female mice were used per genotype.


title: Comparison of gene expression signatures in human melanocytes after indirect cold physical plasma treatment and direct UV-irradiation

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

summary: Cold atmospheric plasma is assembled out of various components such as UV-radiation, electrons, ions and an electromagnetic field at low temperature. In recent years cold atmospheric plasma gains interest as a medical tool used for improved healing of chronic wounds. In order to examine the impact of cold atmospheric plasma on the melanogenesis in human skin, the gene expression signature of differently treated lightly pigmented primary human melanocytes was analysed. Melanocytes were either treated in vitro indirectly by cold atmospheric plasma or irradiated by UV-radiation. After 2 h incubation the microarray analysis was performed.

overall_design: Gene expression induced by treatment of primary human melanocytes with 60 s plasma-treated liquid (ptl) or direct UV-irradiation (91mJ/cm2) was analysed after 2 h incubation. Primary melanocytes (purchased from PromoCell, Heidelberg, Germany) were seeded 24 h before treatment. The gene expression analysis was carried out 5x for untreated control cells, 6x for plasma-treated cells and 4x for UV-irradiated cells.

first: M-C

last: Sommer

first: A

first: G

last: Liebelt


title: Haploid and Deploid for Candida auris

status: Public on Sep 13 2020

first: Jian

last: Bing

address: Songhu Road, Yangpu District

institute: Fudan University

summary: The expression difference for haploid and deploid of Candida auris

overall_design: Total RNA profiles of Candida auris

first: Guanghua

last: Huang

first: Shuru

last: Fan


title: Gene expression changes in SSK41 lymphoma cells upon CABIN1 KD

city: Miami

first: Marco

last: Magistri

state: FL

address: 1501 NW 10th Ave

department: Psychiatry

institute: University of Miami

summary: CABIN1 is frequently mutated and affected by copy number losses in marginal zone lymphoma from the ocular adnexa. We wanted to examine gene expression changes after CABIN1 KD.

overall_design: CABIN1 was knocked down using shRNA in SSK41 B cell lymphoma cells. RNA was extracted from wild type (WT) or KD cells before and after anti-IgM stimulation.

first: Izidore

last: Lossos


title: p53 activation during ribosome biogenesis regulates normal erythroid differentiation.

first: Ismael

last: Boussaid

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

overall_design: Refer to individual Series


title: longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth

status: Public on Sep 12 2020

city: Eugene

first: Gabriel

last: Yette

state: Oregon

address: 1229 University of Oregon 1318 Franklin Blvd

department: Biology- Institute of Molecular Biology

institute: University of Oregon

summary: longfin mutant zebrafish grow and regenerate abnormally long fins. We sought to determine misregulated transcripts in the distal regenerate of 96 hpa caudal fins that could contribute to fin overgrowth or be the longfin causal gene.

overall_design: We used RNA-Seq to compare gene expression between replicates of microdissected distal regenerating fin tissue, distinguished by GFP-negative tissue distal to sp7:GFP expressing cells, collected from longfin heterozygous adult fish and homozygous wildtype clutchmates. Each replicate consisted of pooled tissue from four caudal fins.

first: Scott

last: Stewart

first: Heather

last: Le Bleu

first: Astra

middle: L

last: Henner

first: Joshua

last: Braunstein

first: Kryn

last: Stankunas


title: Protein stability buffers the cost of translation attenuation following eIF2⍺ phosphorylation

city: Cambridge

first: Anne

last: Bertolotti

address: Francis Crick Avenue

department: Neurobiology

institute: MRC Laboratory of Molecular Biology

summary: Quantification of total and polysome-associated RNAs from mouse liver following tunicamycin (Tm) treatment

overall_design: Total and polysome-associated RNAs were collected 0, 2, 4, and 10 hours following Tm treatment. The 0h samples are used as references for comparisons with the later timepoints.

first: Kim

last: Schneider

first: Geoffrey

last: Nelson

first: Joseph

last: Watson

first: Jorg

last: Morf

first: Maximillian

last: Dalglish

first: Laura

last: Luh

first: Annika

last: Weber


title: Molecular characterization of chick anterior and posterior half-scleorotomes by RNA-sequencing.

city: Marseille

first: Julia

last: Schaeffer

address: Parc Scientifique de Luminy

department: IBDM, CNRS UMR7288

institute: Aix-Marseille Université

summary: During amniote peripheral nervous system development, segmentation ensures the correct patterning of the spinal nerves relative to vertebral column. Along the antero-posterior (rostro-caudal) axis, each somite-derived half-sclerotome has intrinsic molecular properties that govern this segmentation process. Posterior half-sclerotomes express repellent molecules to restrict axon growth and neural crest migration to anterior half-sclerotomes. Here, we report an RNA-sequencing-based molecular characterization of anterior and posterior half-sclerotomes, using the chick embryo as a model organism.

overall_design: RNA-sequencing of pooled anterior half-sclerotomes (A) and posterior half-sclerotomes (P) microdissected from chick embryos, embryonic day 3 (stage Hamburger and Hamilton 18).

first: J

first: D

last: Tannahill

first: R

last: Keynes


title: Expression data from livers of control and IlrunKO mice

status: Public on Sep 11 2020

city: Philadelphia

first: Daniel

last: Rader

address: 3400 Civic Center Blvd

institute: University of Pennsyvania

summary: Genome wide association studies of plasma lipid traits suggest a potential link between ILRUN and plasma cholesterol homeostasis. In this study, we sought to study the in vivo role of ILRUN in lipid metabolism. The transcriptional effects of Ilrun deficiency on mouse liver was unknown. We isolated livers from control and global IlrunKO mice for transcriptomic profiling.

overall_design: Livers from 4 hour fasted control WT and global IlrunKO mice were used for RNA extraction and hybridization on Agilent microarrays. Biological replicates: 4 controls and 4 IlrunKO samples.

first: Xin

last: Bi

middle: J


title: mir-284-dependent dynamics of the Drosophila antennal transcriptome during aging

city: Oxford

first: Aron

last: Szabo

address: John Radcliffe Hospital, Headley Way

department: Radcliffe Department of Medicine

institute: Weatherall Institute of Molecular Medicine, University of Oxford

summary: We isolated mir-284 from a genetic screen for age-dependent axon degeneration in Drosophila melanogaster. mir-284 levels show a steep decline with aging. Therefore we embarked on a transcriptome-wide analysis after mir-284 depletion in aging flies.

overall_design: To shed light on the mir-284-regulated transcriptome, we performed RNA sequencing (RNA-seq) on wild-type (w1118) and mir-284 KO  (w1118;;mir-284 KO) antennae at 3 and 25 days of age in three biological replicates (2 biological replicates for mir-284 KO at 25d) on an Illumina NextSeq.

first: Yale

last: Michaels

first: David

last: Knapp

first: Markus

last: Toegel

first: Stacy

last: Gladman

first: Catherine

last: Collins

first: Tudor

last: Fulga


title: Transcriptomic analysis of Kupffer cells in patients with cirrhosis

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Background and aims:  Patients with decompensated cirrhosis present serious infections of bacterial origin. During homeostasis, resident macrophages from the liver or Kupffer cells (KCS) play a key role in the phagocytosis of circulating bacteria. The objective of this study was to characterize the transcripomic and functional profile of KCs in liver cirrhosis and its relationship with the risk of infections. Methods: KCs were isolated from livers of patients with cirrhosis (n = 4) and controls (n = 5) and the profile was determined by RNA sequencing. The phenotype and altered molecular pathways of the isolated KCS were analyzed through GSEA . Results: The expression profile of KCs is specific and different depending on whether they reside in a cirrhotic or control liver. The GO analysis revealed that the pathways differentially expressed in KCs isolated from cirrhotic liver are implicated in the immune response. The GSEA showed that KCs isolated from patients with cirrhosis present a greater overexpression of M1 markers with respect to M2 (normalized enrichment score, NES: 1.68, p <0.01 vs. NES: 0.8, p <0.01). Conclusion: The KCS of patients with cirrhosis have a unique and distinct gene expression profile characterized by up-regulation of M1 markers.

overall_design: KC were isolatrd from decompensated cirrhosis that underwent liver transplantation (n=4) and a control group of patients with liver tumours (except hepatocellular carcinoma) and without underlying liver disease (n=5). Morever, whole liver tissue from the same patients were aso sequenced.

first: E

last: Pose

first: M

last: Coll

first: P

last: Ginès


title: Effect of Panax Notoginseng on gene expression in rats with cerebral ischemia-reperfusion injury

city: Baise

first: huang

last: qing

address: No.18, Zhongshan 2nd Road, Youjiang District

institute: Youjiang Medical University for Nationalities

summary: Methods: Panax notoginseng was used to treat MCAO model rats, and the differentially expressed genes between Panax notoginseng group and model group were identified by RNA SEQ, and the possible mechanism of Panax notoginseng in regulating ischemic stroke was analyzed

overall_design: The differentially expressed genes were compared between Panax notoginseng group and control group

first: Lanqing

last: Meng

first: Qing

last: Huang


title: Wnt/planar cell polarity primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells [MoGene-2_0-st]

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Imbalance in intestinal stem cell (ISC) homeostasis leads to cancer and metabolic disease. Therefore intense efforts are underway to understand ISC hierarchy and the niche signals that control stem cell fate. Several ISC populations have been described according to their marker expression, cell-cycle behavior and lineage potential. Actively cycling Lgr5+ ISCs ensure homeostatic renewal. A less well-defined and minor population of quiescent and label-retaining cells (LRCs) is viewed as a reserve stem cell pool. However, the existence of quiescent stem cells distinct from the Lgr5+ ISCs is controversial. Indeed, recent findings identified quiescent intestinal cells as a subpopulation of Lgr5+ ISCs that are committed to the secretory fate, but the signals that maintain and activate quiescent cells/LRCs remain elusive.

overall_design: We compared intestinal stem cells expressing high levels of Lgr5 and GFP with Flattop-expressing intestinal crypt cells

first: Anika

last: Böttcher

first: Maren

last: Büttner

first: Sophie

last: Tritschler

first: Michael

last: Sterr

first: Alexandra

last: Aliluev

first: Ingo

last: Burtscher

first: Steffen

last: Sass

first: Martin

last: Irmler

first: Christoph

last: Ziegenhain

first: Wolfgang

last: Enard

first: Andrea

last: Schamberger

first: Fien

last: Verhamme

first: Oliver

last: Eickelberg

first: Fabian

last: Theis

first: Heiko

last: Lickert


title: RNA-seq of Poeciiopsis retropinna and turrubarensis maternal follicles

city: Stanford

middle: Warren

last: Guernsey

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

summary: Characterization of the pregnant maternal follicle transcriptome of a placental (P. retropinna) and non-placental (P. turrubarensis) Poeciliopsis species

sample_organism:
Poeciliopsis retropinna
Poeciliopsis turrubarensis

overall_design: Expression profiling of three replicates from four river populations of P. retropinna and three replicates of P. turrubarensis

middle: W

first: Julie

last: Baker


title: Wnt/planar cell polarity primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

first: Johannes

last: Beckers

summary:
A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required for better treatment options for a variety of chronic intestinal diseases, however, current models of ISC lineage hierarchy and segregation are still under debate. Here we report the identification of Lgr5+ ISCs that express Flattop (Fltp), a Wnt/planar cell polarity (PCP) reporter and effector gene. Functional analysis and lineage tracing revealed that Wnt/PCP-activated Fltp+ ISCs are primed towards either the enteroendocrine or Paneth cell lineage in vivo, while retaining self-renewal and multi-lineage capacity in vitro. Surprisingly, canonical Wnt/beta-catenin- and non-canonical Wnt/PCP-activated Lgr5+ ISCs are indistinguishable by the expression of stem-cell signature or secretory lineage-specifying genes, suggesting that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch of canonical to non-canonical Wnt signalling. Pseudotemporal ordering of targeted single-cell gene expression data allowed us to delineate the ISC differentiation path into enteroendocrine and Paneth cells. Strikingly, both lineages are directly recruited from ISCs via unipotent transition states, excluding the existence of formerly predicted bi- or multipotent secretory progenitors. Transitory cells that mature into Paneth cells are defined by label-retention and co-expression of stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ label-retaining cells (LRCs). Taken together, we identified the Wnt/PCP pathway as a new niche signal and polarity cue regulating stem cell fate. Active Wnt/PCP signalling represents one of the earliest events in ISC lineage priming towards the Paneth and enteroendocrine cell fate, preceding lateral inhibition and expression of secretory lineage-specifying genes. Thus, our findings provide a better understanding of the niche signals and redefine the mechanisms underlying ISC lineage hierarchy and segregation.
Here we establish the Wnt/Planar cell polarity (PCP) gene Flattop (Fltp) as a unique marker for intestinal LRCs and their distinct secretory fate. We show that Fltp+ cells are characterized by a combined stem cell and secretory gene signature. A subset of Fltp+ cells is classified by label-retention and predominantly locates at position +4, indicative of quiescent stem  cells. Strikingly, Fltp+ LRCs are specified by Wnt/PCP signaling in contrast to actively cycling stem cells that rely on the canonical Wnt/β-catenin pathway. In mice with disturbed Wnt/PCP signaling, the differentiation of enteroendocrine cells from LRCs is impaired. These findings establish Fltp as a novel marker for intestinal LRCs and implicate Wnt/PCP signaling in cell-cycle exit and commitment of ISCs to the secretory lineage. Taken together, we not only provide a marker to study LRCs in homeostatic and diseased conditions, but also identify the Wnt/PCP signaling pathway as a therapeutic target for colorectal cancer and metabolic disease.

overall_design: We analysed three crypt cell populations distinguishable by Fltp-Venus reporter (FVR) expression

last: Böttcher


title: Genome-wide expression analysis of sh-Ctrl and sh-PRLR SW-1990 cells

city: Shanghai

first: PeiQi

last: Huang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: The study is to explore differentially expressed genes in SW-1990 cells infected with sh-Ctrl or sh-PRLR.

overall_design: The genome-wide cDNA microarrays were performed to investigate the differentially expressed genes in PRLR knockdown SW-1990 cells compared to control cells estabilished by our own lab using Affymetrix U133 Plus 2.0 whole-genome chips.Each group contains three biological replicates.

first: Huizhen

last: Nie

first: Wuqing

first: ShuHeng

last: Jiang

first: Qin

last: Yang

first: Lipeng

last: Hu

first: XiaoMei

first: Jun

last: Li

first: YaHui

last: Wang

first: Qing

first: Lei

last: Zhu

first: Gary

last: Xiao

first: Jan

last: Sundquist

first: Kristina

first: Yongwei

last: Sun

first: Jianguang

last: Ji

first: Zhigang

last: Zhang


title: Small RNA sequencing of cerebrospinal fluid exosome fraction in medulloblastoma patients

city: Goyang

first: Ho-Shin

last: Gwak

address: 323 Ilsan-ro

department: Department of Cancer Control

institute: National Cancer Center Graduate School of Cancer Science and Policy

type: Non-coding RNA profiling by high throughput sequencing

summary: We reported that the microRNA profiling of exosome isolated from 58 cerebrospinal fluid (CSF) of 38 medulloblastoma (MBL) patient with or without letomeningeal metastases (LM). CSF exosome was precipitated using Exo2DTM for RNA assay (EXOSOME plus, Suwon, South Korea) according to the manufacture’s protocol (Kim, et al. 2017). 2 ml of CSF were added to Exo2DTM reagent B following mixing by inverting, and incubated at room temperature for 30 min. The supernatant was discarded and the exosome containing pellet was resuspended in 100 ul of PBS to further RNA isolation. Total RNA was extracted from the CSF exosome fraction using a microRNA purification kit (Norgen Biotek corp., Thorold, Canada) according to the manufacture’s protocol. Briefly, samples were mixed with lysis buffer, and the lysate was added to absolute ethanol. The lysate was applied up to the column and centrifuged at 8,000 rpm for 1 min. The column was washed with wash solution and centrifuged at 14,000 rpm for 1 min. Finally, the column was applied to 20 ul of elution solution and centrifuged at 14,000 rpm for 2 min, and the flow-through was stored at –80 ℃ for storage. RNA precipitates were quantified and qualified with Bioanalyzer Pico 6000 Chip (Agilent Technologies, Santa Clara, CA). The 10 ng of total RNA was provided to the cDNA library generation using SMARTer smRNA-Seq kit (Illumina Inc., San Diego, CA), according to the user manual. The cDNA library was subjected to sequencing using Truseq SBS Kit and HiSeq 2500 System (Illumina Inc., San Diego, CA), according to user guide.

overall_design: 58 cerebrospinal fluid (CSF) samples of medulloblastoma patients


title: p53 activation during ribosome biogenesis regulates normal erythroid differentiation. [ChIP-Seq]

first: Ismael

last: Boussaid

address: 22 Rue Mechain

institute: Inserm

summary: The role of ribosome biogenesis in erythroid development is supported by the recognition of erythroid defects in ribosomopathies in both Diamond-Blackfan anemia and 5q- syndrome. Whether ribosome biogenesis exerts a regulatory function on normal erythroid development is still unknown. In the present study, a detailed characterization of ribosome biogenesis dynamics during human and murine erythropoiesis shows that ribosome biogenesis is abruptly interrupted by the drop of rDNA transcription and the collapse of ribosomal protein neo-synthesis. Its premature arrest by RNA polI inhibitor, CX-5461 targets the proliferation of immature erythroblasts. We also show that p53 is activated spontaneously or in response to CX-5461 concomitantly to ribosome biogenesis arrest, and drives a transcriptional program in which genes involved in cell cycle arrest, negative regulation of apoptosis and DNA damage response were upregulated. RNA polI transcriptional stress results in nucleolar disruption and activation of ATR-CHK1-p53 pathway. Our results imply that the timing of ribosome biogenesis extinction and p53 activation are crucial for erythroid development. In ribosomopathies in which ribosome availability is altered by unbalanced production of ribosomal proteins, the threshold of ribosome biogenesis down-regulation could be prematurely reached and together with pathological p53 activation prevents a normal expansion of erythroid progenitors.

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: Eric

last: Soler

first: Mohammad

last: Salma


title: Regulatory role of PIF4 in C24xCol Arabidopsis hybrid and moderate and high ambient temperatures

city: Ratchathewi

first: Varodom

last: Charoensawan

state: Bangkok

address: 272 Rama 6 road

department: Biochemistry

country: Thailand

institute: Mahidol University

summary: The transcriptomic dataset was constructed to investigate the role of PIF4 in response to high ambient temperature in Arabidopsis hybrids by comparing the genome-wide transcriptomic changes of C24xCol and C24xpif4-101 hybrids in two temperature conditions, 22˚C and 27˚C

overall_design: RNA-seq dataset were generated using C24xCol and C24xpif4-101 seedlings grown at 22˚C and 27˚C for 4 and 7 days after sowing.

first: Kawinnat

last: Sue-ob

first: Sandra

last: Cortijo

first: Mathew

last: Box

first: Philip

last: Wigge


title: Calcium signaling induces a partial EMT in carcinoma cells

first: Robert

middle: Joesph

last: Norgard

state: PA

address: 421 Curie Blvd, 531 BRB II/III

country: USA

institute: University of Pennsylvania

summary: Purpose: Next generation RNA-sequencing data to understand the genetic changes that occur during partial EMT (P-EMT) or classical EMT (C-EMT)

overall_design: Murine pancreatic cancer cells were treated with either DMSO, ionomycin, or TGFb for 48 hours

first: Ben

middle: Z

last: Stanger

first: Kathryn


title: Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [RNA-Seq]

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Currently, it is unclear if all monocyte subsets exhibit osteoclastogenic potential. Furthermore, the role of lineage determining TFs in regulating OC differentiation on a genome-wide scale remains poorly understood. In this study, we utilized a novel Irf8 conditional knockout (Irf8 cKO) mouse model to characterize the importance of IRF8 in OC progenitor development and epigenetic regulation of OC differentiation. We performed RNA-seq on Irf8 gWT, gKO, cWT and cKO BMMs, preosteoclasts (PreOCs), and OCs. Cells were analyzed prior to (BMMs) and 3 days (PreOCs) and 6 days (OCs) after RANKL stimulation. Here we show that greater a number of genes are significantly upregulated in Irf8 cKO OCs when compared to WT and Irf8 gKO OCs. Altogether, our data shows that Irf8 cKO mice provide more precise/reliable OC-specific transcriptomic results when compared to Irf8 gKO mice.

overall_design: RNA-seq analysis of transcriptional changes in BMMs stimulated with MCSF (day 0) and MCSF plus RANKL (day 3 (preOCs) and day 6 (OCs)). Both male and female mice and cells obtained from both genders were analyzed in this study.

first: Vivek

last: Thumbigere-Math

first: Amitabh

last: Das


title: Transcriptional characterization of hippocampi from novel preclinical model of drug-resistant epilepsy

city: Braine-l'Alleud

first: Jonathan

last: van Eyll

address: UCB Pharma - Building S2C

department: NewMedicines

institute: UCB Pharma

summary: A novel model of drug-resistant epilepsy based on the selection of mice treated with phenytoin (PHT) in the 6 Hz seizure model was developed. It leads to the identification of subpopulations of drug-responder and non-responder mice. Transcriptional characterization of the hippocampi from these 2 sub-populations was performed and compared. No significant difference has been observed between the 2 sample groups.

overall_design: expression profile from 15 PHT non-responder hippocampi was compared to 15 PHT responder hippocampi as a control.

first: Patrice

last: Godard

first: Karine

last: Leclercq

first: Catherine

last: Vandenplas

first: Rafal

last: Kaminski