title: Comparative transcriptomic analysis of iron deficiency response in roots of Oryza sativa and O. rufipogon

city: Porto Alegre

first: Andriele

last: Wairich

state: Rio Grande do Sul

address: Av. Bento Gonçalves, 9500

department: Center for Biotechnology

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. sativa and its wild progenitor O. rufipogon. A total of 622 and 2,017 genes were found to be differentially expressed in O. sativa and O. rufipogon, respectively. Among the genes regulated in both species, we found the Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2.

sample_organism:
Oryza rufipogon
Oryza sativa

platform_organism:
Oryza rufipogon
Oryza sativa

overall_design: We analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: Oryza sativa (cv. Nipponbare) and Oryza rufipogon (BRA 00004909-8 accession from EMBRAPA). Plants were grown in lab conditions under control and Fe deficiency treatments up to three-leaf stage. Two biological replicates, each composed of roots from three plants, were collected after five days of treatment. Total RNA was extracted from roots and libraries were generated and sequenced at Fasteris® using HiSeq Illumina 2000 and single-end sequencing (50 bp).

first: Ben

middle: H

last: Oliveira

first: Ezequiel

last: Arend

first: Guilherme

last: Duarte

first: Lucas

last: Ponte

first: Raul

last: Sperotto

first: Felipe

last: Ricachenevsky

first: Janette

middle: P

last: Fett


title: De novo transcriptome assembly of the tree swallow (Tachycineta bicolor): tissue-specific expression profiles and positive selection analysis

status: Public on Nov 19 2019

city: Bloomington

first: Kimberly

last: Rosvall

state: IN

address: 1001 E Third Street

department: Biology

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, molecular resources are scarce. Thus, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,747 transcripts, which we aligned to 14,717 protein-coding genes. We then characterized tissue-specific expression profiles and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird, and in doing so, further advance the utility of this system for biologists across disciplines.

overall_design: 6 tissues (blood, liver, spleen, brain, ovary, and muscle) were collected from 2 female tree swallows and total RNA was prepared into equimolar pools for each tissue which were run on both Nextseq and Miseq platforms

first: Alexandra

middle: B

last: Bentz

first: Gregg

middle: W

last: Thomas

first: Douglas

last: Rusch

middle: A


title: Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease [RNA-seq]

city: Berlin

first: Ferah

last: Yildirim

address: Charitéplatz 1, Virchowweg 6

country: Germany

institute: Charité Berlin

summary: Huntington’s disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27 acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.

overall_design: RNA-seq in R6/1 (4 weeks and 8 weeks old), CHL2 (1 year old) and wild type animals.

first: Christopher

last: Ng

first: Tobias

last: Ehrenberger

first: Anthony

middle: R

last: Soltis

first: David

middle: E

last: Housman

first: Ernest

last: Fraenkel


title: RNAseq of Extracellular vesicle RNAs and cellular RNAs from HPASMCs with or without TGF-b1 or BMP4 treatment

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

summary: Excessive TGF-β signalling has been shown to underlie pulmonary hypertension (PAH). Human pulmonary artery smooth muscle cells (HPASMCs) can release extracellular vesicles (EVs) but their content and significance have not yet been studied. Here, we analysed the content and biological relevance of HPASMC-derived EVs. We used low-input RNA-Seq to analyse the RNAs of EVs released by HPASMC under basal conditions. This data was compared to cellular RNAs. The same experiments (RNA-seq of EV and cellular RNAs) were carried out on HPASMC treated with TGF-b1 and BMP4, recapitulating pathological conditions.

overall_design: Extracellular vesicles were isolated from HPASMC with or without TGF-b1 or BMP4 treatment. Low-input RNA-seq was performed on EV and cellular RNAs by BGI. Three replicates were carried out and sequenced for most conditions except for EV from untreated and BMP4 treated HPASMC with 2 replicates due to failure of the library preparation of one replicate.

first: Fernando

last: De la Cuesta

first: Andrew

last: Baker


title: RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

country: Canada

institute: University Health Network

summary: To elucidate the biological pathways altered by sphingolipid modulation with N-(4-hydroxyphenyl) retinamide (4HPR) treatment in human HSPC that may contribute to the restraint in proliferation while promoting persistence of HSC self-renewal as well as determine the mechanism of synergy in enhancement of HSC self-renewal with CB CD34+ agonists UM171 and StemRegenin 1 (SR1), we performed RNA-sequencing (RNA-Seq) of 3 pools of lin-CB cells following 2 or 4 days with DMSO, 4HPR, UM171+SR1 or 3-Factor (4HPR+UM171+SR1). We identified modulation of sphingolipid metabolism regulates self-renewal through activating coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs.

overall_design:
Gene expression profiling of RNA from 3 pools of human cord blood enriched for stem and progenitor cells by lineage depletion (lin- CB) cultured with the indicated small molecules at the indicated times

>>>Submitter states that raw data have been submitted to EGA due to patient privacy concerns<<<

middle: Z

first: Veronique

last: Voisin


title: Defining transcriptional signatures of human hair follicle cell states

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young

institute: UCLA

summary: Single Cell RNA sequencing of human hair follicles

overall_design: Human hair follicles were isolated from scalp, single cell suspensions were generated, cells were subjected to Drop-seq protocol

first: Thomas

last: Allison

first: Rie

last: Takahashi


title: ATAC-seq and RNA-seq of cord blood cells in cytokine-rich ex vivo culture conditions following sphingolipid modulation

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: ATAC-seq of immunophenotypic LT-HSC and ST-HSC from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

summary: To investigate how ex vivo culture affects chromatin accessibility in cultured HSC, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-Seq) on cLT (CD34+CD90+CD45RA-) and cST populations purified from 8 day cultured lineage depleted cord blood (lin- CB) cells treated with 3-Factor (4HPR+UM171+SR1), U+S or 4HPR as well as untreated and vehicle-treated (DMSO) control populations. The subsequent ATAC-seq data was compared to chromatin accessibility signatures generated from uncultured hematopoietic stem and progenitor populations (Takayama, et al.). We found that ex vivo culture shifted cLT and cST cells isolated from control or untreated samples to a chromatin accessibility profiles not found in LT-HSC, suggesting some loss of a stem-cell associated chromatin state. By contrast, 4HPR-treated, to some extent, and 3-Factor-treated HSC maintained chromatin accessibility features of uncultured LT-HSC.

overall_design:
ATAC-seq profiling of RNA from 4 pools of human cord blood enriched for stem and progenitor cells by lineage depletion (lin- CB) cultured with the indicated small molecules at the indicated times

>>>Submitter states that raw data have been submitted to EGA due to patient privacy concerns<<<

first: Alex

last: Murison


title: MYC, together with Cohesin and Mediator complexes, predetermines the sensitivity of gastrointestinal cancer to antifolate drugs

city: shanghai

first: Tingting

last: Liu

address: 320,yueyang road

country: China

institute: insititute of health sciences

overall_design: GeCKO library screen with NUGC3 using RTX treatment.


title: Molecular phenotyping of rejection in mucosal biopsies from lung transplant recipients

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary: Diagnosing lung transplant rejection currently depends on histologic assessment of transbronchial biopsies (TBB) with limited reproducibility and considerable risk of complications. Mucosal biopsies are safer but not histologically interpretable. Microarray-based diagnostic systems for TBBs and other transplants suggest such systems could assess mucosal biopsies as well.

overall_design: We studied 243 mucosal biopsies from the third bronchial bifurcation (3BMBs) collected from seven centers and classified them using unsupervised machine learning algorithms. Using the expression of a set of rejection-associated transcripts annotated in kidneys and validated in hearts and lung transplant TBBs, the algorithms identified and scored major rejection and injury-related phenotypes in 3BMBs without need for labeled training data. No rejection or injury, rejection, late inflammation, and recent injury phenotypes were thus scored in new 3BMBs. The rejection phenotype correlated with IFNG-inducible transcripts, the hallmarks of rejection. Progressive atrophy-related changes reflected by the late inflammation phenotype in 3BMBs suggest widespread time-dependent airway deterioration, which was especially pronounced after two years post-transplant. Thus molecular assessment of 3BMBs can detect rejection in a previously unusable biopsy format with potential utility in patients with severe lung dysfunction where TBB is not possible, and provide unique insights into airway deterioration. ClinicalTrials.gov NCT02812290


title: Next Generation  Sequencing  Analysis of Colorectal Cancer Tissue Transcriptomes

city: Ningbo

first: Jiaxin

last: Ge

state: Zhejiang

address: 247 Renmin Road

institute: The Affiliated Hospital of Medical School, Ningbo University

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-codingRNAs play an important roles in cancers. However, the expression profiles of circRNAs (circRNAs) in human colorectal cancer are largely unclear. The present study aimed at screening the differentially expressed circRNAs, microRNAs (miRNAs) and mRNA in CRC tissues and paired adjacent normal tissues, investigating the function and mechanism of them through analyzing related miRNAs and mRNAs, especially star mRNAs in CRC, such as gut-enriched Krüppel-like factor (KLF4).

overall_design: Three pairs of colorectal cancer tissues and their matched adjacent nontumorous tissues obtained from surgical patients who were histologically confirmed to have CRC based on surgical histopathological examinations were randomly selected for human RNA deep sequencing.

first: Xinjun

last: Zhang


title: β-catenin activation down-regulates cell-cell junction-related genes and induces epithelial-to-mesenchymal transition in colorectal cancers

status: Public on Nov 18 2019

city: Seoul

first: YUJIN

last: KWON

address: 50 Yonsei-fo, Seodaemun-gu

country: South Korea

institute: YONSEI UNIVERSITY

summary: Purpose: WNT signaling activation in colorectal cancers (CRCs) occurs mainly through APC inactivation or, more uncommonly, β-catenin activation. Both processes promote β-catenin nuclear accumulation, which transcriptionally up-regulates epithelial-to-mesenchymal transition (EMT)-related genes.  Experimental Design: We investigated β-catenin localization, downstream gene expression, and phenotypic alterations in HCT116 cells containing a wild-type (HCT116-WT) or mutant β-catenin allele (HCT116-MT), or parental cells with both WT and mutant alleles (HCT116-P). We then analyzed β-catenin localization and associated phenotypes in CRC tissues.  Results: Wild-type β-catenin mainly localized at the cell membrane, whereas mutant showed predominantly nuclear localization; membranous, cytoplasmic, and nuclear localization was observed in HCT116-P cells. Microarray analysis revealed significant down-regulation of Claudin-7 and E-cadherin in HCT116-MT vs. HCT116-WT cells. Claudin-7 was also down-regulated in HCT116-P vs. HCT116-WT cells, although E-cadherin expression was unaffected. Altered expression of cell-cell junction-related molecules led to tight junction (TJ) impairment in HCT116-P, and dual loss of TJs and adherens junctions (AJs) in HCT116-MT. TJ loss increased migration and invasion activities of HCT116-WT, whereas AJ loss was required to further up-regulate these activities in HCT116-P. Immunohistochemistry analysis of 101 stage III CRC tissues revealed high nuclear β-catenin expression (≥30% of tumor cells) in 15 (14.9%) samples, low nuclear expression (1-29%) in 53 (52.5%) samples, and undetectable nuclear expression in 33 (32.6%) samples, with a trend toward more frequent down-regulation of Claudin-7 and E-cadherin, and increased metastasis in CRCs with high vs. low nuclear β-catenin.   Conclusions: β-catenin activation and nuclear translocation induce EMT progression by modifying cell-cell junctions, and are associated with aggressive behaviors of CRCs.

overall_design: HCT116-WT and HCT116-MT cells were used in duplicate samples.

first: Won

middle: K

last: Kim

first: Yujin

last: Kwon

first: Hoguen


title: Effect of Neutrophil Extracellular Traps and Psoriasis-Associated TRAF3IP2 Genotype on Induction of Human Th17 Cells

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Using RNA-sesq to assess effects of NET exposure under different activation conditions, and assessing effects of homozygosity vs. nullizygosity for the Act1 D10N genotype

overall_design: PBMC from 12 different individuals of known Act1 genotype were subjected to 4 conditions (Control; CD3/CD28; NET; NET+LPS) at 2 different times (0h and 6h PMA/lonomycin).

first: Sylviane

last: Lambert

middle: C

first: Rajan

last: Nair

first: James

middle: T

last: Elder


title: Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

institute: The University of Edinburgh

summary: BACKGROUND: The release of small non-coding RNAs (sRNAs) has been reported in parasitic nematodes, trematodes and cestodes of medical and veterinary importance. However, little is known regarding the diversity and composition of sRNAs released by different lifecycle stages and the portion of sRNAs that persist in host tissues during filarial infection. This information is relevant to understanding potential roles of sRNAs in parasite-to-host communication, as well as to inform on the location within the host and time point at which they can be detected. METHODOLOGY & PRINCIPAL FINDINGS: We have used small RNA (sRNA) sequencing analysis to identify sRNAs in replicate samples of the excretory-secretory (ES) products of developmental stages of the filarial nematode Litomosoides sigmodontis in vitro and compare this to the parasite-derived sRNA detected in host tissues. We show that all L. sigmodontis developmental stages release RNAs in vitro, including ribosomal RNA fragments, 5’-derived tRNA fragments (5’-tRFs) and, to a lesser extent, microRNAs (miRNAs). The gravid adult females (gAF) produce the largest diversity and abundance of miRNAs in the ES compared to the adult males or microfilariae. Analysis of sRNAs detected in serum and macrophages from infected animals reveals that the class of parasite miRNAs are preferentially detected in vivo, compared to their low levels in the ES products, and identifies miR-92-3p and miR-71-5p as L. sigmodontis miRNAs that are stably detected in host cells in vivo. CONCLUSIONS: Our results suggest that gravid adult female worms secrete the largest diversity of extracellular sRNAs compared to adult males or microfilariae. We further show differences in the parasite sRNA biotype distribution detected in vitro versus in vivo. We identify macrophages as one reservoir for parasite sRNA during infection, and confirm the presence of parasite miRNAs and tRNAs in host serum during patent infection.

sample_organism:
Meriones unguiculatus
Litomosoides sigmodontis

overall_design: We examined the content of several tissues and in vitro Excretory/Secretory (ES) products by next generation DNA sequencing

first: Juan

middle: F

last: Quintana

first: Al

last: Ivens

first: Sujai

last: Kumar


title: Dichotomous Regulation of Group 3 Innate Lymphoid Cells by Non-gastric Helicobacter Species from an Immunocompromised Mouse

city: Gainesville

first: Liang

last: Zhou

state: FL

department: Department of Infectious Diseases and Immunology

institute: University of Florida

summary: Intestinal innate lymphoid cells (ILCs) contribute to the protective immunity and homeostasis of the gut, and the microbiota are critically involved in shaping ILC function. However, the role of the gut microbiota in regulating ILC development and maintenance still remains elusive. Here, we identified opposing effects on ILCs by two Helicobacter species, Helicobacter apodemus and Helicobacter typhlonius, isolated from immunocompromised mice. We demonstrated that the introduction of both Helicobacter species activated ILCs and induced gut inflammation; however, these Helicobacter species negatively regulated RORγt+ Group 3 ILCs (ILC3s), especially T-bet+ ILC3s, and diminished their proliferative capacity. Thus, these findings underscore a previously unknown dichotomous regulation of ILC3s by Helicobacter species, and may serve as a model for further investigations to elucidate the host-microbe interactions that critically sustain the maintenance of intestinal ILC3s.

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome

overall_design: (1) RNA-seq (2 replicates) of whole proximal colon tissue from Rag1‒/‒ mice gavaged with Rag1‒/‒ and Rag1‒/‒ Selplg‒/‒ (RPS) feces; (2) 16S rRNA gene sequencing of fecal DNA from Rag1‒/‒ and RPS mice; (3) 16S rRNA gene sequencing of fecal DNA from Rag1‒/‒ mice gavaged with Rag1‒/‒ and RPS feces and treated with antibiotics.

first: John

last: Bostick

first: Yetao

last: Wang

first: Yong

first: Mansour

last: Mohamadzadeh


title: Detection and Integrated Analysis of LncRNA and mRNA Relevant to Plateau Adaptation of Yak

city: Chengdu

first: Jiabo

state: Sichuan

address: First Roll street, 4th south part, NO.16

institute: Southwest Minzu University

summary: Analysis of RNA-seq of cerebellum and cerebrum in Yak, Yakow and Cattle.The result reveal the relationship between modules and Plateau Adaptation trait

sample_organism:
Bos taurus
Bos grunniens
Bos grunniens x Bos taurus

overall_design: 18 samples, 3 individuals as replication for each species. Two tissues are cerebellum and cerebrum.

first: Jincheng

last: Zhong


title: Expression data to parental A431 VS CD109 KO A431

city: Montreal

first: Anie

last: Philip

address: 1650 Cedar Avenue

institute: Mcgill university

summary: analysis the gene expression alteration upon the loss of CD109

overall_design: Knockout CD109 by CRISPR/case9 in  squamous cell carcinoma  A431 cell line

first: Shufeng


title: Mapping microglia diversity in the human brain through the integration of high-dimensional techniques

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: Microglia are tissue-resident macrophages of the central nervous system (CNS) that orchestrate local immune responses and contribute to several neurological and psychiatric diseases. Little is known about human microglia and how they orchestrate their highly plastic, context-specific adaptive responses during pathology. Here, we combined two high-dimensional technologies, single-cell RNA-sequencing (scRNA-seq) and time-of-flight mass cytometry (CyTOF), to identify microglia states in the human brain during homeostasis and disease. This approach enabled us to identify and characterize a previously unappreciated spectrum of transcriptional states in human microglia. These transcriptional states are determined by their spatial distribution, and they further change with aging and brain tumor pathology. The description of multiple microglia phenotypes in the human CNS may open promising new avenues for subset-specific therapeutic interventions.

overall_design: Human surgery samples from controls and Glioblastoma multiforme patients were collected prospectively, FACS sorted on lineage-negative live CD45-positive cells and sequenced using the mCEL-Seq2 protocol.

first: Roman

last: Sankowski

last: Sagar

first: Dominic

last: Gruen

first: Marco

last: Prinz


title: CADM1-overexpression ES-2 cells

status: Public on Nov 16 2019

city: Lanzhou

first: Wang

last: Hui

state: Gansu

address: QIlihe, Jiangouyan, NO.335

institute: Chinese Academy of Agricultural Scien

summary:
CADM1, an immunoglobulin superfamily member, frequently inactivated but function as a tumor suppressor in many solid tumors. However, how CADM1 expression in ovarian cancer cells and the mechanisms of its tumor suppressor function is not fully understood.
We created ovarian cancer ES-2 cell lines in which CADM1 was stably up-regulated. Genes differentially expressed in CADM1-overexpressing ES-2 cells.

overall_design: To uncover the upstream regulatory pathways of CADM1 as a tumor suppressor in ovarian cancer, we performed RNA microarray profiling on both CADM1-overexpressed group ES-2 cells and mock control group cells. Gene expression profiles were obtained by microarray analysis using Affymetrix GeneChip® PrimeView™ Human Gene Expression Array.

first: Feixue

last: Xu

first: Xiaoqiang

last: Si


title: Gene expression data of livers from C57BL/6 treated with low dose tunicamycin

city: Shanghai

first: Yan

last: Lu

address: 180 Fenglin Road

department: Department of Endocrinology and Metabolism

institute: Zhongshan Hospital, Fudan University

summary: Sustained ER stress is tightly associated with hyperglycemia and type 2 diabetes.However, the molecular mechanisms remain largely unknown.In order to identify genes that are potentially involved in ER stress-associated hyperglycemia, transcriptomics analyses were performed using RNA-sequencing,which revealed that many genes were dys-regulated in the livers of mice treated with tunicamycin.

overall_design: Eight weeks old male C57BL/6 mice were purchased from the Shanghai Laboratory Animal Company (SLAC). Sustained ER stress was induced with daily intraperitoneal injections of 0.2 mg/kg tunicamycin (654380, Sigma-Aldrich) for 14 days.Then mice were sacrificed and total RNAs were isoloated from liver tissues. Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.

first: Bin

last: Liu


title: Gene expression profiling of CD31+/CD45- cells from normal lung and dissected metastases

status: Public on Nov 17 2019

city: New York

first: Wei

last: Zheng

state: NY

address: 1468 Madison Ave, Annenberg Building, Room 24-60A

institute: Icahn School of Medicine at Mount Sinai

summary: To understand if cancer cells that metastasize to the lung induce changes of gene expression in associated endothelial cells to promote metastatic growth, we profiled the gene expression of CD31+/CD45- cells sorted from unchallenged normal mouse lungs and dissected metastatic nodules.

overall_design: Lung metastases were induced by tail vein injection of syngenic mouse mammary tumor cells, dissected and processed in parallel with normal lungs for FACS sorting for CD31+/CD45- cells. RNA from these cells was analyzed by RNA-seq.

first: Hui

last: Zhang

first: Dejian

last: Zhao

first: Jeffrey

last: Pollard


title: Widespread chromatin activation underlies pathogenic mechanisms in multiple myeloma

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

summary: RNA-seq analysis comparing the transcriptional landscape of PRDM5 silenced vs mock KMS-11 multiple myeloma cell line

overall_design: KMS-11 multiple myeloma cell line was transduced with an inducible shRNA expressing lentiviral system (Tet-pLKO-puro, Addgene #21915) targeting PRDM5 gene. shRNA expression was induced by adding 1 μg/ml doxycycline (Sigma) to the culturing media and replaced every 48 hours. Samples were harvested after 4 days of shRNA expression induction with doxycycline.

first: Felipe

last: Cardoso

last: Ena

first: Raquel

middle: O

last: Ciriza


title: Global gene expression analyses of SeVdp-based somatic cell reprogramming

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary: SeVdp(KOSM) vector can efficiently induce a somatic cell reprogramming in many types of cells. In contrast to SeVdp(KOSM), SeVdp(GKOSM) only induce partially-reprogrammed cells.

overall_design: Total RNA were isolated from MEF, mouse iPSCs, and cells reprogrammed by SeVdp(KOSM) or SeVdp(GKOSM) at day 2.

first: Koji

last: Hisatake


title: Organelle-based therapy for immune mediated disease: mitochondrial transfer elicits Tregs reprogramming

city: Santiago

first: Vinicius

last: Maracaja-Coutinho

state: Santiago

address: Santos Dumont 964

country: Chile

institute: Universidad de Chile

summary: Mesenchymal stem cells (MSCs) have fueled ample translation for the treatment of immune mediated diseases. They exert immunoregulatory and tissue restoring effects. MSCmediated transfer of mitochondria (MitoT) had been demonstrated to rescue target organs from tissue damage. While the mechanism remains to be fully resolved, we explored the effect of MitoT on lymphoid cells. Here, we describe dose dependent MitoT from mitochondria-labelled MSCs mainly to T CD4+ rather than to T CD8+ or CD19+ B-cells. Artificial transfer of isolated MSC-derived mitochondria increased the expression of mRNA transcripts involved in T cell activation and T-regulatory cell differentiation including FOXP3, IL2RA, CTLA4 and TGFβ1, leading to an increase of a highly suppressive CD25+FoxP3+ population. In a GVHD mouse model, transplantation of MitoT-induced human T cells led to significant improvement in survival and reduction in tissue damage and organ T CD4+, CD8+ and IFNγ+ expressing cell infiltration. These findings point to a unique CD4+ T cell reprogramming mechanism with pre-clinical proof of concept data that pave the way for the exploration of organelle-based therapies in immune diseases.

overall_design: RNA profiles of mitocepted (MitoT+) or not (MitoT-) CD3+ facs sorted cells were generated by deep sequencing, using an Illumina HiSeq instrument

first: Angela

last: Court

first: Alice

last: Le-Gatt

first: Patricia

last: Luz-Crawford

first: Eliseo

last: Parra-Crisóstomo

first: Victor

last: Aliaga-Tobar

first: Luis

last: Bátiz

first: Rafael

last: Contreras

first: María

middle: I

last: Ortúzar

first: Mónica

last: Kurte

first: Roberto

last: Elizondo-Vega

first: Karina

last: Pino-Lagos

first: Fernando

last: Figueroa

first: Maroun

last: Khoury


title: RNA-seq data from T cells in vitro

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

summary: Comparison of athymic T cells generated in vitro with iPSC-derived recent thymic emigrant (iRTE) generated from 3D thymic culture and natural splenocytes.

overall_design: We generated CD4+CD8+ T cells on OP9-DL1, CD8+ T cells on OP9-DL1, and CD8+ T cells in 3D thymic culture. We compared them with naive CD8+ T cells from a spleen. Cells were recovered by FACS based on expression of CD45, CD8, CD4, and TCRab, as well as being negative for a dump gate including NK1.1, TCRgd, CD11c.

first: Nicholas

middle: D

last: Klemen

last: Restifo


title: The effects of virus-induced maternal inflammation on offspring methyaltion patterns in skeletal muscle

city: Urbana

first: Anna

last: Dilger

state: Il

address: 1503 S Maryland Ave

department: Animal Sciences

institute: University of Illinois

type: Methylation profiling by high throughput sequencing

summary: The objective of this study was to examine the effects of maternal infection on offspring muscle methylation when the offspring themselves did not become infected during gestation. Gilts were inoculated with either PRRSV or sterile culture medium at 80d gestation. LD muscle samples were taken from uninfected male offspring at birth. Genomic DNA was extracted and underwent reduced representation bisulfite sequencing. Differential methylation went through pathway and gene ontology analysis.

overall_design: 3 control gilts provided 8 offspring (control); 2 PRRSV inoculated gilts provided 8 offspring (PRRSV); total of 16 piglets in study

first: Elizabeth

last: Hogan

first: Jonathan

last: Beever


title: Suppressive function of MDSC is under bidirectional control of intrinsic and immunotherapy-induced type I IFN in pancreatic cancer

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Tumors entertain a highly immunosuppressive network by merging features of regulatory cytokines and cell populations to evade immune control. Myeloid-derived suppressor cells (MDSC) comprise populations of immature myeloid cells in tumor-bearing hosts with a highly immunosuppressive capacity. We could previously identify RIG-I-like helicases (RLH) as targets for the immunotherapy of pancreatic cancer inducing immunogenic tumor cell death and type I interferons (IFN), as key mediators linking innate with adaptive immunity. Here, we show that autochthonous type I IFN signaling is critical for MDSC to gain suppressive function. In contrast, RNA sequencing of MDSC from RLH-ligand-treated mice showed an IFN-driven gene signature and a switch from a M2/G2- towards a M1/G1-polarized phenotype. Functional assays confirmed the loss of the T cell suppressive capacity. Our study identifies a dual role of type I IFN signaling in MDSC´s suppressive function, and RLH-mediated tumor control.

overall_design: T110299 pancreatic cancer cells, that derived from a genetically engineered spontaneous pancreatic cancer mouse (Ptf1a-Cre LSL-KrasG12DLSL-Trp53fl/R172H), were implanted orthotopically in eight C57BL6 mice. Four Mice were treated twice with poly(I:C)-PEI and four mice were treated with glucose as a control. PMN-MDSC as well as M-MDSC were isolated from tumor and spleen. Whole transcriptome of isolated MDSC was then analyzed by RNA sequencing.

first: Philipp

last: Metzger

first: Sabrina

middle: V

last: Kirchleitner

first: Michael

last: Kluge

first: Lars

middle: M

last: König

first: Christine

last: Hörth

first: Daniel

last: Böhmer

first: Julia

last: Ahlfeld

first: Sebastian

last: Kobold

first: Stefan

last: Endres

first: Max

last: Schnurr

first: Peter

last: Duewell


title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue [array]

status: Public on Nov 15 2019

city: Stockholm

first: Simon

last: Lecoutre

address: Huddinge

department: MedH

country: Sweden

institute: Karolinska Institutet

summary:
SP1-regulated transcriptome: Gene expression microarray following SP1 RNAi to define the SP1-regulated transcriptome in human in vitro differentiated adipocyte.
Glutamine-regulated transcriptome: Gene expression microarray in human in vitro differentiated adipocyte incubated in high (10 mM) and low (0.5 mM) concentrations of glutamine.

overall_design: 6 samples were analysed for the SP1-regulated transcriptome and 6 samples were analysed for the glutamine-regulated transcriptome.

first: Paul

last: Petrus

first: Hui

last: Gao

first: Mikael

last: Rydén


title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue [ChIP-seq]

summary: Mapping of O-GlcNAcylated proteome along the genome by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) in in vitro differentiated human adipocytes incubated with low (0.5 mM) or high (10 mM) glutamine.

overall_design: 6 samples were analysed for the O-GlcNAcylated ChIP-seq.


title: Continuous and discrete neuron types of the adult murine striatum

city: San Francisco

first: Stephen

last: Quake

address: 499 Illinois St

institute: Chan-Zuckerberg Biohub

summary: The mammalian striatum is involved in many complex behaviors and yet is largely composed of a single neuron class: the spiny projection neuron (SPN). It is unclear to what extent the functional specialization of the striatum is due to the molecular specialization of SPN subtypes. We sought to define the molecular and anatomical diversity of adult SPNs using single-cell RNA-seq and quantitative RNA in situ hybridization (ISH). We computationally distinguished discrete versus continuous heterogeneity in scRNA-seq data and found that SPNs in the striatum can be classified into four major discrete types with no implied spatial relationship between them. Within these discrete types, we find continuous heterogeneity encoding spatial gradients of gene expression and defining anatomical location in a combinatorial mechanism.  Our results suggest that neuronal circuitry has a substructure at far higher resolution than is typically interrogated which is defined by the precise identity and location of a neuron.

overall_design: 1207 single neurons isolated from the striatum of 9 male mice. Sequenced using Smart-Seq2 amplification and Illumina high throughput short read sequencing.

first: Geoffrey

last: Stanley


title: Muscle-derived Dpp regulates feeding initiation via endocrine modulation of brain dopamine biosynthesis

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: In animals, the brain regulates feeding behavior in response to local energy demands of peripheral tissues, which secrete orexigenic and anorexigenic hormones. Although skeletal muscle is a key peripheral tissue, it remains unknown whether muscle-secreted hormones regulate feeding. In Drosophila , we find that decapentaplegic (dpp), the homolog of human bone morphogenetic proteins BMP2 and BMP4, is a muscle-secreted factor (a myokine) that is induced by nutrient sensing and that circulates and signals to the brain. Muscle-restricted dpp RNAi promotes foraging and feeding initiation whereas dpp overexpression reduces it. This regulation of feeding by muscle-derived Dpp stems from modulation of brain tyrosine hydroxylase (TH) expression and dopamine biosynthesis. Consistently, Dpp receptor signaling in dopaminergic neurons regulates TH expression and feeding initiation via the downstream transcriptional repressor Schnurri. Moreover, pharmacologic modulation of TH activity rescues the changes in feeding initiation due to modulation of dpp expression in muscle. These findings indicate that muscle-to-brain endocrine signaling mediated by the myokine Dpp regulates feeding behavior.

overall_design: 15 skeletal muscle Drosophila samples:  3  dpp RNAi construct #1, 3  dpp RNAi construct #2, 3  dpp RNAi control, 3  control

first: Maricela

last: Robles-Murguia

first: Deepti

last: rRao

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Fabio

last: Demontis


title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue

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

overall_design: Refer to individual Series


title: Comprehensive analysis of the mRNA-lncRNA profile between HBV-related Hepatocellular carcinoma (HBCC) and no HBV-related Hepatocellular carcinoma (HNCC)

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

institute: Zhejiang University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
To explore the lncRNAs and mRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma
To performe microarray analysis to detect the lncRNAs and mRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma

overall_design: To determine the expression profiles of lncRNAs and mRNAs in between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma

first: Hongyan

last: Diao


title: Derivation of Porcine Extraembryonic Endoderm-like Cells from from Blastocysts

city: Harbin

first: Yan

last: Li

address: ,600 Changjiang Road,Xiangfang District

institute: Northeast Agriculture University

summary: Extraembryonic endoderm stem (XEN) cells are isolated from PrE (primitive endoderm) of blastocysts. We directly obtained cell lines with XEN characteristics from porcine embryos for the first time.  the RNA-seq data indicated highly reproducible gene expression patterns among piPSCs or pXEN-like cell.the gene expression patterns of pXEN-like cells were significantly different from those of piPSCs

overall_design: mRNA profiles of Porcine XEN like cells were and Porcine induced pluripotent stem cells  generated by deep sequencing,

first: Shuang

last: Wu

first: Yang

last: Yu

first: Heng

last: Zhang

first: Renyue

last: Wei

first: Jiawei

last: Lv

first: Mingming

last: Cai

first: Xu

last: Yang

first: Yu

first: Zhonghua

last: Liu


title: Molecular characterization of BRSK2 and BRSK1 kinases as negative regulators of the NRF2 transcription factor

city: St. Louis

first: Micheal

middle: Benjamin

last: Major

state: MO

address: 4624 Cancer Research Building

department: Department of Cell Biology and Physiology  Department of Otolaryngology

institute: Washington University in St. Louis

summary: We found that the understudied Brain Specific Kinase 2 and 1 (BRSK2/1) proteins suppress NRF2-dependent transcription and NRF2 protein levels in a kinase-dependent fashion. Integrative phosphoproteomic screens, RNAseq profiling and follow-up validation studies revealed BRSK2/1-driven activation of AMPK and suppression of MTOR signaling. BRSK2 over-expression suppressed global protein synthesis and decreased ribosome-RNA associations, which results in decreased NRF2 protein levels. Overall, our data establish the BRSK1 and BRSK2 kinases as negative regulators of NRF2 via the AMPK/MTOR signaling axis.

overall_design: Evaluation of BRSK2/1 induced changes in RNA via overexpression in HEK293Ts.

first: Tigist

middle: Y

last: Tamir

first: Travis

middle: P

last: Schrank


title: Genome regulation by long noncoding RNAs during amelogenesis

city: Los Angeles

first: Michael

last: Paine

address: 2250 Alcazar Street

institute: USC

summary: We conducted the genome-wide lncRNA and mRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for lncRNA regulators.

overall_design: RNA sampels were obtained from the mandibular incisor enamel organs of 5 rats from three developmental stages-maturation, secretory and cervical loop. Gene expression profiling was done separately for each of the 15 RNA samples.

first: Kaifeng

last: Yin


title: Differentially expressed genes in Day 3 and Day 14 partially resected mouse submandibular salivary glands compared to Day 3 mock surgery control

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

summary: We used microarray to examine the effects of salivary gland resection on gene expression at two time points compared to a mock surgery control.

overall_design: We analyzed gene expression from mock surgery control, Day 3 resected, and Day 14 resected mice using the Clariom S Array platform. Array data was processed using Transcriptome Analysis Console (TAC 4.0) Software. There were 3 biological replicates per condition

first: Amber

middle: L

last: Altrieth

first: Kevin

middle: J

last: O'Keefe

first: Sridar

last: Chittur


title: Gene expression profiling of resting and stimulated CD4+CD45RO+ T cells from Sezary syndrome patients and normal donors

city: Little Rock

first: Henry

last: Wong

state: Arkansas

address: 4301 W. Markham St.

department: Dermatology

institute: University of Arkansas for Medical Science

type:
Expression profiling by array
Third-party reanalysis

summary:
Sezary syndrome is an aggressive cutaneous T cell lymphoma with pruritic skin inflammation and immune dysfunction, driven by neoplastic, clonal memory T cells in both peripheral blood and skin.  To gain insight into how abnormal gene expression in Sezary syndrome promotes T cell dysfunction, lymphoproliferation and transformation, we first compared functional transcriptomic profiles of both resting and activated memory T cells from Sezary syndrome patients and normal donors.
To differentiate gene expression associated with malignancy vs. benign inflammation and proliferation, we performed a within-platform meta-analysis of our data for Sezary syndrome and a GEO data set (GSE12079) for lymphocytic variant hypereosinophilic syndrome (L-HES).  L-HES is a benign lymphoproliferation of clonal memory T cells that produces skin symptoms very similar to Sezary syndrome.
This approach revealed gene expression changes unique to either Sezary syndrome or L-HES, and a subset of genes dysregulated in both SS and L-HES.  L-HES patient 1 progressed to peripheral T cell lymphoma, and acquired Sezary-like gene expression during progression, suggesting that these genes contribute to neoplastic transformation.

overall_design:
Original Sezary data: CD4+CD45RO+ T cells from three Sezary syndrome patients and three normal donors.  To obtain functional gene expression, T cells were stimulated with PMA + A23187 for 0, 2, and 6 hours.  Total RNA was then extracted and hybridized on Affymetrix HG U133 Plus 2.0 microarrays (1 microarray per sample).
L-HES data: 23 samples from GEO series GSE12079.  One replicate of L-HES patient 3 (GSM304966) was excluded.  This series includes single microarrays for normal donor samples and 2-3 microarray replicates for L-HES samples.  Normalized signal intensities from replicate L-HES microarrays were averaged prior to determining fold changes.
Meta-analysis: Genes differentially expressed between cases and controls (within each study), or between stimulated and unstimulated conditions were identified using RankProd.  The threshold for differential expression was log2FC ≥ |1|, and percentage of false prediction (pfp) < 0.05. Genes differentially expressed in Sezary only, L-HES only, or both diseases were identified using GeneVenn by comparing the lists of differentially expressed genes from each study.

first: Andrea

last: Moerman-Herzog

first: Daniel

middle: A

last: Acheampong

first: Amanda

middle: G

last: Brooks

first: Suzan

last: Blair

first: Ping-Ching

last: Hsu


title: Transcriptional differences between skin from patients with atopic dermatitis and control skin obtained from the healthy margins of Mohs surgery patients

first: Brian

last: Kim

address: 660 S Euclid Ave

institute: Washington University in Stl

summary:
Purpose: To determine the transcriptional differences between skin from patients with atopic dermatitis and control skin obtained from the healthy margins of Mohs surgery patients
Methods: 4 mm skin biopsies of skin from atopic dermatitis patients or deidentified healthy margin surgical tissue were obtained and stored in RNA Later (-80C). Whole tissue RNA was isolated from tissue processed with a bead homogenizer using the QIAGEN RNeasy kit. Following DNase treatment (TurboDNase, Invitrogen), ribosomal RNA was removed (Ribo-zero kit, Illumina). mRNA was then fragmented in buffer containing 40 mM Tris acetate (pH 8.2), 100 mM potassium acetate, and 30 mM magnesium acetate and heated to 94C for 150 s. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Invitrogen, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield dscDNA. cDNA was blunt ended, had an A base added to the 30 ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
Samples were sequenced to an average depth of 32 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Homo_sapiens reference build Ensembl_R76 using STAR, gene counts were determined with Subread:featureCount, transcript counts were produced by Sailfish, and sequence performance was assessed with RSeQC v2.3.

overall_design: 4 AD and 4 control patients

first: Madison

middle: R

last: Mack

middle: S


title: Integrative analysis of microRNAs and mRNAs in liver tissue and exosomes from blood of hepatitis C virus (HCV) related hepatocellular carcinoma (HCC) patient to identify biomarker and regulators of HCC [Small RNA-Seq]

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

country: India

institute: Institute of Post Graduate Medical Education & Research

summary: Chronic hepatitis C (CHC) is one of the major risk factor for the progressive development of end stage liver diseases including liver cirrhosis (LC) and HCC worldwide. A deep insight into the molecular mechanism of development and progression of liver fibrosis into cirrhosis and HCC following chronic HCV infection leads to characterization of multiple cellular processes and the underlying regulatory mechanisms. Small Non-coding RNAs (sncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are found to be the prime regulators of multiple cellular pathways. Next generation sequencing is now an emerging tool to identify genome wide altered sncRNAs which are either abundant or present in low copy in diseased condition. Using such tools several studies have identified myriads of differentially regulated miRNAs in HCV infected liver tissue by mapping to the annotated sequences in the miRNA database (miRbase). Our study attempted to identify the candidate miRNA and genes involved in HCV related HCC which has a potential to serve as diagnostic molecule as well as therapeutic target for HCC surveillance and management. In addition, considering our current knowledge about eukaryotic genomes and gene expression patterns there could be many more functional sncRNAs with low copy number yet to be discovered and characterized. We also explored this part to address the complexity of the pathogenesis and disease progression as well as the heterogeneity of the disease.

overall_design:
Identify the candidate miRNAs involved in HCV-related HCC.
[contributor] Medgenome Inc.

first: Shaleen

last: Aggarwal

first: Subash

last: Gupta

first: Sukanta

last: Roy


title: CRISPRa-mediated Kcna1 upregulation decreases neuronal excitability and suppresses seizures in a rodent model of temporal lobe epilepsy [II]

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Epilepsy is a major health burden, calling for new mechanistic and therapeutic insights. CRISPR–mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex-vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can be effective to treat acquired focal epilepsy.  We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonic-clonic seizures in a model of temporal lobe epilepsy. The focal treatment minimizes concerns about off-targets effects in other organs and brain areas. This study provides the proof of principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability.

overall_design: 3x Primary neurons treated with sgLacZ, 3x Primary neurons treated with sgKcna1

first: Gaia

last: Colasante

first: Gabriele

last: Lignani

first: Vania

last: Broccoli


title: CRISPRa-mediated Kcna1 upregulation decreases neuronal excitability and suppresses seizures in a rodent model of temporal lobe epilepsy [I]

overall_design: 6x Epileptic treated with sgLacZ, 6x Epileptic treated with sgKcna1, and 5x Control treated with sgLacZ adult mouse hippocampi


title: Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

summary: we compared changes in the transcriptome and the translatome of M. truncatula roots upon rhizobial infection using direct RNA-seq and Translating Ribosome Affinity Purification (TRAP) combined with RNA-seq (TRAP-seq), respectively. TRAP is a ribosome immunopurification approach that has been extensively used in plants and mammals to assess translational changes

overall_design: Transcriptional and translational changes at an early stage of the symbiotic association were examined and compared by performing RNA sequencing (RNA-seq) on both Total and TRAP RNA samples (see below) from M. truncatula roots inoculated with water (mock) or with S. meliloti. Root tissue samples from two biological replicates were collected at 48 hours post-inoculation (hpi) from seedlings grown on agar-Fahraeus plates.

first: Mauricio

last: Reynoso

first: Karen

last: Hobecker

first: Marcos

last: Lancia

first: Maureen

last: Hummel

first: Christhopher

last: Town

first: Benjamin

last: Rosen

first: Julia

last: Bailey-Serres

first: Flavio

last: Blanco

first: Maria Eugenia

last: Zanetti


title: Transcriptome of P1 wild-type and RykSL/SL mutant lungs

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Transcriptomic analysis between P1 wild-type and RykSL/SL mutant lungs (Left lobs)

overall_design: Lung mRNA profiles of P1 wild-type and RykSL/SL lungs were generated by deep sequencing.

first: Hyun-Taek

last: Kim

last: Guenther

first: Didier

last: Stainier


title: Role of cis-zeatin in root responses to phosphate starvation

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

summary: In this work we show that root illumination influences Pi starvation responses, enhancing the root and shoot growth arrest and limiting the root/shoot ratio as well as root hair elongation.  A comparative transcriptomic study using dark-grown roots (DGR) roots seedlings taht were grown with or without phosphate identifies several genes that respond to Pi deficiency that were not previously reported, likely by the negative effect of the root illumination.

overall_design: Random sequencing of poly A RNA from Arabidopsis thaliana wild type roots grown for 8 days in a medium 1/2MS with (+Pi 625 µM) or without (5 µM) of phosphate.

middle: C


title: Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Chromatin organization in Phaeodactylum tricornutum

overall_design: ChIP-seq of Trimethylation of H3K4 in Pt18.6

first: Xue

last: Zhao

first: Leila

last: Tirichine

first: Anne

last: Flore Deton


title: Analysis of human classical and non-classical monocytes compared to their dendritic cell counterpart.

city: Buffalo

first: Jason

last: Muhitch

address: Elm & Carlton Sts.

department: Urology

institute: Roswell Park Cancer Institute

summary: Peripheral blood monocytes are the starting material utilized in conventional dendritic cell (DC) vaccination for the treatment of a broad range of malignancies. While the use of cytokines and growth factors to polarize monocyte-derived DC to distinct phenotypes is well-established, little is known about the contributions of distinct human monocyte subsets to monocyte-derived DC function and patient responses to vaccination. To investigate the status of monocyte subsets in cancer patients and following culture into DC, we isolated classical (C-Mo), intermediate (I-Mo), and non-classical (NC-Mo) from the peripheral blood of renal cell carcinoma (RCC) patients prior to DC vaccination (NCT00085436) and from anonymous healthy donors. Patients treated with DC vaccination who were long term survivors (>100 months survival) had a unique monocyte signature with a two-fold higher percentage of NC-Mo in pretreatment peripheral blood compared to other RCC patients. RCC patient monocytes from each subset were transcriptionally distinct from healthy donor monocytes. Further transcriptional analysis determined that each monocyte subset was characterized by a discrete gene expression profile before and after DC maturation. Phenotypic analysis showed that DC derived from NC-Mo expressed higher levels of CD80, CD83, CD86, HLA-DR, and CD40 compared to DC originating from C-Mo and secreted increased amounts of IL-12p70 following CD40L stimulation. Collectively, these findings establish that DC derived from NC-Mo are potent antigen presenting cells and provide the foundation for future vaccination strategies that enrich NC-Mo prior to DC maturation.

overall_design: Classical and non-classical monocytes were FACS purified from peripheral blood obtained from 3 healthy donors and either used for transcriptional analysis or cultured into dendritic cells for analysis.


title: Gene expression changes in ovaries of oocyte-specific conditional knockout of Ubc9 in juvenile mice

city: Houston

first: Stephanie

last: Pangas

address: One Baylor College of Medicine

department: Pathology & Immunology

institute: Baylor College of Medicine

summary: The reproductive lifespan in mammals is largely determined by the abundance and quality of oocytes residing within the primoridial ovarian follicular pool. Critical oocyte-expressed genes driving ovarian function have been identified, buta role for post-translational modifications, such as SUMOylation of these key factors is not well understood. Oocyte-specific genetic ablation of the sole E2 SUMOylation enzyme, UBC9,  cause female sterility. Preantral and antral stage ovarian follicles are depleted by sexual maturity, and loss of the ovarian reserve in early adulthood causes premature ovarian failure, a condition associated with infertility in women. Gene expression changes indicate atered  function of multiple POI candidate genes, including the transcription factors, NOBOX and SOHLH1. Together, these studies show that SUMOylation is required in the mammalian oocyte for regulating key genetic determinants of oocyte growth and differentiation.

overall_design: Ovarian mRNA profiles of 14-day old control (Ubc9flox/flox) and Ubc9flox/flox Gdf9iCre+ mice were generated by RNA sequencing, in triplicate pools, using an Illumina HiSeq 2500 system.

first: Amanda

last: Rodriguez

first: Shawn

last: Briley

first: Swamy

last: Tripurani

first: Bethany

last: Patton

first: Kimal

last: Rajapakshe

first: Robert

last: Rydze

first: Alexander

last: Rajkovic

first: Alexandria

last: Andrieux

last: Dejean

first: Cristian

last: Coarfa


title: Analysis of classical monocytes from healthy donors, pretreatment RCC patients, and RCC long term survivors.

overall_design: Classical monocytes from healthy donor controls, pretreatment RCC patients, RCC long term survivors, and a recent blood draw from the long term survivors up to 8 years post-treatment initiation.


title: Analysis of monocyte subsets from pretreatment RCC patients compared to healthy donors.

overall_design: Blood monocyte subsets from 8 pretreatment RCC patients were compared to 4 healthy donor controls.


title: Expression data examining DNA damage responses in murine Abl Pre-B cells with genetic deficiencies in damage response genes

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Genotoxic damage is known to disrupt cellular functions and is lethal if not repaired properly. We compare the transcriptional programs activated in response to genotoxic DNA damage induced by ionizing radiation (IR) in pre-B cells from mice deficient in various DNA damage response (DDR) genes.
We used microarrays to detail the global gene expression of mutated cells compared to WT cells, with and without exposure to the DNA damaging agent ionizing radiation (IR), and identified differentially-regulated genes and associated pathways responding to the damage.

overall_design: Each cell line was treated or untreated with IR and gene expression was compared for an IR-response transcription program activated in that particular cell line.  Each genotype's IR-response was compared to the WT response, as well as that of the other mutated cell lines.

first: Cynthia

last: Innes

first: Jill

middle: E

last: Hesse

first: Abigail

last: Morales

first: Beth

last: Helmink

first: Shepherd

middle: H

last: Schurman

first: Barry

last: Sleckman

first: Richard

last: Paules


title: Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

summary: Elevated level of circulating cell-free DNA (cfDNA) has been associated with poor prognosis and relapse in patients with diffuse large B-cell lymphoma (DLBCL), but the tumor-specific molecular alterations in cfDNA with prognostic significance remain unclear. We investigated the association between 5-hydroxymethylcytosines (5hmC), a mark of active demethylation and gene activation, in cfDNA from blood plasma and prognosis in DLBCL. We used the 5hmC-Seal, a highly sensitive chemical labeling technique, to profile genome-wide 5hmC in plasma cfDNA samples from 48 newly diagnosed patients with DLBCL at the University of Chicago between 2010 and 2012. Patients were followed through December 31, 2017. We found a distinct genomic distribution of 5hmC in cfDNA marking tissue-specific enhancers, consistent with their potential roles in gene regulation. The 5hmC profiles in cfDNA differed by cell-of-origin, and were associated with clinical prognostic features including Ann Arbor stage, serum lactate dehydrogenase (LDH) level, and the International Prognostic Index (IPI). We developed a 29 gene-based weighted prognostic score (wp-score) for predicting event-free survival (EFS) and overall survival (OS), by applying the elastic net regularization on the Cox proportional hazard model. The wp-scores showed significantly improved prognostic accuracy and/or sensitivity/specificity than the established prognostic factors. In multivariate Cox models, patients with high wp-scores were associated with worse event-free survival (Hazard Ratio [HR] = 9.17, 95% confidence interval [CI] = 2.01- 41.89, p = 0.004), compared with those in the low risk group. Our findings suggest that the 5hmC signatures in cfDNA at the time of diagnosis are associated with clinical outcomes in DLBCL and may provide a novel non-invasive prognostic approach for DLBCL.

first: Brian

last: Chiu

first: Zhou

first: Qiancheng

last: You

first: Chang

last: Zeng

first: Elizabeth

last: Stepniak

first: Paige

last: Bracci

first: Girish

last: Venkataraman

first: Chuan

last: He

first: Sonali

last: Smith


title: Moderate blast exposure alters gene expression and levels of amyloid precursor protein

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary:
Objective: Blast induced traumatic brain injuries are a signature injury of recent war campaigns; yet little is known about the biological mechanisms underlying blast exposures.
Methods: In a group of military personnel (N = 69), prior to, and on each day of a blast training program (10 days total), blood was collected; throughout training, blast exposure measures were detected by helmet sensors to determine the mean peak pressure in pounds per square inch (psi). On day 7, some participants (n= 29) sustained a moderate blast (mean peak pressure = 7.9 psi) and were matched to participants with no/low blast exposure during the training (n = 40).
Results: RNA-seq identified 1,803 dysregulated genes, including 746 up-regulated genes and 1,058 down-regulated genes following a moderate blast exposure. The IPA showed the APP gene network to be most dysregulated following blast, with an IPA network score of 43.  Real-time qPCR was used to validate the expression changes for four genes 4 genes, namely: amyloid precursor protein (APP), amyloid precursor-like protein 2 (APLP2), nicastrin (NCSTN) and NEDD8 Activating Enzyme E1 Subunit 1 (NAE1) and significant dysregulation of these genes was confirmed (p = 0.00083476, p = 0.000105, p = 0.000673 and p = 0.043145, respectively).
Conclusions: Moderate blast exposure results in a signature biological profile that includes acute APP reductions, followed by genetic expression increases and normalization of APP levels; these changes likely influence neuronal recovery.

overall_design: miRNA profiling of 24 human blood samples at two time points to study PTSD

first: Yun

last: Sijung

first: Jessica

last: Gill


title: Transcriptional profiling of endothelial cells in the cerebral cortex of a Abcb1a-TRAP (ES3026) mouse line

status: Public on Nov 14 2019

city: New York

first: Eric

middle: F

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in endothelial cells in the cerebral cortex of adult Abcb1a-EGFP/Rpl10a (ES3026) mice.

overall_design:
TRAP-Seq of endothelial cells in the cerebral cortex of adult Abcb1a-EGFP/Rpl10a (ES3026) control mice.

Please note that the ES and JL are the initials of the investigators that extracted the RNA. There is no other functional distinction between the samples.

first: Jim

last: Li

first: Nathaniel

last: Heintz


title: Transcriptional changes involved in inhibition of biofilm formation by ε-Polylysine in Salmonella Typhimurium

city: fukuoka nishi ward

first: Cunkuan

last: Shen

state: fukuoka

address: Motooka

institute: kyushu university

summary: Salmonella Typhimurium is one of the major foodborne pathogens due to its biofilm formation on food contact surfaces. A polymer of positively charged lysine, ε-Polylysine has been demonstrated to inhibit biofilm formation of both Gram-positive and -negative bacteria. To elucidate the mechanism for inhibition of biofilm formation by ε-Polylysine, transcriptional profiles were compared between the cells before and after treatment with ε-Polylysine in Salmonella Typhimurium. A genome-wide DNA microarray analysis was performed after cultivation in 0.1% bacto soytone in the presence of 0.001% ε-Polylysine at 30°C for 2 h. Genes involved in curli and cellulose production, quorum sensing, and flagellar motility were down-regulated, whereas genes associated with colanic acid synthesis were up-regulated. The data from microarray was validated by RT-qPCR. Furthermore, production of colanic acid in S. Typhimurium decreased in the presence of ε-Polylysine. The outcome of this study provides a basic understanding of the anti-biofilm mechanisms of ε-Polylysine and may contributes to develop new disinfectant to control biofilm during food manufacturing and storage.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Gene expression during initial adhension (2 hours) were measured with or withour exposure to  0.001% ε-Polylysine. Three dependent experiments were performed at each time.

first: Tariqul

last: Islam

first: Yoshimitsu

last: Masuda

first: Ken-ichi

last: Honjoh

first: Takahisa

last: Miyamoto


title: JMJ17, a H3K4 demethylase, regulates chlorophyll biosynthesis during the transition from dark to light in Arabidopsis seedlings [light treatments]

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: We have reported that JMJ17 act as a repressor to a set of genes involved in  photosynthesis, tetrapyrrole biosynthesis and light response related development  in the dark, while during dark to light irradiation it  acts as an activator of same set of genes.

overall_design: Global gene regulation by JMJ17 were analysed in  wild type (WT) and jmj17-1 seedling  by deep micro-array analysis, Affymetrix Gene Chip Arabidopsis ATH1 Genome Array

first: Md

middle: T

first: Long-Chi

last: Wang


title: Generation of diffuse intrinsic pontine glioma mouse models by brainstem targeted in utero electroporation

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary: Diffuse intrinsic pontine gliomas (DIPGs) are highly lethal childhood brain tumors. Their unique genetic makeup, pathological heterogeneity, and brainstem location all present challenges to treatment. Developing mouse models that accurately reflect each of these distinct features will be critical to advance our understanding of DIPG development, progression, and therapeutic resistance. The aim of this study was to generate new mouse models of DIPG, and characterize the role of specific oncogenic combinations in DIPG pathogenesis. We used in utero electroporation (IUE) to transfect neural stem cells in the developing brainstem with PiggyBac DNA transposon plasmids. Combinations of PDGFB or PdgfraD842V, dominant negative Trp53 (DNp53), and H3.3K27M expression induced fully penetrant brainstem gliomas.   IUE enabled the targeted transfection of brainstem neural stem cells. PDGFB + DNp53 induced the rapid development of grade-IV gliomas. PdgfraD842V + DNp53 produced slower forming grade-III gliomas. Addition of H3.3K27M only significantly accelerated PdgfraD842V DIPG development. Glioma subgroup molecular signatures were associated with differences in bulk PDGFB and PdgfraD842V tumor composition. H3.3K27M induced both overlapping and unique gene expression changes in PDGFB and PdgfraD842V tumors. Paracrine effects of PDGFB promote disruption of pericyte-endothelial interactions and angiogenesis in PDGFB DIPG mouse models.  Brainstem targeted in utero electroporation provides a rapid and flexible system to generate diverse DIPG mouse models. Using IUE to investigate mutation and pathohistological heterogeneity of DIPG will provide a valuable tool for future genetic and preclinical studies.

overall_design: Two to three biological replicates were analyzed for each of 6 conditions (six genotypes; two-three samples per genotype)

first: Smruti

last: Patel


title: Combined use of astragalus polysaccharide and berberine attenuates insulin resistance in IR-HepG2 cells via regulation of the gluconeogenesis signaling pathway

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

summary: Insulin resistance (IR) is likely to induce metabolic syndrome and type 2 diabetes mellitus (T2DM). Gluconeogenesis (GNG) is a complex metabolic process that may result in glucose generation from certain non-carbohydrate substrates. Chinese herbal medicine astragalus polysaccharides and berberine have been documented to ameliorate IR, and combined use of astragalus polysaccharide (AP) and berberine (BBR) are reported to synergistically produce an even better effect. However, what change may occur in the GNG signaling pathway of IR-HepG2 cells in this synergistic effect and whether AP-BBR attenuates IR by regulating the GNG signaling pathway remain unclear. For the first time, we discovered in this study that the optimal time of IR-HepG2 cell model formation was 48 hours after insulin intervention. AP-BBR attenuated IR in HepG2 cells and the optimal concentration was 10mg. AP-BBR reduced the intracellular H2O2 content with no significant effect on apoptosis of IR-HepG2 cells. In addition, a rapid change was observed in intracellular calcium current of the IR-HepG2 cell model, and AP-BBR intervention attenuated this change markedly. The gene sequencing results showed that the GNG signaling pathway was one of the signaling pathways of AP-BBR to attenuate IR in IR-Hepg2 cells. The expression of p-FoxO1Ser256 and PEPCK protein was increased and the expression of GLUT2 protein was decreased significantly in the IR-HepG2 cell model, and both of these effects could be reversed by AP-BBR intervention. AP-BBR attenuated IR in IR-HepG2 cells, probably by regulating the GNG signaling Pathway.

overall_design: HepG2 cells (Cell Bank of the Chinese Academy of Sciences, Shanghai, China) were cultured in 1640 medium (Hyclone, Beijing, China) containing 10% fetal bovine serum (FBS, Hyclone, Beijing, China) and 1 × streptomycin in a 37 ℃ 5% CO2 saturated humidity incubator. The normally cultured HepG2 cell lines in log phase were centrifuged at 100grpm for 5 min, and 20000 cells/well were placed in a 96-well plate and incubated at 37°C.The experiment was performed in 24-h control group, 24-h model group, 36-h control group, 36-h model group, 48-h control group, 48-h model group, 72-h control group and 72-h model group. Insulin (Gibco, NY, USA) was diluted to a final concentration of 10-6 mol/L in complete medium. 200µl insulin preparation was added into each well for the model group and an equal amount of complete medium was added into each well for the control group. Culture was performed in a 37 ℃ 5% CO2 and saturated humidity incubator. The supernatant of the corresponding medium was collected according to the time point by centrifugation at 3000 r/min for 5 min and stored at-80 ℃ for use. RNA isolation, purification and quantification: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample were quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.cDNA Library Construction: Poly(A) RNA was purified from total RNA (5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then, the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which was subsequently used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base was then added to the blunt ends of each strand, which were prepared for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified by PCR under the following conditions: initial denaturation at 95℃ for 3 min, 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The mean insert size for the final cDNA library was 300 bp (±50 bp). Finally, 150bp paired-end sequencing was performed on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.Pathway enrichment analysis: Using the DAVID database and mouse genome as background control, the differentially expressed genes were analyzed by gene ontology under "FunctionalAnnotation Chart" functional module. The differentially expressed genes were divided into three categories according to their functions: the biological process, the cell component and the molecular function. Pathway analysis was carried out by KEGG analysis function.

first: Zhu-Jun

last: MAO

first: Lu-Ping

last: Qin


title: Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants (DenseTimeCourse)

city: San Francisco

first: Jason

middle: V

last: Rogers

state: CA

address: 1170 Veterans Boulevard

institute: Calico Life Sciences LLC

summary: Here we sought to comprehensively characterize the role of the electron transport chain in yeast models of aging.  Using a panel of ETC mutants, we observed that ETC mutants fail to survive starvation when grown to saturation in standard SD growth medium.  This starvation lethality is associated with a significantly lower cytosolic pH and dysregulated gene expression compared to wild type cells.  In an unbiased genetic suppressor screen, we found that loss of function mutations in major cellular nutrient sensing/signaling pathways (Ras/PKA, Tor, PP2A) along with a number of gene expression regulators can prevent starvation lethality in these mutants.  Together our results suggest that the ETC plays a critical regulatory role in mounting an appropriate response to starvation through communication with major nutrient sensing/signaling pathways in the cell.

overall_design: Dense time course comparison of Saccharomyces cerevisiae strains S288C w.t. (cDBY001) to mutants nde1∆ nde2∆ ndi1∆ (cDBY0085) and cox4∆ (cDBY0045) grown in YNB + NH4 + glucose

first: Patrick

last: Gibney

first: Robert

last: Caldwell

first: David

last: Botstein


title: Genetic identification of vagal sensory neurons that control feeding

first: Ling

last: Bai

address: 1550 4th St., Rock Hall Rm 346

department: Physiology

institute: UCSF

summary: Energy homeostasis requires precise measurement of the quantity and quality of ingested food. The vagus nerve innervates the gut and can detect diverse interoceptive cues, but the identity of the key sensory neurons and corresponding signals that regulate food intake remains unknown. Here we use an approach for target-specific, single-cell RNA sequencing to generate a map of the vagal cell types that innervate the gastrointestinal tract. We show that unique molecular markers identify vagal neurons with distinct innervation patterns, sensory endings, and function. Surprisingly, we find that food intake is most sensitive to stimulation of mechanoreceptors in the intestine, whereas nutrient-activated mucosal afferents have no effect. Peripheral manipulations combined with central recordings reveal that intestinal mechanoreceptors, but not other cell types, potently and durably inhibit hunger-promoting AgRP neurons in the hypothalamus. These findings identify a key role for intestinal mechanoreceptors in the regulation of feeding.

overall_design: Nodose ganglion single cell mRNA profiles of 6 to 12-week-old C57BL/6JN mice were generated by deep sequencing, using either 10x Genomics (sample 1) or Smart-seq2 protocol (all other samples).


title: Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants (ETC_Mutants)

overall_design: Gene expression time courses in which Saccharomyces cerevisiae S288C wild type strain is compared to 1) electron transport chain (ETC) mutants coq2d and cox4d, 2) suppressors of ETC mutant starvation lethality ras2d, rts1d and tco89d and 3) strains in which the ETC mutants are suppressed. The time courses extend across the wild type diauxic shift. Cells were grown in YNB + NH4 + 2% glucose. Sampling for all strains was at at t=0 hours (log phase), 12 and 16 hours as technical replicates.

middle: M


title: Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants

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

overall_design: Refer to individual Series


title: FXYD5 (dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer

city: Brescia

first: Antonella

last: Ravaggi

state: Brescia

address: Viale Europa 11

department: Department of Clinical and Experimental Sciences

institute: University of Brescia

summary:
High-grade serous ovarian carcinoma (HGSOC) is generally associated with a very dismal prognosis. Nevertheless, patients with similar clinicopathological characteristics can have markedly different clinical outcomes. Our aim was the identification of novel molecular determinants influencing survival.
Gene expression profiles of 12 HGSOC long-term and 27 short-term survivors (training set) were generated by microarray, and a prognostic signature was identified and further evaluated on an independent extensive HGSOC dataset through a meta-analysis approach.

overall_design: Snap-frozen tumor biopsies were obtained at primary surgery from 39 HGSOC patients: 27 short-term survivors, who lived less than 3 years after initial diagnosis, and 12 long-term survivors, who lived more than 7 years. Total RNA was extracted and hybridized to Affymetrix  oligonucleotide microarray chips.  On the basis of their Platinum Free Interval (PFI), defined as  the time between the last dose of first-line carboplatin-based chemotherapy  and the date of tumor progression, HGSOC patients were defined as “resistant” (PFI<6 months), “partially sensitive” (PFI 6-12 months), and “sensitive” (PFI>12 months).

first: Renata

last: Tassi


title: Transcriptome differences between white and brown adipose tissue from wildtype and uncoupling protein 1 knockout mice exposed to different diets and ambient temperatures

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed  transcript abundance in interscapular brown and inguinal white adipose tissue of wildtype and UCP1-KO mice either adpated to 20°C or 30°C and fed a high fat or control diet.

overall_design: Male C57BL/6J mice of wildtype or Ucp1-KO genotype were fed a high fat diet (48% energy from fat) or control diet (13% energy from fat) at thermoneutrality (30°C). Control diet was also fed at 20°C, resulting in a total of 6 groups of 8 animals each. After 4 weeks, we prepared interscapular brown adipose tissue and inguinal white adipose tissue, resulting in 96 samples. Of these, we sequenced total RNA and determined transcript abundance.

first: Stefanie

last: Maurer

first: Sabine

last: Mocek

first: Anika

last: Zimmermann

first: Martin

last: Klingenspor


title: 2-Methylcitrate cycle: a well-regulated controller in Bacillus sporulation

city: Wuhan

first: Xinfeng

last: Li

address: Shi zi shan street

institute: Huazhong Agricultural University

summary: To understand which gene(s) are affected by 2-methylcitrate to lead to the delayed sporulation in ∆prpD, we extracted the total RNA from BMB171 and ∆prpD at 12 h for whole genome transcription analysis by RNA sequencing (RNA-Seq). Our RNA-seq data showed that transcriptions of almost all of the SigF regulon genes, as concluded from the B. subtilis regulon, were significantly down-regulated in ∆prpD compared with the wild type BMB171. However, almost all the regulon genes of SigH, a sigma factor that functions upstream of SigF, were significantly up-regulated in ∆prpD. Those genes included spo0A, the early-expressed operon spoIIA and sigF itself. These results indicated that dysregulation of genes occurred on various levels. In particular, though, post-transcriptional inhibition of sigF functionality might subsequently lead to down-regulation of SigF regulon genes in the ∆prpD mutant.

overall_design: BMB171 and ΔprpD strains were cultured in GYS medium for 12 h, RNA samples were isolated and sequenced, each with two repetitions.

first: Cao

last: Zheng

first: Jin

last: He


title: Endogenous beta-galactosidase activity marks TREM2-expressing Kupffer cell population in the livers of carbon tetrachloride-treated Lgr5-LacZ mice

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Lgr5+ cells isolated from liver organoids act as bipotent liver progenitors. Beta-galactosidase (beta-gal)-expressing cells appear in injured livers of Lgr5-LacZ mice, however, their origin and identity has remained controversial. Here we sought to clarify this issue. The majority of beta-gal+ cells emerged in pericentral regions of the liver lobule. Lineage tracing demonstrated that beta-gal+ cells did not originate from hepatocytes or cholangiocytes. Beta-gal+ cells were negative for hepatocyte and cholangiocyte markers; but positive for Kupffer cell markers.  Transcriptome analysis revealed the expression of endogenous beta-galactosidase Glb1 and genes characteristic of TREM2+ macrophages that may regulate stem cell maintenance. We were not able to detect the expression of the Lgr5-LacZ transgene and concluded that the transgene was silenced.

overall_design: Lgr5-LacZ transgene-bearing mice (aged 7-12 weeks) were subjected to liver injury by single intraperitoneal injection of CCl4 (1µl/g body weight) diluted in rapeseed oil. Liver samples were collected 6 days after the injection. We analysed the transcriptional profiles of sorted b-gal+ F4/80high cells (sample name FITCpos), b-gal- F4/80high cells (sample name FITCneg), EpCAM+ cholangiocytes and hepatocytes (HEP). Each sample contains pooled cells from 2 individual mice.

first: Viljar

last: Jaks


title: RNA-seq of PC3 prostate cancer cell line xenografts in mice administered the ghrelin receptor antagonist [D-Lys3]-GHRP-6 or PBS for two weeks

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

country: Australia

institute: Queensland University of Technology

summary: The ghrelin receptor antagonist [D-Lys3]-GHRP-6 (or PBS control) was administered for two weeks to NOD/SCID mice with PC3 prostate cancer cell line xenografts. Daily intraperitoneal injections of 20 nmoles/mouse/day [D-Lys3]-GHRP-6 significantly reduced xenograft tumour size at day 9 to 14. RNA-sequencing was performed on xenograft tumours at experimental endpoint (14 days).

overall_design: RNA sequencing of PC3 prostate cancer cell line xenografts from NOD/SCID mice. Subcutaneous tumours were allowed to grow until a volume of approximately 100 mm3 was reached, when mice were divided into two experimental groups. Mice then received daily intraperitoneal (i.p.) injections of 20 nmoles/mouse [D-Lys3]-GHRP-6, Sigma-Aldrich, St-Louis, MO, USA) (n=3) or PBS control (n=3) for 14 days.


title: Embryonic response to high beta-hydroxybutyrate (BHB) levels in postpartum dairy cows [gene expression]

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: This project is meant to document the effect of the negative energetic balance on the embryo quality and as it happens, to identify ways to improve the fertility of dairy bovines. Measurement of the β-Hydroxybutyric acid (BHB) has been taken between 45 and 60 days post-partum on twelve Holstein cows. Cows have been ranked according to the sanguine measurement as high or low in BHB in order to get 6 cows per group. After having synchronized the heat with hormones and an ovarian stimulation, cows have been inseminated and the embryos were selected as so to be transferred in at least two heifers. This project aim at isolating the differences created on the transcriptomic expression in morulas and blastocysts grown in cows with an energetic inbalance.

overall_design: This is a 2 conditions experiment with morula and blastocysts collected in cows with low or high BHB.  Four biological replicates for each treatment and each were hybridized in a dye swap design.

first: Catherine

last: Chaput


title: Embryonic response to high beta-hydroxybutyrate (BHB) levels in postpartum dairy cows [methylation]

summary: This project is meant to document the effect of the negative energetic balance on the embryo quality and as it happens, to identify ways to improve the fertility of dairy bovines. Measurement of the β-Hydroxybutyric acid (BHB) has been taken between 45 and 60 days post-partum on twelve Holstein cows. Cows have been ranked according to the sanguine measurement as high or low in BHB in order to get 6 cows per group. After having synchronized the heat with hormones and an ovarian stimulation, cows have been inseminated and the embryos were selected as so to be transferred in at least two heifers. With this transfer it is possible to isolate the impact of the energetic level of the mother before and during the gestation on the performances of the future progeny.

overall_design: This is a 2 conditions experiment with morula (4 per pool) and blastocysts (1 per pool) collected in cows with low or high BHB.  Four biological replicates for each treatment and each were hybridized in a dye swap design.


title: Chromatin blueprint of glioblastoma stem cells reveals new subtypes with unique drug sensitivities [methylation]

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

summary: We identified three novel chromatin-driven subtypes of gliblastoma stem cells, regualted by specific essential transcription factors and with specific drug sensitivities

overall_design: Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium EPIC Human Methylation BeadChip.

first: Mathieu

last: Lupien

first: Peter

middle: B

last: Dirks


title: Chromatin blueprint of glioblastoma stem cells reveals new subtypes with unique drug sensitivities [ATAC-seq]

summary: We identified three novel chromatin-driven subtypes of glioblastoma stem cells, regulated by specific essential transcription factors and with specific drug sensitivities.

overall_design:
Glioblastoma cells were profiled for open chromatin using ATAC-seq (total = 43 samples).

Raw data files (fastq) are under controlled access. Contact the Princess Margaret Cancer Centre Genomics Core/University Health Network (geneservice@pmgenomics.ca) for access using the identifiers outlined below and the file names in the Sample 'description' field.


title: RNA sequencing analysis shows that titanium dioxide nanoparticles induce endoplasmic reticulum stress, which has a central role in mediating plasma glucose in mice

city: Harbin

first: Ning

last: Gu

address: No. 92 West Da-zhi Street

institute: School of Life Science and Technology, Harbin Institute of Technology

summary: Titanium dioxide nanoparticles (TiO2 NPs) constitute the top five NPs in use today. A recent study determined that oral administration of TiO2 NPs increases plasma glucose in mice. In the current study, RNA sequencing (RNA-seq) technology was used to investigate genome-wide effects of TiO2 NPs. Clustering analysis of the RNA-seq data showed the most significantly enriched gene ontology terms and KEGG pathways related to the endoplasmic reticulum (ER) and ER stress. Molecular biology verification showed that TiO2 NPs activated a xenobiotic biodegradation response and increased expression of cytochrome P450 family genes in mouse livers, thus inducing ER stress in mice. ER stress activated MAPK and NF-B pathways and induced an inflammation response, resulting in phosphorylation of the insulin receptor substrate 1 and, consequently, insulin resistance. This was the main mechanism by which TiO2 NPs increased plasma glucose in mice. Meanwhile, ER stress disturbed the monooxygenase system, and thus generated reactive oxygen species (ROS). Relief of ER stress with 4-phenylbutyric acid inhibited all the above effects of TiO2 NPs, including the generation of ROS. Therefore, TiO2 NP-induced ER stress was a decisive factor with a central role in plasma glucose disturbance in mice.

overall_design: Examination of genome-wide expressions in Control and NP groups

first: Hailong

last: Hu


title: Embryonic response to high beta-hydroxybutyrate (BHB) levels in postpartum dairy cows

type:
Expression profiling by array
Methylation profiling by array


title: Comparative transcriptome analysis reveals naked mole rat liver adaptations to hypoxia

summary: This study compares the transcriptional response to hypoxia in liver of the hypoxia-tolerant naked mole rat (NMR) and the hypoxia-sensitive rat.

sample_organism:
Rattus norvegicus
Heterocephalus glaber

platform_organism:
Rattus norvegicus
Heterocephalus glaber

overall_design: Liver mRNA profiles (Illumina HiSeq 2000) of naked mole rat (NMR) and rat exposed to short-term hypoxia (8% O2, 8 hours). Compared to normoxia samples.

first: Vadim

last: Gladyshev


title: Understanding the role of miRNAs in controlling metabolic master regulators

city: Mumbai

first: Ullas

middle: Kolthur

last: Seetharam

state: Maharashtra

address: Homi Bhabha Road, Colaba

department: Department of Biological Sciences

institute: Tata Institute of Fundamental Research

summary: Our study unravels a novel network of miR dependent regulation of metabolic genes and their contribution towards maintainance of cellular energy homeostasis

overall_design: MicroRNAs sequencing from the liver of 2-3 months old fed mice using Illumina HiSeq1000

last: Kolthur-Seetharam


title: RNA sequencing of lesional and nonlesional skin from patients with atopic dermatitis

status: Public on Nov 13 2019

city: Saint Louis

first: Ting-Lin

last: Yang

state: Missouri

address: 660 S. Euclid Ave., CB 8123

country: USA

institute: Washington University of St Louis

summary:
Purpose: To determine the transcriptional differences between lesional skin and nonlesional skin from patients with atopic dermatitis
Methods: Skin biopsies of lesional and non-lesional sites on atopic dermatitis patients were obtained and stored in RNA Later. Ribosomal RNA was removed and cDNA was generated with the SMARTer kit (CloneTech) with 10 ng of total RNA per sample.
Samples were sequenced to an average depth of 34 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Ensembl release 76 using STAR, gene counts were determined with Subread:featureCount, and sequence performance was assessed with RSeQC.

overall_design: Six atopic dermatitis patients

first: Madison

last: Mack

first: Brian

last: Kim


title: Tet2 interacts with SCAN domain and regulates Zscan4-associated events during cell reprogramming

city: Shanghai

first: Zhouli

last: Cheng

address: Mingdao Building, 131 Dong’An Rd, Shanghai, China

institute: Key Laboratory of Medical Epigenetics and Metabolism, and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences


title: Tet2 interacts with SCAN domain and regulates Zscan4-associated events during cell reprogramming (ChIP-Seq)

summary: Evolutionarily conserved SCAN domain-containing zinc finger transcription factors (ZSCAN) have been found in both the mouse and human genomes. Of which, Zscan4 is crucial for zygotic genome activation (ZGA) in preimplantation embryos, and induced pluripotent stem cell (iPSC) reprogramming. However, little is known about the mechanism of Zscan4 underlying these processes of cell fate control. Here we show that Zscan4f, a representative of ZSCAN proteins, is able to recruit Tet2 through its SCAN domain. The Zscan4f-Tet2 interaction promotes DNA demethylation and regulates the expression of target genes, particularly those encoding glycolytic enzymes and proteasome subunits. Disruption of the Zscan4f-Tet2 interaction impairs cellular metabolism, proteasome function, and ultimately compromises iPSC generation. These results identify Tet2 as a major cooperator for the function of Zscan4f, and suggest a common mechanism shared by SCAN family transcription factors to recruit TET DNA dioxygenases to regulate diverse cellular processes.

overall_design: Examinate the target genes of Zscan4f in D4-OSKM-2ndMEFs

first: Dan

last: Ye


title: Tet2 interacts with SCAN domain and regulates Zscan4-associated events during cell reprogramming (RNA-Seq)

overall_design: Transcriptome analysis was performed in D4-OSKM-2ndMEFs (3 groups, n=3 per group).


title: miRNA expression in Abelson virus transformed fetal liver B cell progenitors

city: Innsbruck

first: Verena

last: Labi

address: Innrain 80-82

department: Developmental Immunology

country: Austria

institute: Medical University Innsbruck

summary: Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental defect and blocked B lymphopoiesis. We validated the equally widely expressed Bcl2l11 gene as joint target of miR-17~92 cluster members. Bcl2l11 encodes the pro-apoptotic protein BIM, central to life-death decisions in most mammalian cells. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3’UTR in the mouse. Blocking miR-17~92:Bim interaction early in development phenocopied the lethal developmental defect of miR-17~92 ablation. In contrast, hematopoietic and B lineage specific mutagenesis, while selectively compromising B lineage cell fitness, left hematopoietic cell compartments untouched as long as the cells expressed Bim biallelically. Thus, despite hundreds of overall predicted targets vital miRNA functions can be mediated by a single target gene, depending on cellular context and level of target gene expression.

overall_design: Total RNA was extracted from 5 wild type and 5 Bim3'UTRmut/mut Abelson transformed B cell progenitors derived from E14.5 fetal liver. 100 ng of total RNA per sample was used as input for nCounter gene expression analysis (NanoString Technologies).

first: Klaus

last: Rajewsky

first: Filippos

last: Klironomos