title: Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (EZH2_KO_HSC)

first: Atsushi

last: Iwama

summary: Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Epigenetic alterations are one of the hallmarks of HSC aging, and profiling of DNA methylation and histone modifications has provided potential mechanisms that contribute to HSC aging. Chromatin accessibility reflects a comprehensive transcriptional network operating in cells; however, it has not yet been investigated in HSC aging. Here we performed an integrated analysis of aged HSCs on transcriptome, chromatin accessibilities, and histone modifications. Alterations in chromatin accessibility preferentially took place in HSCs with aging, the cells at the top of hematopoietic hierarchy, suggesting that the age-associated alterations in chromatin accessibility are memorized in HSCs and are inherited to downstream progenitor cells. However, most genes with differentially accessible regions (DARs) were not actively transcribed and kept poised for activation in aged HSCs. Motifs of ATF/CREB, STAT, and CNC family transcription factors were significantly enriched at DARs in aged HSCs. These transcription factors are activated in response to external stresses such as cytokine and inflammation signals and oxidative stresses, suggesting that the long-term exposure to such stress signals have changed chromatin accessibility in HSCs to augment responses by such trained HSCs to subsequent stimuli. In contrast, aged HSC-specific gene expression occurred mainly at gene loci with poised accessible regions but not DARs without accompanying drastic chromatin reorganization, suggesting that altered cell-extrinsic stimuli or signals from aged niche largely account for this process. Our findings provide key epigenetic molecular insights into HSC aging and serve as a reference for future analysis.

overall_design: RNA-seq of Ezh2 knock out HSCs

first: Naoki

last: Itokawa

first: Motohiko

last: Oshima

first: Wakako

last: Kuribayashi

first: Naoya

last: Takayama

first: Shuhei

last: Koide

first: Yaeko

last: Nakajima-Takagi

first: Aoyama

last: Kazumasa

first: Satoshi

last: Yamazaki

first: Koji

last: Eto


title: Steady-state expression of Giardia lamblia transcripts

status: Public on Sep 24 2020

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

country: USA

institute: University of Colorado Denver

type: Expression profiling by high throughput sequencing

summary: RNASequencing and RNA level measurements of G. lamblia transcripts during trophozite stage to compare expression between genes of interest

overall_design: Poly(A) RNASequencing of G. lamblia trophozoites

first: Daniel

middle: R

last: Eiler

first: Brian

middle: T

last: Wimberly

first: Danielle

middle: Y

last: Bilodeau

middle: S

first: Jeffrey

last: Kieft


title: Gene expression profiles of human spinal cord organoids derived from human pluripotent stem cells

status: Public on Sep 10 2020

city: SEOUL

first: Ju-Hyun

last: Lee

address: 73 Inchon-ro

country: South Korea

institute: Korea University College of Medicine

summary: We used microarrays to examine that human spinal cord organoids reflect the characteristics of spinal cord development.

overall_design: Multiple organoids pooled together were used for microarray analysis.

first: Woong

last: Sun


title: Genome wide analysis of Open Chromatin Regions in memory OT-I cells

status: Public on Sep 30 2020

city: Bronx

first: Shu Shien

last: Chin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cognate antigen signals control CD8+ T cell priming, expansion size and effector versus memory cell fates, however, it is not clear whether they can also modulate the functional features of memory CD8+ T cells.  We observed that OT-I cells that were primed with weak cognate antigen signals incorporate more cytokine signals, leading to a hypothesis that CD8+ T cells that receive weak TCR signals require cytokine signals to form functional memory. Using a previously described mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, the “Il2ramut/mut” mouse, we conducted a comparative analysis of gene expression and epigenetic landscape of Il2ramut/mut and WT OT-I memory cells that were primed with strong (Lm-Ova N4) versus weak (Lm-Ova T4). RNA seq data showed that both TCR and IL-2 priming signals have minimal effect on gene expression in resting memory CD8 T cells, but they significantly modify the epigenetic landscape of the memory CD8 T cells. These findings have important contributions to the current understanding of how priming signals program memory CD8 T cells in vivo.

overall_design: We adoptively transferred Il2ramut/mut and WT OT-I cells to sets of hosts and immunized them with Lm-Ova N4 (2 replicates)  or Lm-Ova T4 (2 replicates). Spleens of the hosts were harvested 3-4 weeks later and memory OT-I cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq).

first: Shu

first: Fabien

last: Delahaye

first: Gregoire

last: Lauvau


title: Immunogenic chemotherapy enhances recruitment of CAR-T cells to solid tumors and improves anti-tumor efficacy when combined with checkpoint blockade

status: Public on Sep 18 2020

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

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

overall_design: Refer to individual Series


title: Single-Cell Transcriptomic Profiling of subpopulations of vascular endothelial cells following acute lung injury

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: We utilized high-throughput single-cell transcriptomics to identify endothelial subpopulations and track their responses to inflammatory injury.

overall_design: Single cell RNA-sequencing of 35,973 lung endothelial cells were obtained during homeostasis and defined injury time points ( 6 hours, 1 day, 2 days, 3 days and 7 days) following systemic in vivo exposure to the bacterial endotoxin lipopolysaccharide (LPS).

first: Lianghui

last: Zhang

first: Shang

last: Gao

first: Zachary

last: White

first: Yang

last: Dai

first: Asrar

middle: B

last: Malik


title: Application of singe nuclei RNA sequencing to assess the hepatic effects of   2,3,7,8-tetrachlorodibenzo-p-dioxin

status: Public on Sep 01 2020

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Cell-specific transcriptional responses are lost in the averages of bulk RNA sequencing. We performed single nuclei RNA sequencing (snSeq) on frozen liver samples from male C57BL/6 mice in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Approximately 19,907 hepatic genes were detected across 16,015 sequenced nuclei from control and treated samples. Eleven cell-(sub)types were identified including distinct hepatocyte sub-populations, consistent with the cell diversity of the liver. TCDD increased macrophages from 0.5% to 24.7%, while neutrophils were only present in treated samples. The number of differentially expressed genes correlated with the basal expression level of Ahr. In addition to expected functional enrichments within each cell-(sub)type, RAS signaling was enriched in nonparenchymal cells. snSeq also identified a Kupffer cell subtype highly expressing Gpnmb, consistent with a dietary NASH model. Overall, snSeq distinguished cell-specific transcriptional changes and population shifts consistent with the hepatotoxicity of TCDD.

overall_design: Male C57BL/6 mice aged postnatal day 28 mice (N = 2) were orally gavaged with sesame oil vehicle or 30 μg/kg TCDD every 4 days for 28 days. On day 28 (PND 52) livers were immediately collected, frozen in liquid nitrogen, and stored at -80°C. Nuclei were isolated from frozen livers, stained with DAPI, and subjected to FACS in order to generate a single nuclei suspension which was loaded onto the 10X Genomics Single Cell 3' V3 platform.

first: Kelly

middle: A

last: Fader

first: Sudin

last: Bhattacharya

first: Tim

last: Zacharewski


title: The transcriptome of a murine model of melanoma initiation and progression unravels molecular signatures of phenotype switch and novel independent prognostic factors for melanoma patients

status: Public on Aug 31 2020

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

summary: Despite advances in therapeutics, the progression of melanoma to metastasis still confers a poor outcome to patients. Nevertheless, there is a lack of biological models to understand cellular and molecular changes taking place along disease progression. Here, we analyzed the transcriptome of a multi-stage murine model of melanoma progression comprising a non-tumorigenic melanocyte lineage (melan-a), pre-malignant melanocytes (4C), non-metastatic (4C11-) and metastasis-prone (4C11+) melanoma cells. Clustering analyses have grouped the four cell lines according to their differentiated (melan-a and 4C11+) or undifferentiated/“mesenchymal-like” (4C and 4C11-) morphologies, suggesting dynamic gene expression patterns associated with the transition between these phenotypes. The cell plasticity observed in the murine melanoma progression is corroborated by molecular markers described for cell subtypes during human melanoma differentiation, as the differentiated cell lines in our model exhibit upregulation of transitory and melanocytic markers, whereas mesenchymal-like cells show increased expression of markers from undifferentiated and neural crest-like states. Sets of differentially expressed genes (DEGs) were detected at each transition step of tumor progression, and transcriptional signatures related to malignancy, metastasis and epithelial-to-mesenchymal transition were identified. Finally, DEGs were mapped to their human orthologs and subsequently evaluated in uni- and multivariate survival analysis using gene expression and clinical data of 703 drug-naïve primary melanoma patients, revealing several independent candidate prognostic markers. Altogether, these results provide novel insights into the molecular mechanisms underlying the phenotypic switch taking place during melanoma progression, reveal potential drug targets and prognostic biomarkers, and corroborate the translational relevance of this unique sequential model of melanoma progression.

overall_design: Total RNA-seq strand-oriented libraries (triplicate) from nonmalignant melanocytes (melan-a), non-tumorigenic pre-malignant melanocytes (4C), non-metastatic melanoma (4C11-)  and metastatic melanoma (4C11+) were pair-sequenced (2 x 100nt) in a Illumina HiSeq 1500 platform.

middle: M

first: Miriam

middle: G

last: Jasiulionis

first: Diogo

middle: O

last: Pessoa


title: MicroRNA expression profile of Apis mellifera ligustica brain tissue

status: Public on Dec 02 2020

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

country: China

institute: 6/5000 Shandong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We analyzed the changes in the brain tissue of Apis mellifera ligustica at the molecular level by sequencing after using fluvalinate. We found that the differentially expressed miRNAs (DEM) may be involved in hippocampal cell apoptosis and damage to memory functions. This result may be related to behaviors observed after the administration of this medication, such as a lack of homing at night and behavioral disturbances. Overall, our results provide new information about the molecular mechanisms and pathways of fluvalinate action in the brain tissue of Apis mellifera ligustica.

overall_design: Find the differentially expressed miRNAs in the brain tissues of Apis mellifera ligustica at different times after fluvalinate administration

last: Liuxu

first: Lou

last: Delong

first: Fan

last: Yunhan

first: He

last: Yu

first: Shan

last: Xueqing

first: Xia

last: Haitao

first: Wang

last: Guizhi


title: RNA-seq analysis of Ralstonia solanacearum treated with nitrosative and oxidative stress

status: Public on Oct 26 2020

city: Madison

first: Caitilyn

last: Allen

state: WI

address: Russell Labs 1630 Linden Drive

department: Plant Pathology

institute: University of Wisconsin-Madison

summary: Ralstonia solancearum causes bacterial wilt disease on diverse plant hosts. R. solanacearum cells enter a host from soil or infested water through the roots, then multiply and spread in the water-transporting xylem vessels. Despite the low nutrient content of xylem sap, R. solanacearum grows extremely well inside the host, using denitrification to respire in this hypoxic environment. R. solanacearum growth in planta also depends on the successful deployment of protein effectors into host cells using a Type III Secretion System (T3SS). The T3SS is absolutely required for R. solanacearum virulence, but it is metabolically costly and can trigger host defenses. Thus, the pathogen’s success depends on optimized regulation of the T3SS. We found that a byproduct of denitrification, the toxic free-radical nitric oxide (NO), positively regulates the R. solanacearum T3SS both in vitro and in planta. Using chemical treatments and R. solanacearum mutants with altered NO levels, we show that the expression of a key T3SS regulator is induced by NO in culture. Analyzing the transcriptome of R. solanacearum responding to varying levels of NO both in culture and in planta revealed that the T3SS and effectors were broadly upregulated with increasing levels of NO. This regulation was specific to the T3SS and was not shared by other stressors. Our results suggest that R. solanacearum experiences an NO-rich environment in the plant host and may use this NO as a signal to activate T3SS during infection.

overall_design: We analyze gene expression of WT R. solanacearum strain GMI1000 grown in denitrification-promoting low oxygen conditions in culture and when grown in tomato stems. Two mutant R. solanacearum strains, ∆narG, which cannot denitrify, and ∆norB, which accumulates nitric oxide (NO), were also analyzed both in culture and in tomato stems. In addition, we included two culture treatments, one with 100 uM hydrogen peroxide to induce oxidative stress, and one with the NO donor CysNO (1mM) to induce nitrosative stress. Each treatment or mutant included three biological replicates from separate overnight R. solanacearum cultures.

first: Connor

last: Hendrich

first: Alicia

middle: N

last: Truchon

first: Beth

middle: L

last: Dalsing


title: Suppression of p53 response by blocking p53–Mediator binding with a stapled peptide

status: Public on Aug 01 2020

city: Boulder

first: Dylan

middle: J

last: Taatjes

address: 3415 Colorado Ave JSC Biotechnology Building Campus Box 596

institute: University of Colorado at Boulder

summary: DNA-binding transcription factors (TFs) have been challenging to target with molecular probes.  Many TFs function in part through interaction with Mediator; we sought to block p53 function by disrupting the p53-Mediator interaction.  Through rational design and activity-based screening, we characterized a stapled peptide, with functional mimics of both p53 activation domains, that selectively disrupted p53- and Mediator-dependent transcription in vitro. This “bivalent peptide” also suppressed p53 transcriptional response in human cancer cells.  Our strategy circumvents the TF and instead targets the TF-Mediator interface, with desired transcriptional outcomes.  Different TFs target Mediator through different subunits, suggesting this strategy could be generalizable.

overall_design: Examination of p53 transcriptional activity by RNAseq with and without the inhibitory peptide in the presense of the p53 activator Nutlin3a.

first: Cecilia

last: Levandowski

first: Benjamin

first: Jonathan

last: Rubin

first: Timothy

last: Read


title: Metabolic Regulations by ceRNA under Grass-fed and Grain-fed regimens in Angus Beef Cattle

status: Public on Aug 06 2020

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University


title: Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

status: Public on Jul 23 2020

city: Tel Aviv

first: Aldema

last: Sas-Chen

state: Israel

address: Tel Aviv University

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel Aviv University

summary: N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification, present on tRNA, rRNA and recently investigated in eukaryotic mRNA. We report ac4C-seq, a chemical genomic method for single-nucleotide resolution, transcriptome-wide quantitative mapping of ac4C. While we did not find detectable ac4C sites in human and yeast mRNAs, ac4C was induced via ectopic overexpression of eukaryotic acetyltransferase complexes, invariably at a conserved sequence motif. In contrast, cross-evolutionary profiling reveals unprecedented levels of ac4C across hundreds of residues in rRNA, tRNA, ncRNA and mRNA from hyperthermophilic archaea. Ac4C is dramatically induced in response to temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Cryo-EM visualization of WT and acetyltransferase-deficient archaeal ribosomes furnishes structural insights into the temperature-dependent distribution of ac4C and its potential thermoadaptive role. Our studies quantitatively define the ac4C landscape, providing a technical and conceptual foundation for unravelling this modification’s role in biology and disease.

sample_organism:
Methanocaldococcus jannaschii
Pyrococcus furiosus
Saccharolobus solfataricus
Saccharomyces cerevisiae
Homo sapiens
Thermococcus sp. AM4
Thermococcus kodakarensis

overall_design: polyA-enriched RNA from HEK-293T WT (single sample) or Nat10+Thumpd1 overexpressing (2 replicates) cells under NaCNBH3, deacetylation or mock treatment. Total RNA from HeLa WT or Nat10 depleted cells (3 replicates each)  under NaCNBH3, deacetylation or mock treatment. polyA-enriched RNA from HeLa WT (3 replicates) or Nat10 depleted (2 replicates) cells under NaCNBH3 or mock treatment. Total RNA from M. jannaschiae  under NaCNBH3, deacetylation or mock treatment.  Total RNA from S. solfataricus  under NaCNBH3, deacetylation or mock treatment. Total RNA from T. sp. AM4 under NaCNBH3 or mock treatment, grown in 65, 75 and 85 degrees celsius. Total RNA from P. furiosus under NaCNBH3 or mock treatment, grown in 75, 85 and 95 degrees celsius. Total RNA from T. kodakarensis (T.kod) under NaCNBH3 or mock treatment, grown in 55 (1 sample), 65 (2 samples), 75 (2 samples), 85 (4 samples) and 95 (1 sample) degrees celsius. One of the replicates of 85 degree of T.kod underwent also deacetylation. Total RNA from T. kod strains deleted for TK0754 or TK2097 grown at 85 degrees and treated with NaCMBH3 or mock (in duplicates). T.kod purified ribosomes treated with NaCNBH3. rRNA-depleted RNA from WT T.kod grown at 85 and 95 degrees were treatedd with NaCNBH3 or NaCNBH3 and mock, respectively.

first: Schraga

last: Schwartz


title: Tramscriptomic and genomic analysis highlights the basis of ZYMV tolerance in zucchini

status: Public on Oct 20 2020

city: Cercola

first: Ciro

middle: Gianmaria

last: Amoroso

address: Viale Giotto 15

department: Agricultural science

country: Italy

institute: university of Naples Federico II

summary: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance.  In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days after inoculation (DPI) at transcriptomic and genomic levels. A comparative RNA-seq experiment, allowed to evaluate more than 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus and two synaptotagmin (SYTA) genes, key regulators of plant virus intercellular movement. Finally, transcripts mapping allowed the identification of two regions rich in SNPs (Single Nucleotide Polymorphisms) on linkage group 1 and linkage group 8, putatively introgressed from C. moschata, containing a putative disease resistance protein (CNL gene) exclusively expressed in 381e. In conclusion, 381e transcriptome analysis confirmed a globally improved plant fitness by reducing the effect of viral infection and showed the activation of genes putatively involved in tolerance to ZYMV. Our work provides new insight into plant virus recovery process to ZYMV.

overall_design: The RNA-seq experiment was conducted at 12dpi (days post inoculation) on two isogenic lines, a tolerant ZYMV line (381e) and a susceptible line (True French).

first: Giuseppe

last: Andolfo

first: Claudio

last: Capuozzo

first: Antimo

last: Di Donato

last: Martinez

first: Laura

last: Tomassoli

first: Maria

last: Ercolano


title: Single Cell RNA Sequencing of Human Milk-Derived Cells Reveals Sub-Populations of Mammary Epithelial Cells with Molecular Signatures of Progenitor and Mature States: a Novel, Non-invasive Framework for Investigating Human Lactation Physiology

status: Public on Nov 12 2020

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary: Milk derived live mammary epithelial cells were characterized by single cell RNA sequencing.

overall_design: Cells were pelleted from mid-feed milk samples prior to cryopreservation and subsequent analysis by single cell RNA sequencing.

first: Jayne

middle: F

last: Martin Carli

middle: C


title: microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs (RNA-seq)

status: Public on Jul 17 2020

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

summary: RNA-seq of RNA isolated form costal chondrocytes of mice at post-natal day 7

overall_design: RNA-seq of costal chondrocytes from wild-type (n=4) and MiR140-null mice (n=4). All mice lines initially generated from heterozygous miR140+/- mice

first: Yao

last: Hao

first: Kathleen

last: Cheung


title: microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: exosomal ELNAT1 promotes lymphatic metastasis of bladder cancer

status: Public on Nov 16 2020

city: Guangzhou

first: Yuming

last: Luo

state: Guangdong

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

institute: Sun yat-sen Memorial Hospital

summary: The crosstalk between tumor cells and LECs triggers the LN metastasis in bladder cancer (BCa), but the underlying mechanisms are not completely understood. Previously, we identified that BCa-secreted extracellular vesicles (EVs)-packaged lncRNAs mediated the communication with LECs and promoted LN metastasis. To evaluate whether EV-packaged lncRNAs triggered the LN metastasis of BCa, next-generation sequencing (NGS) to the global expression profiles of lncRNAs was utilized in the urinary EVs (urinary-EV) of five MIBC patients and five healthy volunteers.

overall_design: To identify EV-packaged lncRNAs involved in the progression of bladder cancer, NGS was performed in the urinary EVs of five MIBC patients and five healthy volunteers. The RNA from urinary EVs was extracted and enriched with PCR to create the final cDNA library, which was sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System.

first: Changhao

last: Chen

first: Tianxin

last: Lin


title: Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model (ATAC-Seq)

status: Public on Jul 09 2020

city: Beijing

first: Yaqi

last: Wang

address: Changchun Street No.45

institute: Xuanwu Hospital,Capital Medical University

summary: The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was used to investigate the AD-associated chromatin reshaping in the APPswe/PS1dE9 (APP/PS1) mouse model. ATAC-seq data in the hippocampus of 8-month-old APP/PS1 mice were generated, and the relationship between chromatin accessibility and gene expression was analyzed in combination with RNA-sequencing.We identified 1690 increased AD-associated chromatin accessible regions in the hippocampal tissues of APP/PS1 mice and 1003 decreased chromatin accessible regions were considered to be related with declined AD-associated biological processes.In the APP/PS1 hippocampus, 1090 genes were found to be up-regulated and 1081 down-regulated. Interestingly, enhanced ATAC-seq signal was found in approximately 740 genes, with 43 exhibiting up-regulated mRNA levels.Our study reveals that alterations in chromatin accessibility may be an initial mechanism in AD pathogenesis.

overall_design: ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2015).

first: X

last: Zhang

first: Q

last: Song

first: Y

last: Hou

first: J

last: Liu

first: P


title: Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

status: Public on Aug 21 2020

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

summary: Alternative RNA 3’-end processing provides an important source of transcriptome diversification, which impacts various biological processes and the etiology of diseases, including cancer. A prime example of this is the transcript isoform switch that leads to the read-through expression of the long non-coding RNA NEAT1_2, at the expense of the shorter polyadenylated transcript NEAT1_1. Expression of NEAT1_2 is required for the formation of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. Searching for proteins that modulate this isoform switching event we identified factors involved in the 3’-end processing of polyadenylated (pA+) RNA as well as several components of the Integrator complex. Perturbation experiments established that, by promoting the cleavage of NEAT1_2, Integrator forces NEAT1_2 to NEAT1_1 isoform switching and, thereby, restrains PS assembly. Consistently, low expression levels of several Integrator subunits correlated with poorer prognosis of cancer patients exposed to chemotherapeutics. Our study identifies Integrator as a key regulator of PS biogenesis and establish a link between Integrator, cancer biology and chemosensitivity, which may be exploited therapeutically.

overall_design: enhanced UV crosslinking and immunoprecipitation (eCLIP) is a method for identifying protein binding sites to RNA. INTS11 is the catalytic subunit of the Integrator complex. eCLIP followed by high-throughput sequencing of INTS11 in HeLa cells. Two different antibodies of INTS11 (ab75276, HPA029025), size-matched input and IgG controls in duplicates

first: Jasmine

last: Barra

first: Gabriel

last: Gaidosh

first: Ezra

last: Blumenthal

first: Mina

last: Tayari

first: Nina

last: Kirstein

first: Tobias

middle: K

last: Karakach

first: Torben

middle: H

last: Jensen

first: Francis

last: Impens

first: Kris

last: Gevaert

first: Eleonora

last: Leucci

first: Ramin

last: Shiekhattar

first: Jean-Christophe

last: Marine


title: Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model (RNA-Seq)

first: Yaqi

last: Wang

overall_design: Hippocampal mRNA profiles of 8-month old wild type(WT) and  APPswe/PS1dE9(APP/PS1) double transgenic mice were generated by deep sequencing, in triplicate,using Illumina Hiseq 150PE.

first: X

last: Zhang

first: Q


title: RNA-Sequencing of Chronic hypersensitivity pneumonitis compared with Idiopathic Pulmonary Fibrosis and Control Lung

status: Public on Jul 01 2020

city: Aurora

first: Ivana

last: Yang

institute: University of Colorado Anschutz Medical Campus

summary: Chronic hypersensitivity pneumonitis (CHP) is caused by an immune response to antigen inhalation and is characterized by variable histopathological and clinical features. A subset of CHP subjects have usual interstitial pneumonia and appear to be clinically similar to subjects with idiopathic pulmonary fibrosis (IPF). However, the molecular relationship between CHP and IPF is not well understood. We report an RNA-seq based transcriptomic analysis for whole lung tissues from CHP, IPF and control subjects.

overall_design:
To determine the common and unique molecular features of CHP and IPF, transcriptome analysis of lung samples from CHP (N=82), IPF (N=103), and unaffected controls (N=103) was conducted. Differential gene expression was determined adjusting for sex, race, age and smoking history, and using false discovery rate (FDR) to control for multiple comparisons.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: H

last: Furusawa

first: David

last: Schwartz

first: Jonathan

last: Cardwell


title: Single-nucleus RNA-seq reveals dysregulation of striatal cell identity due to Huntington’s disease mutations

status: Public on Jul 11 2020

city: Baltimore

first: Sonia

last: Malaiya

state: Maryland

address: 209, Roundhouse Ct.

department: Institute of Genome Science

institute: University of Maryland

summary: Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide expansion in exon 1 of the huntingtin (Htt) gene. Cell death in HD occurs primarily in striatal medium spiny neurons (MSNs), but the involvement of specific MSN subtypes and of other striatal cell types remains poorly understood. To gain insight into cell type-specific disease processes, we studied the nuclear transcriptomes of 4,524 cells from the striatum of a genetically precise knock-in mouse model of the HD mutation, HttQ175/+, and from wildtype controls. We used 14-15-month-old mice, a time point roughly equivalent to an early stage of symptomatic human disease. Cell count distributions indicated selective loss of D2 MSNs and increased microglia in aged HttQ175/+ mice. Thousands of differentially expressed genes were distributed across most striatal cell types, including transcriptional changes in glial populations that are not apparent from RNA-seq of bulk tissue. Reconstruction of cell type-specific transcriptional networks revealed a striking pattern of bidirectional dysregulation for many cell type-specific genes. Typically, these genes were repressed in their primary cell type, yet de-repressed in other striatal cell types. Integration with existing epigenomic and transcriptomic data suggest that partial loss-of-function of the Polycomb Repressive Complex 2 (PRC2) may underlie many of these transcriptional changes, leading to deficits in the maintenance of cell identity across virtually all cell types in the adult striatum.

overall_design: Single nucleus RNA sequencing of striatums of three wild type (WT) and four HttQ175/+ 14-15 month old mice

first: Marcia

last: Cortes-Gutierrez

first: Brian

middle: R

last: Herb

first: Sydney

last: Coffey

first: Samuel

last: Legg

first: Jeffrey

middle: P

last: Cantle

first: Carlo

last: Colantuoni

last: Carroll

first: Seth

last: Ament


title: Memory OT-I cells

status: Public on Sep 30 2020

city: Bronx

first: Shu Shien

last: Chin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

overall_design: Refer to individual Series


title: Integrative transcriptomic characterization of matched primary and hepatic metastases of pancreatic ductal adenocarcinoma

status: Public on Jun 02 2020

city: Shanghai

first: Ping

last: Lin

address: No.320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

summary:
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers due to its high metastasis rate in liver. However, little is known about the molecular features of hepatic metastases due to difficulty in obtaining fresh tissues and low tumor cellularity.
Methods and Results: We conducted RNA sequencing for synchronous surgically resected PTs and the paired HMs from 14 hepatic oligometastatic PDACs and experimentally validated our findings in specimens from 35 of such cases. The comprehensive analysis of gene expressions showed largely similarity between PTs and HMs. However, hepatic metastases also showed unique characteristics, such as stronger abilities of proliferation, downregulation of EMT activity and metabolic rewiring. More interesting, altered tumor microenvironments were observed in hepatic metastases, especially higher proportion of tumor infiltrating M2 macrophage and upregulation of complement cascade. Further experiments demonstrate that expression of C1q increased continuously from normal to PTs to HMs, C1q was mainly produced from M2 macrophage, and C1q promoted migration and invasion of PDAC cells.
Conclusion: Taken together, we found potential factors that contribute to different stages of PDAC metastasis. Our study broadens the understandings of molecular mechanisms driving PDAC metastasis.

overall_design:
To decipher the transciptomic heterogeneity between HMs and paired PTs and unravel the molelcular mechanisms of PDAC metastasis, 33 freshly frozen specimens from 14 treatment-naϊve PDACs (6 N-PT-HM trios, 7 PT-HM pairs, and 1 HM) were subjected to RNA sequencing.
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Authors state "Raw data was available from National Omics Data Encyclopedia (NODE) database (http://www.biosino.org/node/project/detail/OEP000481). Restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of NODE committee."

first: Yongwei

last: Sun

first: Hong

last: Li

first: Yixue

first: Jing

last: Xue

first: Jianyu

first: Minwei


title: Cell type-specific oxidative stress genomic signatures in the globus pallidus of dopamine depleted mice

status: Public on Sep 07 2020

city: Pittsburgh

first: Alyssa

last: Lawler

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: We developed a new viral affinity purification strategy, Cre-Specific Nuclear Anchored Independent Labeling (cSNAIL), to isolate Cre recombinase-expressing (Cre+) nuclei from the adult mouse brain. cSNAIL is an AAV that delivers a modified version of the nuclear-anchored protein tag developed for INTACT nuclei isolation (Deal & Henikoff, Dev Cell. 2010. 18:1030-1040; Mo et al., Neuron. 2015. 86(6):1369-1384). Applying cSNAIL technology in Pvalb-2A-Cre mice, we performed targeted assessment of the cell type-specific transcriptomic and epigenetic effects of dopamine depletion on parvalbumin-expressing (PV+) neurons and PV- nuclei. We recovered signatures of oxidative stress response involving Hif2a signaling that was specific to external globus pallidus (GPe) PV+ neurons, a consequence of dopamine depletion that may have theraputic implications for Parkinson's disease.

overall_design: We collected RNA-seq and ATAC-seq from cSNAIL-isolated populations of PV neurons and remaining cells in the mouse isocortex, striatum, and GPe. The subjects were either dopamine depleted via acute, bilateral 6-hydroxydopamine (6-OHDA) lesion, or healthy controls that recieved a sham surgery. Both sexes were represented in both treatment groups.

first: Ashley

last: Brown

first: Rachel

middle: S

last: Bouchard

first: Noelle

last: Toong

first: Yeonju

last: Kim

first: Nitinram

last: Velraj

first: Grant

last: Fox

first: Michael

last: Kleyman

first: Byungsoo

last: Kang

first: Aryn

last: Gittis

first: Andreas

last: Pfenning


title: Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment

status: Public on May 12 2020

city: Lausanne

first: Ana

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

summary: Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted. Several computational methods to estimate RNA processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate RNA processing and degradation rates from a single sample. To this end, we use the Zeisel model and take advantage of its analytical solution, reducing the problem to solving a univariate non-linear equation on a bounded domain. The approach is computationally rapid and enables inference of rates that correlate well with previously published datasets. In addition to saving experimental work and computational time, having a sample-based rate estimation has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and perform quality control. Finally the method and theoretical results described here are general enough to be useful in other settings such as nucleotide conversion methods.

overall_design: Wildtype mouse embryonic stem cells (mESCs) were labeled with 4-thiouridine for 10 minutes. Biochemical separation was then used to separate the pool of transcripts containing 4sU (newly transcribed RNA) from the preexisting RNA. Newly transcribed and preexisting RNA were sequenced on Illumina HiSeq 2500.

first: Micha

last: Hersch

first: Adriano

last: Biasini

first: Sven

last: Bergmann


title: Single cell transcriptomics analysis of bone marrow mesenchymal lineage cells

status: Public on May 01 2020

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

summary: Bone marrow mesenchymal lineage cells are a heterogeneous cell population involved in bone homeostasis and diseases such as osteoporosis. While it is long postulated that they originate from mesenchymal stem cells (MSCs), the true identity of MSCs and their in vivo bifurcated differentiation routes into osteoblasts and adipocytes remain poorly understood. Here, by employing large scale single cell transcriptome analysis, we computationally defined MSCs and delineated their bi-lineage differentiation paths in young, adult and aging mice. One identified subpopulation is a unique cell type that expresses adipocyte markers but contains no lipid droplets. As non-proliferative precursors for adipocytes, they exist abundantly as pericytes and stromal cells that form a ubiquitous 3D network inside the marrow cavity. Functionally they play critical roles in maintaining marrow vasculature and suppressing bone formation. Therefore, we name them marrow adipogenic lineage precursors (MALPs) and conclude that they are a new component of marrow adipose tissue.

overall_design: 4 batches of single cell libraries for sequencing: endosteal Td+ bone marrow cells from 1-month-old (n=2), 1.5-month-old (n=3), 3-month-old (n=3) and 16-month-old (n=3) male Col2/Td mice. 20,000 cells were loaded in aim of acquiring one single library of 10,000 cell for each age group by Chromium controller (V3 chemistry version, 10X Genomics Inc, San Francisco, USA), barcoded and purified as described by the manufacturer, and sequenced using a 2x150 pair-end configuration on an Illumina HiSeq platform at a sequencing depth of ~400 million reads.

first: Leilei

last: Zhong

first: Robert

last: Tower

first: Yulong

last: Wei

first: Zhen

last: Miao

first: Jihwan

last: Park

first: Rojesh

last: Shrestha

first: Luqiang

last: Wang

first: Wei

last: Yu

first: Nicholas

last: Holdreith

first: Yejia

last: Zhang

last: Tong

first: Yanqing

last: Gong

first: Jaimo

last: Ahn

first: Katalin

last: Susztak

first: Nathaniel

last: Dyment

first: Mingyao

last: Li

first: Fanxin

last: Long

first: Chider

last: Chen

first: Patrick

last: Seale

first: Ling

last: Qin


title: Ribosome Footprinting of WT and mutant yeast cells at different temperatures

status: Public on Apr 30 2020

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

summary: We use ribosome footprinting to assess the gene expression changes occuring after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C). We find that between 40°C and 42°C there is a shift in gene expression from the expression of genes harboring long and structured 5'UTRs to the expression of genes harboring thranscripts with short and unstructure 5'UTRs. We performed these experiments for WT yeast cells as well as for mutant yeast cells in which the RNA helicase Ded1 condensates at lower temperatures (Ded1-IDRm). We find upon comparing mutant and WT cells at 42°C, that Ded1-IDRm has increased expression of genes harboring unstructured 5'UTRs and decreased expression of genes harboring structured 5'UTRs.

overall_design: Ribosome Footprinting of WT and mutant yeast cells after 10 minutes at 30, 40 or 42°C

first: Ulrike

last: Friedrich

first: Christiane

last: Iserman

first: Lena

last: Hersemann

first: Günther

last: Kramer

first: Simon

last: Alberti


title: RNA-sequencing of CWR22Rv1 cell line following shRNF8 and DHT treatment

first: Tingting

last: Zhou

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area

department: Institute of Translational Medicine

institute: China Medical University

summary: RNA sequencing for 6 samples.

overall_design: Examing 2 conditions, each with 3 replicates


title: Integration of transcriptome and proteome analyses reveiled molecular mechanisms for formation of replant disease in Nelumbo nucifera

city: Zhengzhou

first: chen

last: dong

address: 100 Lianhua Street

institute: Henan University of Technology

summary: The normal growth of Nelumbo nucifera, a widely planted aquatic crop in Asia, was severely ruined by replant disease. To investigate changes of transcripts in response to replant disease, transcriptomic analyses were performed by comparing seedings of first-year planting  (FP) and consecutive planting  (CP). 9810 differentially expressed genes (DEGs) were identified between FP and CP. Based on the biological function of these target genes, the signal pathway of consecutive monoculture was illustrated in N.nucifera. The experiments aimed to provide data for unveiling the molecular characteristics of replant disease, and explore our understanding of replant disease in aquatic botony.

overall_design: mRNA profiles of first-year planting group (FP) and consecutively planting group (CP) in rhizomes of N.nucifera were generated by deep sequencing, in triplicate.

first: Chen

last: Dong


title: Intergenic DNA organization in the mammalian nervous system

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

summary: Eukaryotic genomes largely consist of non-coding DNA regions. Most non-coding DNA resides in intergenic DNA regions located between a gene and its nearest gene. Here, we demonstrate the relationship between intergenic DNA and gene regulation throughout the mammalian nervous system.

overall_design: Examination of total RNA profiles of mouse ES cell-derived spinal motor neurons by deep sequencing.

first: Ravneet

last: Jaura

first: Kaitlin

last: Montanera

first: Ho


title: Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model

first: Yaqi

last: Wang

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


title: A complex regulatory landscape involved in the development of external genitals [CnR]

status: Public on Apr 25 2020

first: Ana Rita

middle: Amandio

last: Lhopitallier

address: SV2842, Station 19

department: SV-ISREC-EPFL

institute: EPFL

summary: In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we use a TAD flanking the HoxD gene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. We suggest that this TAD can be considered as a coherent functional unit in itself, with several regulatory sequences acting together to elicit a transcriptional response. With one notable exception, the deletion of each of these sequences in isolation did not produce any substantial modification in the global transcriptional outcome of the system, a result at odds with a conventional view of long-range enhancer function. Likewise, both the deletion and inversion of a CTCF site located in a region rich in such sequences did not affect transcription of the target gene. In the latter case, however, slight modifications were observed in interaction profiles in vivo in agreement with the loop extrusion model, despite no apparent functional consequences. We discuss these unexpected results by considering both conventional explanations and an alternative possibility whereby a rather unspecific accumulation of particular factors within the TAD backbone may have a global impact upon transcription.

overall_design: CUT&RUN analysis of HOXA13 in genital tubercle (GT) or in the cloaca region (CR) of wildtype mouse embryonic tissues. CTCF CUT&RUN analysis of Inv(V) E13.5 GT.

first: Ana

first: Denis

last: Duboule


title: A complex regulatory landscape involved in the development of external genitals


title: Fra-2 overexpression upregulates pro-metastatic cell-adhesion molecules, promotes pulmonary metastasis and reduces survival in a spontaneous xenograft model of human breast cancer

status: Public on Apr 06 2020

city: Moscow

first: Diana

last: Maltseva

address: Myasnitskaya str. 13/4

department: Faculty of Biology and Biotechnology

country: Russia

institute: National Research University Higher School of Economics

summary:
The effect of Fra-2 overexpression in two stable Fra-2 overexpressing clones of the human breast cancer cell line MDA-MB-231 on survival and metastatic load was studied after subcutaneous injection into scid and E- and P-selectin deficient scid (select) mice. To identify Fra-2 target genes, we performed cDNA microarrays with mRNA isolated from xenograft tumour tissue.
Fra-2 overexpression lead to a significantly shorter overall survival and a higher amount of spontaneous metastases in scid mouse lungs and compared to select mice indicating that Fra-2 regulates selectin binding sites on the tumour cell surface, which directly influence overall survival. By using cDNA microarray analysis of resected primary tumours a multitude of deregulated genes, which are known to be involved in metastasis formation

overall_design: The cells of two clones of MDA-MB231 line with Fra-2 overexpression (clone 1 and clone 2) as well as control cells were injected subcutaneously into scid mice and E- and P-selectin double knock-out scid mice (select). mRNA was isolated from xenograft tumour tissue (three tumours per group) and analyzed using Affimetrix transcriptome arrays.

first: Sabrina

last: Arnold

first: Jan

last: Kortland

middle: V

first: Timur

last: Samatov

first: Susanne

last: Lezius

first: Alexander

last: Tonevitsky

first: Karin

last: Milde-Langosch

first: Daniel

last: Wicklein

first: Udo

last: Schumacher

first: Christine

last: Stürken


title: MicroRNA-based subtypes in head and neck squamous cell carcinoma

status: Public on Apr 01 2020

city: Memphis

first: Jeremiah

middle: Ray

last: Holt

state: TN

address: 19 S. Manassas, Room 202

department: Medicine

institute: UTHSC

summary:
Highly coordinated, deregulated expressions of microRNAs (miRNA) have been implicated in the development of various cancers, including head and neck squamous cell carcinoma (HNSCC). Outside of HPV infection, molecular classification of HNSCC is lacking, and patient stratification by anatomical location and stage does not account for the heterogenous clinical courses seen. Previous studies have proposed molecular classifications based on gene expression, but none describe the role of microRNA expression in HNSCC subtyping.
In this study, we identified reliable miRNA clusters that can be used to subclassify HNSCC tumors as well as other squamous tumors of other anatomic locations. An institutional discovery cohort was generated using miRNA expression data from microarrays, and this was validated using publicly available next-generation microRNA sequencing data from TCGA. Further analysis of these subtypes revealed distinct biological and clinical features of HNSCC tumors based on the miRNA expression profiles, which provides new insights into the pathogenesis and treatment of HNSCC.

overall_design: A total of 115 tumor samples were considered. Quality control procedures were applied to microarray probe-level intensity files, and a total of 88 tumor arrays remained after removal of duplicate arrays, low-quality arrays, and arrays from non-HNSCC samples. Probe-level data was quantile normalized, and RMA expression values were used from probes matched to 825 mature microRNA sequences. Samples HN008 - HN159 were used to profile mRNA expression in a previous study (Series GSE39366).


title: State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Leukemia Development

status: Public on Apr 23 2020

city: Duarte

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: Temporal dynamics of gene expression are informative of changes associated with disease development and evolution. Given the complexity of high-dimensionaltemporal datasets, an analytical framework guided by a robust theory is needed to interpret time-sequential changes and to predict system dynamics. Herein, we use acute myeloid leukemia as a proof-of-principle to model gene expression dynamics in a transcriptome state-space constructed based on time-sequential RNA-sequencing data. We describe the construction of a state-transition model to identify state-transition critical points which accurately predicts leukemia development. We show an analytical approach based on state-transition critical points identifies step-wise transcriptomic perturbations driving leukemia progression. Furthermore, the gene(s) trajectory and geometry of the transcriptome state-space provides biologically-relevant gene expression signals that are not synchronized in time, and allows quantification of gene(s) contribution to leukemia development. Therefore, our state-transition model can synthesize information, identify critical points to guide interpretation of transcriptome trajectories and predict disease development.

overall_design: We conducted a longitudinal study in a mouse AML model induced by the Cbfb-MYH11 (CM) oncogene to observe the temporal evolution of the transcriptome from healthy state to leukemia state. In the conditional CM knock-in mouse model (Cbfb+/56MMx1Cre), expression of CM in the adult bone marrow alters normal hematopoietic differentiation creating aberrant pre-leukemic progenitor cells which acquire additional genetic, epigenetic alterations needed for malignant transformation and AML development. In a cohort of CM mice (Cbfb+/56MMx1Cre; N=7) and littermate controls (Ctrl; N=7) lacking one or both transgenes (Cbfb+/56M or  Mx1Cre), peripheral blood was sampled prior to and following CM induction (by poly (I:C) treatment) monthly for up to 10 months (or when mice were moribund with leukemia). Blood samples were subjected to bulk RNA-sequencing and flow cytometry analysis.

first: Russell

last: Rockne

first: Sergio

last: Branciamore

first: Jing

last: Qi

first: David

last: Frankhouser

last: O’Meally

first: Wei-Kai

last: Hua

first: Guerry

first: Emily

last: Carnahan

first: Lianjun

last: Zhang

first: Ayelet

last: Marom

first: Herman

last: Wu

first: Davide

last: Maestrini

first: Xiwei

first: Yate-Ching

last: Yuan

first: Zheng

last: Liu

first: Leo

middle: D

first: Stephen

last: Forman

first: Nadia

last: Carlesso

first: Ya-Huei

last: Kuo

first: Guido

last: Marcucci


title: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to tomato media

status: Public on Mar 31 2020

city: Braunschweig

first: Jasper

last: Schierstaedt

address: Messeweg 11-12

department: EP

institute: Julius kühn-Institute

summary:
Summary: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to tomato medium (TM) and tomato root exudates (TX) compared to minimal medium (MM).
Purpose: Salmonella mRNA profile, when grown in different media was compared to minimal medium to reveal environment specific transcriptional changes.
Methods: mRNA profiles were generated using Illumina HiSeq in triplicates. The sequences were analysed using Bowtie2 followed by Cufflinks.

overall_design: mRNA profiles of Salmonella were generated using Illumina HiSeq in triplicates.

first: Sven

last: Jechalke

first: Azhar

last: Zarkani

first: Klaus

last: Neuhaus

first: Adam

last: Schikora


title: Sputum and blood transcriptomics characterization of the PDE4 inhibitor CHF6001 in COPD

status: Public on Mar 30 2020

city: Parma

first: Mirco

last: Govoni

address: Largo Francesco Belloli 11A

department: Global Clinical Development

institute: Chiesi Farmaceutici SpA

summary: The aim of the present study was to characterize the gene expression profile of the phosphodiesterase-4 inhibitor CHF6001 on top of inhaled triple therapy in sputum cells and whole blood of chronic bronchitis patients.  Samples for analyses were collected from a multicenter, three-period, three-way, placebo-controlled, double-blind, complete block crossover study. Eligible patients underwent three, 32-day treatment periods during which they received CHF6001 800 or 1600 µg twice daily (total daily doses of 1600 or 3200 µg) or matching placebo, all via multi-dose dry-powder inhaler (NEXThaler). Treatment periods were separated by a 28–42 day washout. Eligible patients were male or female, ≥40 years of age, current or ex-smokers with a smoking history ≥10 pack-years, a diagnosis of COPD, post-bronchodilator forced expiratory volume in 1 second (FEV1) ≥30% and <70% predicted, ratio of FEV1 to forced vital capacity (FVC) <0.70, COPD Assessment Test score ≥10, and a history of chronic bronchitis (defined as chronic cough and sputum production for more than three months per year for at least two years) and treated with inhaled triple ICS/LABA/LAMA therapy for at least two months prior to enrollment. CHF6001 had no effect in blood, but a strong effect in sputum with 1471 and 2598 significantly differentially-expressed probe-sets relative to placebo (p-value adjusted for False Discovery Rate<0.05) for 800 and 1600µg , respectively. Functional enrichment analysis showed significant modulation of key inflammatory pathways involved in cytokine activity, pathogen-associated-pattern-recognition activity, oxidative stress and vitamin D with associated inhibition of downstream inflammatory effectors. A large number of pro-inflammatory genes coding for cytokines and matrix-metalloproteinases were significantly differentially expressed for both doses; the majority (>87%) were downregulated, including macrophage inflammatory protein-1-alpha and 1-beta, interleukin-27-beta, interleukin-12-beta, interleukin-32, tumor necrosis factor-alpha-induced-protein-8, ligand-superfamily-member-15, and matrix-metalloproteinases-7,12 and 14.  In conclusion inhaled PDE4-Inhibition by CHF6001 on top of triple therapy in patients with chronic bronchitis patients significantly modulated key inflammatory targets and pathways in the lung but not in blood. Mechanistically these findings support a targeted effect in the lung while minimizing unwanted systemic class-effects

overall_design: Sputum cells and whole blood samples were profiled on Affymetrix U133 Plus 2.0 microarrays. Induced sputum was collected for analysis at pre-dose and 2 h post-dose on Days 20 or 26 or 32. Whole blood was collected for analysis at pre-dose on Day 1 and 2 h post-dose on Day 32. In blood,  51, 54 and 55 post-dose samples for placebo, 800 and 1600 µg twice daily, respectively and 45, 48, 45 pre-dose samples for placebo, 800 (mid) and 1600 µg (high) twice daily, respectively, have been used for analysis. In sputum  43, 41 and 41 post-dose samples for placebo, 800 and 1600 µg twice daily, respectively, and 30, 36, 38 pre dose samples for placebo, 800 and 1600 µg twice daily, respectively, have been used for analysis

first: Michele

last: Bassi

first: Stefano

last: Vezzoli

first: Germano

last: Lucci

first: Aida

last: Emirova

first: Marie

middle: A

last: Nandeuil

first: Gianluigi

last: Poli

last: Petruzzelli

first: Gera

last: Jellema

first: Ebenezer

last: Afolabi

first: Brendan

last: Colgan

first: Brian

last: Leaker

first: Oliver

last: Kornmann

first: Kai

middle: M

last: Beeh

first: Henrik

last: Watz

first: Dave

last: Singh


title: African American hepatocyte genotype

status: Public on Mar 27 2020

city: Chicago

first: Minoli

last: Perera

address: 303 E Chicago Ave.

department: Pharmacology

institute: Northwestern Univeristy

summary: African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes.  To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix.  We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL.  These AA-specific eQTLs are less correlated to GTEx eQTL in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs).  We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci.  Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes.  Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.

overall_design: 96 DNA samples from hepatocytes were genotyped using an Illumina Multi-Ethnic Genotyping array (MEGA), including three replicates, and four blank samples.

first: C

last: Park

first: Tanima

last: De

first: Y

last: Xu

first: Yizhen

last: Zhong

first: E

last: Smithberger

first: Cristina

last: Alarcon

last: Gamazon


title: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to soil media

first: Jasper

last: Schierstaedt

summary:
Summary: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to DS soil suspension (DS) and suspension of autoclaved DS soil (DA) compared to minimal medium (MM).
Purpose: Salmonella mRNA profile, when grown in different media was compared to minimal medium to reveal environment specific transcriptional changes.
Methods: mRNA profiles were generated using Illumina HiSeq in triplicates. The sequences were analysed using Bowtie2 followed by Cufflinks.

first: Sven

last: Jechalke

first: Klaus

last: Neuhaus

first: Adam

last: Schikora


title: Extracellular matrix-inducing Sox9 orchestrates basal progenitor proliferation and gliogenesis in developing neocortex

first: Scientific Computing

last: Facility

summary: Neocortex expansion is largely based on the proliferative capacity of basal progenitors (BPs), which is increased by extracellular matrix (ECM) components via integrin signaling. Here we show that Sox9 drives expression of ECM components and that laminin 211 increases BP proliferation in embryonic mouse neocortex. Examination of Sox9 expression reveals that Sox9 is expressed in BPs of developing ferret and human, but not mouse neocortex. Functional studies by conditional Sox9 expression in the mouse BP lineage demonstrate increased BP proliferation, reduced Tbr2 and induction of Olig2 expression, indicative of premature gliogenesis. Conditional Sox9 expression also results in cell non-autonomous stimulation of BP proliferation followed by increased production of upper-layer neurons. Collectively, our findings demonstrate that Sox9 exerts concerted effects on transcription, BP proliferation, neuron production, and neurogenic as well as gliogenic BP cell fate, suggesting that Sox9 acts a master regulator in the subventricular zone to promote neocortical expansion.

overall_design: Comparison of transcriptomes and analysis of differentially expressed genes in embryonic mouse basal progenitors, electroporated with either control construct (referred as control) or with a conditional Sox9 expression construct (referred as Sox9). Control had 3 replicates, Sox9 had 4 replicates.

first: Ayse

last: Guven

first: Marta

last: Florio

first: Holger

last: Brandl

first: Wieland

middle: B

last: Huttner


title: RNA-seq data from Giardia intestinalis WB trohozoites infecting human Caco-2 cells

status: Public on Feb 20 2020

city: Uppsala

first: Feifei

address: Husargatan 3

country: Sweden

institute: Uppsala University

sample_organism:
Giardia duodenalis
Homo sapiens

platform_organism:
Giardia duodenalis
Homo sapiens

overall_design: In this study we compare at the transcriptomic level, how giardia and human gene expresion changes over time when Giardia trophozoites infect human Caco-2 cells

first: Showgy

last: Ma'ayeh


title: Immune microenvironment evolution and tumor metabolism reprograming during treatment of Bevacizumab containing regimen in CLM patients

status: Public on Mar 08 2020

city: Guangzhou

first: Dongqiang

last: Zeng

address: NO.1838 North Guangzhou Avenue

department: Medical oncology

institute: Southern Medical University

summary: We examined how the immune microenvironment molds tumor evolution in a longitudinal dataset of colorectal cancer liver metastases. Through multiplexed analyses, the immune microenvironment exerts a strong selection pressure during treatment of CLM tumor. Increasing infiltration of T cell were associated with favorable outcomes and sensitive response to chemotherapy ± Bevacizumab. Activation of fatty acid metabolism, xenobiotic metabolism, insulin receptor signaling pathway and neutrophils infiltration were observed in progressive tumors. TCR diversity in response metastatic regions was significantly increased compared with non-responder. Bevacizumab containing regimen facilitated T cell infiltrating to the tumor microenvironment which might consequently benefit from checkpoint immunotherapy. In responding patients, mutation load from plasma were reduced from baseline, but changed slightly in tumor tissues. This integrative and comparative omics analysis provides a new paradigm for understanding the evolution and treatment resistance of colorectal cancer liver metastases, with implications for identifying ways to advance treatment regimen and monitoring treatment response of colorectal cancer liver metastases.

overall_design:
We analyzed clinical outcomes and molecular features of longitudinal specimens prospectively collected from 15 patients with CLM

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Wangjun

last: Liao

first: Min

last: Shi

last: Huang

first: Jing

last: Li

first: Yuqi

last: Wang

first: Chunlin

first: Xiaoxiang

last: Rong

first: Yisheng

last: Fang

first: Jin

first: Jiao

first: Miaohong

first: Siting

last: Zheng

first: Yichen

last: Xue

first: Jian

last: Guo

first: Junhao

last: Zhang

first: Zilan

last: Ye

first: Yulin

first: Jianping

last: Bin


title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [CRISPR screen]

status: Public on Jun 22 2020

city: New York

first: Andrew

last: Ji

state: NY

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai

summary: To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and  site-matched normal skin

overall_design: SCC cell lines were infected with a CRISPR sgRNA library of 334 genes (and 136 non-targeting sgRNA controls) and grown either as xenograft tumors in immunocomprised mice or in vitro, followed by sequencing of sgRNAs

middle: L

first: Adam

middle: J

last: Rubin


title: Skeletal and limb anomalies as a result of mutation in hnrnpul1 in zebrafish

status: Public on Feb 05 2020

city: Calgary

first: Sarah

last: Childs

state: AB

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Mutations in RNA binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb and neurological symptoms. Here, we show a developmental role for hnrnpul1 in the zebrafish limb, craniofacial development and in adult onset scoliosis. Furthermore, we demonstrate for the first time a role of hrnpul1 in alternative splicing regulation.

overall_design: 3 wild type bio reps, 3 double homozygous hnrnpul1/1l mutant bio reps

first: Danielle

last: Blackwell

first: Sherri

last: Fraser

first: Oana

last: Caluseriu

first: Claudia

last: Vivori

first: Paul

last: Gordon

first: Amanda

last: Tyndall

first: Ryan

middle: E

last: Lamont

first: Jillian

last: Parboosingh

first: A

last: Innes

first: Francois

last: Bernier


title: To measure extension longevity effect of soraprazan and identify the mechanism

status: Public on Jan 23 2020

city: Seoul

first: Miae

last: Oh

address: Anam 145

institute: Korea University

summary: Lipofuscin is known as intracellular waste substance produced by damaged mitochondrial incompleted decomposition. And it is a biomarker of aging.   As aging, accumulation of the lipofuscin in retinal pigment epithelium induces blindness called Age-related macular degeneration. Soraprazan is developed to reduce the lipofuscin production and cure the age-related macular degeneration.  Soraprazan reducing the age biomarker lipofuscin can be suggested to have effect of longevity extension. C.elegans were treated on NGM agar plate containing 0, 50, 100, 200 μM soraprazan and showed the lipofuscin reduction and extension of longevity.  To identify the mechanism, 0 and 200 μM treated worms’ RNA expression was analyzed through microarray.

overall_design: After 14 days treatment of 0 and 200 μM soraprazan, the gene expression difference was compared. Two independent experiments were performed using about 350 worms at each concentration.

first: Jiah

last: Yeom


title: Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay pathways [CAGE-seq]

status: Public on Feb 17 2020

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

summary: In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs. Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs were identified. We also found that PROMPTs become sources of 21-22 nt small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPT production. In addition, we found ~200 transcription start sites within 3’-UTR-encoding regions that produce long unspliced, exosome-sensitive antisense RNAs. The previously characterized non-coding (nc) RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of ncRNAs. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

overall_design: CAGE-seq sequencing in triplicates of 12 days-old Arabidopsis thaliana whole seedlings (Col-0) for 3 different genotypes, a rrp4-2 mutant, a hen2-4 mutant, and a wild type.

first: Jette

last: Bornholdt

first: Maxim

last: Ivanov

first: Peter

last: Brodersen

first: Albin

last: Sandelin

first: Maria

last: Vigh


title: Effect of lutein on worms lacking complex I subunit nuo-5 (ortholog of human NDUFS1)

status: Public on Jan 31 2020

city: Düsseldorf

first: Silvia

last: Maglioni

state: NRW

address: Auf' m hennekamp 50

institute: IUF-Leibniz Institute

summary: To gain insight into the pathways accounting for the deleterious effects associated with severe mitochondrial dysfunction, we compared the transcriptomic profile in control L3 larvae with that of  strong (arrested) nuo-5 RNAi. We also found that the natural compound lutein was able to rescue some of the defective phenotypes we characterized in nuo-5-depleted animals therefore we compared also the transcriptomic profile of stage-matched (L3) cohorts of C. elegans upon strong nuo-5 RNAi, treated and untreated with lutein, with that of animals fed empty vector control.

overall_design: Three different groups were analyzed, each containing 4 independent samples

first: Natascia

last: Ventura

first: Nuno

last: Raimundo


title: Cycling cancer persisters arise from lineages with distinct transcriptional and metabolic programs

status: Public on May 21 2020

city: Cambridge

first: Yaara

last: Oren

state: Massachusetts

address: 415 Main street cambridge

institute: Broad institute

summary: Non-genetic mechanisms have recently emerged as important drivers of therapy failure in cancer, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment. While most cancer persisters, like their bacterial counterparts, remain arrested in the presence of drug, a rare subset of cancer persisters can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to simultaneously resist therapy and maintain proliferative capacity in the presence of drug. To address this, we developed Watermelon, a new high-complexity expressed barcode lentiviral library for simultaneous tracing each cell's clonal origin, proliferative state, and transcriptional state, and used it to study this rare, transiently-resistant, proliferative persister population and identify what distinguishes it from non-cycling persisters. Analysis of Watermelon-transduced cancer cell lines demonstrated that cycling and non-cycling persisters arise from different pre-existing cell lineages with distinct transcriptional and metabolic programs. The proliferative capacity of persisters is associated with an upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation in specific subpopulations of tumor cells.

overall_design:
10X Genomics single cell RNAseq of PC9 cells treated with Osimertinib
Lung cancer PC9 cells were treated with osimertinib (300nM) and harvested before treatment, after 3,7, and 14 days of continuous drug treatment. At day 14 prior to sequencing, cells were sorted to three groups based on mCherry expression:cycling (low), moderate cyclers (med) and non-cycling (high)
In addition, seven Watermelon lines models from EGFR-driven lung cancer (PC9, HCC827), HER2-driven breast cancer (BT474, EFM192A) and BRAF-driven melanoma (A375, COLO858) and colorectal (HT29) cell lines, treated them with clinically relevant kinase inhibitors for 10 days (300nM osimertinib, 1uM lapatinib or 1uM dabrafenib). At day 10 prior to sequencing, cells were sorted to three groups based om mCherry expression:cycling (low) and non-cycling (high)


title: RNA-seq of prostate cancer cell lines with acquired resistance to AKT inhibitors GDC-0068 (ATP competitive) or MK206 (allosteric)

status: Public on Jan 24 2020

city: South San Francisco

first: Anneleen

last: Daemen

state: CA

address: 1 DNA Way

institute: GENENTECH, INC.

summary:
Goal: Study resistance mechanisms to ATP-competitive vs. allosteric AKT inhibitors, in prostate cancer
Methods: RNA-sequencing
Results: Resistance to the ATP-competitive inhibitor GDC-0068 was driven by compensatory activity of parallel signaling pathways

overall_design: Duplicate results of RNA-seq of the LNCaP prostate cell line (untreated or treated with either AKT inhibitor) and derived clones with acquired resistance to either AKT inhibitor

first: Kui

last: Lin


title: Tissue specific dual RNA-seq defines host-parasite interplay in experimental visceral leishmaniasis caused by Leishmania donovani and Leishmania infantum

status: Public on Jan 17 2020

city: York

first: Paul

last: Kaye

address: Wentworth way

institute: University of York

summary: FIve  6/8 week old female BALB/c mice were infected with the LV9 L. donovani strain,five mice were infected with the L. infantum  NCL strain, five were uninfected, and spleen and liver were taken from mice at day 36 post infection. These tissues were then used to prepare for RNAseq

sample_organism:
Leishmania donovani
Leishmania infantum
Mus musculus

overall_design: 5 mice uninfected, 5 mice infected with L. donovani, 5 mice infected with L. infantum, and spleen and liver tissues taken at day 36 post infection for RNAseq

first: Sarah

last: Forrester

first: Amy

last: Goundry

first: Bruna

last: Torres Dias

first: Thyago

last: Leal Calvo

first: Milton

last: Osório Moraes

first: Jeremy

last: Mottram

first: Ana

last: de Araújo Lima


title: Proteogenomic single cell analysis of skeletal muscle myocytes

status: Public on Jan 15 2020

city: Baltimore

first: Marc

last: Halushka

state: MD

address: 720 Rutland Avenue / Ross Rm 632B

department: Pathology

institute: Johns Hopkins University SOM

summary:
Background:  Skeletal muscle myocytes have evolved into slow and fast-twitch types.  These types are functionally distinct as a result of differential gene and protein expression. However, an understanding of the complexity of gene and protein variation between myofibers is unknown.
Methods: We performed deep, whole cell, single cell RNA-seq on intact and fragments of skeletal myocytes from the mouse flexor digitorum brevis muscle. We compared the genomic expression data of 171 of these cells with two human proteomic datasets.  The first was a spatial proteomics survey of mosaic patterns of protein expression utilizing the Human Protein Atlas (HPA) and the HPASubC tool. The second was a mass-spectrometry (MS) derived proteomic dataset of single human muscle fibers. Immunohistochemistry and RNA-ISH were used to understand variable expression.
Results: scRNA-seq identified three distinct clusters of myocytes (a slow/fast 2A cluster and two fast 2X clusters).  Utilizing 1,605 mosaic patterned proteins from visual proteomics, and 596 differentially expressed proteins by MS methods, we explore this fast 2X division.  Only 36 genes/proteins were mosaic across all three studies, of which nine are newly described as variable between fast/slow twitch myofibers. An additional 414 genes/proteins were identified by two methods. Immunohistochemistry and RNA-ISH generally validated variable expression across methods presumably due to species-related differences.
Conclusions: In this first integrated proteogenomic analysis of mature skeletal muscle myocytes we validate the main fiber types and greatly expand the known repertoire of twitch-type specific genes/proteins. We also demonstrate the importance of integrating genomic and proteomic datasets.

overall_design: This dataset is single cell RNA-sequencing of 763 skeletal myocyte cells from a single C57BL/6J  mouse's flexor digitorus brevis. The mouse was greater than 3 months of age. Of these cells, 171 were used for downstream analyses to compare with single-cell proteomic data.

first: Suraj

last: Kannan

first: Brian

first: Rohan

last: Verma


title: Alpha/Beta Mouse TCR Sequencing of CD4+ thymic regulatory and conventional T-cells

status: Public on Jan 10 2020

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

summary: Thymic regulatory T cells (tTreg) are critical in maintenance of normal T cell immunity and tolerance. The role of TCR in tTreg cell selection remains incompletely understood. Here we assessed TCRa and TCRb sequences of tTreg and conventional thymic CD4+ T (Tconv) cells by high throughput sequencing.  We identified ab TCR sequences that were unique to either tTreg or Tconv cells and found that these were distinct as recognized by machine learning (ML) algorithm and by preferentially used amino acid trimers in ab CDR3 of tTreg cells. In addition, a proportion of ab TCR sequences expressed by tTreg were also found in Tconv cells, and ML classified the great majority of these shared ab TCR sequences as characteristic of Tconv and not tTreg cells. These findings identify two populations of tTreg, one in which Treg fate is associated with unique properties of the TCR, and another with TCR properties characteristic of Tconv cells for which tTreg fate is determined by factors beyond TCR sequence.

overall_design: 3 individual Rag2GFP-Foxp3-RFP mice with Alpha-Beta TCR sequencing data. 3 individual TCRdCreER ZsGreen Foxp3 RAF samples with Alpha-Beta TCR sequencing data (each samples were pooled from 3 mice). 3 individual TCRα +/- TCRβ Tg mice with Alpha TCR Sequencing data. The raw data for this study has been deposited into NCI SRA (BioProject ID: PRJNA541952; SRA Accession: SRP197126).

first: Annette

last: Ko

first: Alvin

last: Shi

first: Thomas

last: Nguyen


title: Regular exercise potentiates energetically expensive hepatic de novo lipogenesis during early weight regain

status: Public on Dec 10 2019

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary: Obese rats were calorically restricted with (EX) or without (SED) treadmill exercise (1 h/day, 6 days/wk, 15 m/min) to induce and maintain weight loss. After 6 weeks of WLM, subsets of WLM-SED and WLM-EX rats were allowed ad libitum access to food for 1 day to promote relapse (REL). An energy gap-matched group of sedentary, relapsing rats (REL-GM) were provided a diet matched to the positive energy imbalance of the REL-EX rats.

overall_design: This dataset is RNA-sequencing performed on the relapsing animals only.

first: David

last: Presby


title: Translation is required for miRNA-dependent decay of endogenous transcripts.

status: Public on Jan 09 2020

city: Lausanne

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

summary: Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cytosolic long noncoding RNAs (lncRNAs). We show, that despite interacting with miRNA loaded RNA-induced silencing complex (miRISC), the steady state abundance and degradation rates of these endogenously expressed non-translated transcripts are minimally impacted by miRNA loss. To validate the requirement of translation to miRNA-dependent decay, we fused a miRISC bound lncRNA, whose levels are unaffected by miRNAs, to the 3’end of a protein-coding gene reporter and shown that this results in its miRNA-dependent transcript destabilization. Furthermore, analysis of the few lncRNAs whose levels are regulated by miRNAs revealed these tend to associate with translating ribosomes and are likely misannotated micropeptides, further substantiating the necessity of target translation to miRNA-dependent transcript decay. Our analyses revealed the strict requirement of translation for miRNA-dependent transcript destabilization and demonstrates that the levels of coding and noncoding transcripts are differently affected by miRNAs.

overall_design: Conditional loss of dicer function was induced in mESCs and small RNA sequencing as well as mRNA metabolic labelling was performed to assess changes in transcript degradation and miRNA loss, between wild-type and Dicer depleted mESCs.

first: Adriano

last: Biasini

first: Stefano

last: de Pretis

first: Jennifer

middle: Y

last: Tan

first: Baroj

last: Abdulkarim

first: Harry

last: Wischnewski

first: Rene

last: Dreos

first: Mattia

last: Pelizzola

first: Constance

last: Ciaudo

middle: C


title: Assessing placental maturity through histological and transcriptomic analyses in idiopathic spontaneous preterm birth

status: Public on Dec 25 2019

city: Gainesville

first: Heather

last: Brockway

department: Physiology and Functional Genomics

institute: University of Florida

overall_design: RNA-sequence based transcriptome profiles of idiopathic spontaneous preterm and normal term placental villous tissue from delivery 1x50bp single end reads generated and 50 million read deapth coverage

first: Louis

last: Muglia

first: Helen

last: Jones


title: Effect of knocking down complex I subunit nuo-5 (ortholog of the human NDUFS1) in C.elegans

first: Silvia

last: Maglioni

summary: In this study we compared the transcriptomic profile in control L3 larvae with that of mild or strong (arrested) nuo-5 RNAi. The two treatment (mild and strong) in fact lead to two very different phenotype. The mild supperssion of nuo-5 induces improved healthspand and has pro longevity effect. The strong suppression of the same gene has, on the contrary, deleterious effects such as arrested development.

first: Natascia

last: Ventura

first: Alfonso

last: Schiavi


title: RNAseq of total, soluble and insoluble fraction of WT and mutant yeast cells after 10 minutes at 30, 40 or 42°C

status: Public on Nov 26 2019

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

institute: MPI-CBG

summary: We use RNAseq to assess the gene expression as well as solubility of transcripts after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C) for wildtype and Ded1-IDRm mutant cells.

overall_design: RNAseq of WT and mutant yeast total, soluble and insoluble fraction after 10 minutes at 30, 40 or 42°C

first: Ulrike

last: Friedrich

first: Christiane

last: Iserman

first: Lena

last: Hersemann

first: Antonio

last: Domingues

first: Günther

last: Kramer

first: Simon

last: Alberti


title: Uncovering the role admixture in health disparities: Association of hepatocyte gene expression and DNA methylation to African Ancestry in African-Americans [Methylation]

status: Public on Oct 31 2019

first: Minoli

last: Perera

state: IL

institute: Northwestern Univeristy

summary: In African Americans (AA), the proportion of West African ancestry (WAA) may explain the genetic drivers of health disparities in disease.  Analysis of RNA sequencing data from sixty AA-derived primary hepatocytes identified 32 gene expression profiles associated with WAA (FDR <0.05) with enrichment in angiogenesis and inflammatory pathways (FDR <0.1).  Association of DNA methylation to WAA identified 1037 differentially methylated regions (FDR <0.05), with hypomethylated genes enriched for drug response pathways.  Within the PharmGKB pharmacogene, VDR, PTGIS, ALDH1A1, CYP2C19 and P2RY1 were associated with WAA (p <0.05) with replication of CYP2C19 and VDR in the GTEx liver cohort.  For every 1% increment in WAA, P2RY1 gene expression increased by 1.6% and CYP2C19 gene expression decreased by 1.4%, suggesting effects on clopidogrel response and platelet aggregation.  We conclude that WAA contributes to variablity in hepatic gene expression and DNA methylation with identified genes indicative of health disparities prevalent in AAs.

overall_design: Bisulphite converted DNA from the 56 samples were hybridised to the Illumina EPIC 850k BeadChip

first: C

last: Park

first: Tanima

last: De

first: Y

last: Xu

first: Yizhen

last: Zhong

first: E

last: Smithberger

first: Cristina

last: Alarcon

last: Gamazon


title: Longitudinal single-cell transcriptomics analysis of mouse lung upon bleomycin-induced injury

status: Public on Dec 02 2019

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: Two single-cell RNA sequencing data sets were generated called "Whole lung" and "High Resolution". The "Whole lung" single-cell mRNAseq libraries were generated with Drop-Seq from whole mouse lungs upon bleomycin-induced injury and followed over time. Samples were taken at days 3 (n = 3), 7 (n = 5), 10 (n = 3), 14 (n = 4), 21 (n = 4) and 28 (n = 2). Control samples (n = 7) were administered saline only, also indicated with PBS or day0. The "High resolution" single-cell mRNAseq libraries were generated with Drop-Seq from the epithelial compartment of mouse lungs upon bleomycin-induced injury and followed over time. Samples were taken daily for two weeks and at days 21, 28, 36, 54 after injury. Control samples (n = 2) were administered saline only, also indicated with PBS or day0.

overall_design: Single-cell transcriptomics time-course experiment.

first: Herbert

last: Schiller


title: Regulation of uterine genes during the peri-implantation period, and its relationship to gene expression changes in the maternal brain in gestating mice

status: Public on Oct 24 2019

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

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

overall_design: Refer to individual Series


title: Uncovering the role admixture in health disparities: Association of hepatocyte gene expression and DNA methylation to African Ancestry in African-Americans [RNA-seq]

city: Chicago

address: 303 E Chicago Ave.

overall_design: 68 RNA samples from cultured liver hapatocytes were used for RNA-Seq

middle: R


title: Regulation of uterine genes during the peri-implantation period, and its relationship to gene expression changes in the maternal brain in gestating mice (FAIRE-seq)

summary: In this study, we conducted an integrated analysis of gene expression and chromatin structure of mouse uterus to understand the regulation of uterine expressed genes on gestation day (GD) 4 during the peri-implantation period.

overall_design: The whole uterus of preganant mice (n=4) were collected at gestatiion day 4 (GD4). Total RNA was isolated from each uterus and sequenced using Illumina platform.

middle: K

first: Andrew

last: Kelleher

first: Thomas

last: Spencer


title: An 'omics approach to unraveling the paradoxical effect of diet on PFOS and PFNA induced NAFLD

status: Public on Oct 09 2019

city: Kingston

first: Marisa

last: Pfohl

state: RI

address: Pharmacy Building, 7 Greenhouse Road

department: BPS

institute: University of Rhode Island

summary: Perfluoroalkyl substances (PFASs) are a family of toxicants universally detected in human serum and known to cause dyslipidemia in animals and humans. Non-alcoholic fatty liver disease (NAFLD) is most prevalent form of liver disease in the United States and has been rising in global prevalence over recent years. This study explored diet-PFAS interactions and their potential role in the increasing global incidence of NAFLD. Male C57BL/6 mice were fed with either a low-fat diet (10% kcal from fat) or a moderately high fat diet (45% kcal from fat) with or without perfluorooctanesulfonic acid (PFOS) or perfluorononanoic acid (PFNA) at a low dose of 0.0003% w/w in feed for 12 weeks.Livers were excised for histology and quantification of PFASs and lipids. Proteomics and transcriptomics were utilized to conduct mechanistic pathway exploration. In a high fat diet, PFOS and PFNA protected against the onset of hepatic lipid accumulation and inflammatory progression. Genes and proteins related to lipid metabolism, synthesis, transport, and storage were modulated by PFAS exposure and further impacted by the presence of dietary fat. When combined with a high fat diet, low dose PFOS and PFNA are protective against the onset of NAFLD suggesting that dietary fat impacts the behavior of PFASs in vivo. Furthermore, both dietary fat content and the chemical functional head group exerted significant influence on tissue partitioning and the resulting hepatic biochemical signature.

overall_design: We analyzed a total of 18 samples, using 3 biological replicates per treatment group. Relative gene expression was compared between the low fat diet (LFD) controls, high fat diet (HFD) controls, low fat-PFOS (L-PFOS), low fat-PFNA (L-PFNA), high fat-PFOS (H-PFOS), and high fat-PFNA (H-PFNA) treatment groups.

first: Christoph

last: Schorl


title: Single cell transcriptional atlas of mouse Achilles tendons

status: Public on Oct 10 2019

city: New York

first: Christopher

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report a single cell transcriptome atlas of Achilles tendon from 6-week-old male C57Bl/6 mice using single cell RNA sequencing.

overall_design: The overall objective of the study was to generate an atlas of the distinct cell populations in tendon using single cell RNA sequencing.

first: Jacob

last: Swanson


title: Expression profiles of HCT116 colorectal cancer cells and HCT116-derived CDKN1A (p21) knockout (ko) cells.

status: Public on Nov 01 2019

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

summary: Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Progression Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain a gene expression signature associated to the kockout of  p21 (i.e. Cyclin Dependent Kinase Inhibitor 1A, CDKN1A) in colorectal carcinoma samples and its association with of epithelial-mesenchymal transition (EMT). We analysed and compared three independent cultures of HCT116 p21 wt cells and three HCT116 p21-/- ko cells.

overall_design: In this study, independent biological replicates of HCT116 wt (n =3) and p21 (CDKN1A) ko cells (n = 3) were screened for gene expression of cancer progression related genes (770 genes including 30 housekeeping genes). Tumor cells were cultured in a 100 mm cell culture dish in RPMI medium supplemented with 1% penicillin/streptomycin and 10% FBS until 80% confluency and harvested via scraping off the plate. RNA was isolated from snap-frozen cell pellets. Gene expression analysis was performed using the human nCounter® PanCancer Progression Panel (NanoString Technologies). Total RNA was isolated from frozen cell pellets by QIAzol-chloroform extraction followed by RNeasy Mini Kit (Qiagen, Hilden, Germany) preparation. Isolated RNA (100 ng) was processed through the NanoString nCounter Prep Station. Subsequently, samples were processed according to the manufacturer’s instructions and signals of reporter probes were counted and tabulated using the nCounter Digital Analyzer (NanoString Technologies). Finally, housekeeping gene (geometric mean of 30 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 3.0 (NanoString Technologies, Hamburg, Germany) and standard settings.

first: S

last: Bueno-Fortes

first: J

last: Muenzner

first: A

last: Berral-Gonzalez

first: P

last: Lindner

first: K

last: Huebner

last: Kunze

first: T

last: Baeuerle

first: R

last: Schneider-Stock


title: Acclimation to a High Salt Diet is Sex-Dependent

status: Public on Sep 14 2019

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary: We report the relative difference in renal inner medulla transcript abundance between male and female rats,

overall_design: 13-15 week old Sprague Dawley rats purchased from Envigo Laboratories were fed a 0.49% NaCl diet TD 96208 (Envigo).  Tissue from the inner medulla of the kidney was isolated, RNA was extracted using the Trizol method (Ambion) and subjected to RNA sequencing.

first: Eman

last: Gohar

first: Carmen

last: De Miguel

first: Ijeoma

last: Obi

first: Elizabeth

last: Daugherty

first: Kelly

last: Hyndman

first: Bryan

last: Becker

first: Chunhua

last: Jin

first: Randee

last: Sedaka

first: Jermaine

middle: G

last: Johnston

first: Pengyuan

last: Liu

first: Joshua

middle: S

last: Speed

first: Tanecia

last: Mitchell

first: Jennifer

last: Pollock

first: David


title: Regulation of uterine genes during the peri-implantation period, and its relationship to gene expression changes in the maternal brain in gestating mice (RNA-seq)

first: Susanta

last: Behura

first: Andrew

last: Kelleher

first: Thomas

last: Spencer


title: HM450K-based DNA methylation analysis of normal brain and glioma samples

status: Public on Sep 09 2019

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

type: Methylation profiling by genome tiling array

summary: Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to transcriptional alteration. Nonetheless, a primary role of this defect in genome-wide cancer-associated gene misregulation is still being questioned.  Here, we used adult glioma, a widespread type of brain tumor, to evaluate the relative contribution of DNA methylation-dependent and -independent mechanisms on transcriptional alteration at CpG-island/promoter-associated genes in cancer cells.   By extensive molecular analyses conducted in both IDH wild-type (IDHwt) and IDH mutated (IDHmut) samples, we show that DNA hypermethylation affects only a minority of genes that show a loss or a gain of expression. In IDHwt samples, for instance, more than 75% of aberrantly repressed genes do not display DNA methylation defect at their CpG-island promoter. Rather, an alteration in the H3K27me3 signature is the predominant molecular defect at misregulated genes. We also observed that a bivalent chromatin signature in stem cell might not only predispose genes to hypermethylation, as widely documented, but more generally to all type of transcriptional alterations. In addition, we evidenced that transcriptional strength in healthy brain influences the choice between DNA methylation- or H3K27me3- associated silencing pathway at repressed genes in glioma. Combined our study supports a model whereby the altered developmental control of H3K27me3 dynamics, and more specifically defects in the interplay between polycomb protein complexes and brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells.  Together our study provides a comprehensive and revisited picture of epigenetic gene deregulations in cancer. Our observations are also of importance for the design of drugs that aims to target cancer epigenetic defects.

overall_design: Bisulfite converted DNA of brain and glioma samples was hybridized to the Infinium Human Methylation 450K BeadChip. DNA bisulfite conversion and hybridization on the arrays were performed by Integragen, SA (Evry, France) following the Illumina Infinium HD methylation protocol.

first: Franck

last: Court

first: Philippe

last: Arnaud