title: RNA-Seq analysis of primary human keratinocytes exposed to Cannabidiol

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

overall_design: Primary human keratinocytes were incubated with either DMSO or CBD (10 µM) for 24 hours (N=3).

first: Laura

last: Casares

first: Víctor

last: García

first: Martín

last: Garrido-Rodríguez

first: Estrella

last: Millán

first: Juan

last: Collado

first: Adela

last: García-Martín

first: Jon

last: Peñarando

first: Marco

last: Calzado

first: Laureano

last: de la Vega


title: Endogenous retroviruses are associated with hippocampus-based memory impairment

status: Public on Dec 31 2019

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

type: Expression profiling by high throughput sequencing

summary: Retrotransposons comprise a staggering 40% of the mammalian genome. Among them, endogenous retroviruses (ERV) represent sequences that closely resemble the proviruses created after exogenous retroviral infection. ERVs make up 8–10% of human and mouse genomes and range from evolutionarily ancient sequences to recent acquisitions. Studies in Drosophila have provided a causal link between genomic retroviral elements and cognitive decline.  However, in mammals, the role of ERVs in learning and memory remains unclear. Here, we studied two independent murine models for ERV activation: muMT strain (lacking B cells and antibody production) and intracerebroventricular injection of streptozotocin (ICVI-STZ). We conducted behavioral assessments (contextual fear memory and spatial learning), as well as gene and protein analysis (RNA sequencing and PCR assays). Mice lacking mitochondrial-antiviral-signaling protein (MAVS) and mice lacking stimulator-of-interferon-genes protein (STING), two downstream sensors of ERV activation, provided confirmation of ERV impact. We found that muMT mice and ICVI-STZ mice induced hippocampal ERV activation as shown by increased gene and protein expression of the Gag sequence of the transposable element intracisternal A-particle (IAP). ERV activation was accompanied by significant hippocampus-related memory impairment in both models. Notably, deficiency of the MAVS pathway was protective against ICVI-STZ-induced cognitive pathology. Overall, our results demonstrate that ERV activation is associated with cognitive impairment in mice. Moreover, they provide a new molecular target for strategies aimed at attenuating retroviral element sensing, via MAVS, to treat dementia and neuropsychiatric disorders.

overall_design: For figure 1, RNA-Seq was conducted from n = 2 muMT and n = 3 wildtype mice; for figure 3, n=3 ICVI-STZ and n=2 ICVI-STZ wildtype mice were analyzed 3 weeks after injection;  for figure 3, n=3 ICVI-STZ and n=4 ICVI-STZ MAVS-KO mice were analyzed 3 weeks after injection

first: Yousef

last: Al-Abed

first: Patricio

middle: T

last: Huerta


title: microRNA-142–mediated repression of phosphodiesterase 3B critically regulates peripheral immune tolerance

status: Public on Dec 20 2019

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tregs play a fundamental role in immune tolerance via control of self-reactive effector T cells (Teffs). This function is dependent on maintenance of a high intracellular cAMP concentration. A number of microRNAs are implicated in the maintenance of Tregs. In this study, we demonstrate that peripheral immune tolerance is critically dependent on posttranscriptional repression of the cAMP-hydrolyzing enzyme phosphodiesterase-3b (Pde3b) by microRNA-142-5p (miR-142-5p). In this manner, miR-142-5p acts as an immunometabolic regulator of intracellular cAMP, controlling Treg suppressive function. Mir142 was associated with a super enhancer bound by the Treg lineage–determining transcription factor forkhead box P3 (FOXP3), and Treg-specific deletion of miR-142 in mice (TregΔ142) resulted in spontaneous, lethal, multisystem autoimmunity, despite preserved numbers of phenotypically normal Tregs. Pharmacological inhibition and genetic ablation of PDE3B prevented autoimmune disease and reversed the impaired suppressive function of Tregs in TregΔ142 animals. These findings reveal a critical molecular switch, specifying Treg function through the modulation of a highly conserved, cell-intrinsic metabolic pathway. Modulation of this pathway has direct relevance to the pathogenesis and treatment of autoimmunity and cancer.

overall_design: ChIP-seq to identify Foxp3 binding sites in murine Treg cells

first: Nelomi

last: Anandagoda

first: Joanna C.

middle: D

last: Willis

first: Arnulf

last: Hertweck

first: Luke

middle: B

last: Roberts

first: Ian

last: Jackson

last: Gokmen

middle: G

first: Jane

middle: K

last: Howard

first: Graham

middle: M

last: Lord


title: Gene expression in brain of interleukin-18 knockout mice at 6 and 12 weeks of age

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Interleukin-18 knockout mice had metabolic syndromes after 24 weeks of age. We examined gene expression profiles in mice brain using genome-wide microarray technology, and compared gene expression profiles between wild-type and interleukin-18 knockout mice. To verify responsible molecules involved in metabolic syndromes such as obesity, we compared the gene expression levels at 6 and 12 weeks of age, and picked up them whose expression was more than 2-fold increase or less than 1/2-fold decrease.

overall_design: The mouse whole brains derived from wild type and interleukin-18 knockout mice at 6 and 12 weeks of age were examined. Each strain was run in triplicate.

first: Kyosuke

last: Yamanishi


title: Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

type: Genome variation profiling by genome tiling array

summary: AIM: To investigate whether chromosomal instability (CIN) is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability) and CIMP (CpG island methylator phenotype) in early onset colorectal cancer (EOCRC). METHODS: Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis) were analyzed by array comparative genomic hybridization (aCGH), in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs) and the MSI/CIMP condition in EOCRC. RESULTS: Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B) and four secondary clusters (A1, A2, B3, B4). The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC), which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected articular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS: Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.

overall_design: A total of 88 individuals diagnosed with CRC at an age of 45 years or younger (range: 16–45 years) were collected at the 12 de Octubre University Hospital in Madrid. Family history of cancer (including at least three generations) and clinicopathological information was obtained for each patient, with a follow-up of at least 60months from surgery. Six patients were excluded because familial adenomatous polyposis was diagnosed Material for array comparative genomic hybridization (aCGH) analysis could be obtained from 60 of the remaining 82 patients.

first: María

last: Arriba

first: Juan

middle: L

last: García

first: Daniel

last: Rueda

first: Jessica

last: Pérez

first: Lorena

last: Brandariz

first: Oana

middle: A

last: Nutu

first: Laura

last: Alonso

first: Yolanda

last: Rodríguez

first: Miguel

last: Urioste

first: Rogelio

last: González-Sarmiento

first: José

last: Perea


title: Differential clinicopathological and molecular features within late-onset colorectal cancer according to tumor location

summary: Background: Since there is a predilection of some clinical and molecular features for a given tumor location, we assessed whether this can be confirmed in late-onset colorectal cancer (LOCRC).  Methods: We analyzed clinical and molecular characteristics of LOCRC at different tumor locations in order to determine if there are differential phenotypes related with the location in the colon.  Results: Right colon cancers showed features associated with sporadic Microsatellite Instability: predominance of female cases and BRAF mutations, and an important mucinous component. Left colon cancers developed a higher number of polyps and multiple primary CRCs, showed the strongest familial component, and had better prognosis. Rectal cancers showed a predominantly sporadic phenotype, with worse prognosis and a CpG Island Methylator Phenotype (CIMP)-High. No copy number alterations (CNAs) greater than or equal to 50% were observed in this LOCRC group, and the most recurrent alterations were losses at 5q13 and 14q11, and gains at 7q11, 7q21-q22, 19p13-p12, 19q13 and 20p11-q11. KRAS and PIK3CA were the only mutated genes showing differences according to the tumor location, mainly for right colon cancers.   Conclusions: Categorizing LOCRC according to tumor location appears to be an adequate first step to resolving the heterogeneity of this subset of CRC.

overall_design: A total of 100 consecutive individuals with colorectal cancer diagnosed at an age of 70 years or older were collected from our institution, starting from January 2002. All patients, or a first degree relative in case of death of the index case, provided written consent. 86 of these samples could be adequately processed for Array Comparative Genomic Hybridisation (a-CGH).

first: Juana

last: Cano

first: Eduardo

last: Rubio

first: Alfredo

last: Vivas

first: Carmen

last: Sánchez

first: Sandra

last: Tapial

last: Pena

first: Mariano

last: García-Arranz

first: Damián

last: García-Olmo


title: Discrimination of dormant and active hematopoietic stem cells by G0 markers reveals dormancy regulation by cytoplasmic calcium

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: Quiescent hematopoietic stem cells (HSCs) are typically dormant, and only a few quiescent HSCs are active. The relationship between “dormant” and “active” HSCs remains unresolved. Here we generated a G0 marker (G0M) mouse line that visualizes quiescent cells. G0M identifies a small population of active HSCs (G0Mlow), which are distinct from dormant HSCs (G0Mhigh), within the conventional quiescent HSC fraction. Single-cell RNA-Seq analyses showed that the gene expression profiles of these populations were nearly identical, yet differed in their Cdk4/6 activity. Furthermore high-throughput small molecule screening revealed that high concentrations of cytoplasmic calcium ([Ca2+]c) were linked to dormancy of HSCs. These findings indicate that G0M separates dormant and active adult HSCs, which are regulated by Cdk4/6 and [Ca2+]c. This G0M mouse line represents a useful resource for investigating physiologically important stem cell subpopulations.

overall_design: RNA sequencing of mouse bone marrow HSCs treated with or without LPS

first: Tsuyoshi

last: Fukushima

first: Yosuke

last: Tanaka

first: Fiona

last: Hamey

first: Chih-Hsiang

last: Chang

first: Toshihiko

last: Oki

first: Terumasa

last: Umemoto

first: Shuhei

last: Asada

first: Yasutaka

last: Hayashi

first: Takeshi

last: Fujino

first: Taishi

last: Yonezawa

first: Reina

last: Takeda

first: Kimihito

middle: C

last: Kawabata

first: Keiko

last: Mikami

first: Tomofusa

last: Fukuyama

first: Susumu

last: Goyama

first: Hitoshi

last: Takizawa

first: Yasushi

last: Ishihama

first: Hiroaki

last: Honda

first: Berthold

last: Göttgens

first: Toshio

last: Kitamura


title: RNA-Seq analysis of inguinal white adipose tissue (iWAT) from control and high fat diet mice treated with THCA and THCA+T007

first: Eduardo

last: Muñoz

summary: Medicinal cannabis has garnered worldwide attention in recent years but has been hampered by the psychotropic activity of Δ9-tetrahydro-cannabinol (Δ9-THC). However, the biological activity of its precursor Δ9-THC acid  (Δ9-THCA) remain largely unexplored; yet, it is known that Δ9-THCA is not psychotropic and displays PPARg agonistic activity. We report here that Δ9-THCA is a partial and selective PPARg, albeit with lower adipogenic activity than the full PPARg agonist, rosiglitazone (RGZ).  In addition, Δ9-THCA enhanced osteoblastogenesis in human mesenchymal stem cells. Docking and in vitro functional assays indicated that Δ9-THCA binds and activated PPARg by acting at both the canonical and the alternative binding sites in the PPARg ligand-binding pocket. Indeed, transcriptomic signature at inguinal white adipose tissue (iWAT) from mice treated with Δ9-THCA confirmed its mode of action at PPARg. Administration of Δ9-THCA for 3-weeks in a mouse model of high fat diet (HFD)-induced obesity significantly reduced fat mass and body weight gain, and markedly ameliorated glucose intolerance and insulin resistance, while largely preventing liver steatosis, adipogenesis and macrophage infiltration in fat tissues. In addition, immunohistochemistry, transcriptomic and plasmatic biomarkers analyses showed that treatment with Δ9-THCA caused browning of iWAT and displayed potent anti-inflammatory actions in HFD mice. Altogether, our studies collectively document the potent biological activity of Δ9-THCA as a PPARggonist with capacity to substantially improve metabolic syndrome and inflammation associated to obesity. Our findings also imply that non-decarboxylated, Cannabis sativa extracts could be added to the arsenal of cannabis preparations already available in countries where medicinal cannabis is authorized.

overall_design: RNA-Seq profiles were generated for C57BL6 mice in five conditions: Control, THCA, THCA+T007, HFD and HFD+THCA (N=2).

first: Belén

last: Palomares

first: Francisco

last: Ruiz-Pino

first: Martín

last: Garrido-Rodríguez

first: Miguel

last: Sánchez-Garrido

first: Inmaculada

last: Velasco

first: María

middle: J

last: Vazquez

first: Xavier

last: Nadal

first: Carlos

last: Ferreiro-Vera

first: Rosario

last: Morrugares

first: Giovanni

last: Appendino

first: Getano

last: Morello

first: Marco

last: Calzado

first: Manuel

last: Tena-Sempere


title: Transcriptomic analysis of Drosophila olfactory projection neurons

status: Public on Dec 19 2019

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

country: USA

institute: Baylor College of Medicine

summary: Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global downregulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. To compare the RNA and protein dynamics of PN surface molecules in the developing-to-mature transition, we also profiled the PN transcriptomes from 36hAPF pupae and 5d adults. We performed bulk RNA-sequencing of PNs with 3 samples for each stage and 2k cells for each sample.

overall_design: 6 samples, 3 from development and 3 from adult

first: Jiefu


title: The IL-4/STAT6/PPARγ signaling axis is driving the extension of the RXR heterodimer cistrome, providing restricted ligand responsiveness in macrophages

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: Retinoid X receptor (RXR) is an obligate heterodimeric partner of several nuclear receptors (NRs), and as such a central component of NR signaling regulating the immune and metabolic phenotype of macrophages. Importantly, the binding motifs of RXR heterodimers are enriched in the tissue-selective open chromatin regions of resident macrophages, suggesting specific roles in subtype specification. Recent genome-wide studies revealed that RXR binds to thousands of sites in the genome, but the mechanistic details how the cistrome is established and serves ligand-induced transcriptional activity remained elusive. Here we show that IL-4-mediated macrophage plasticity results in a greatly extended RXR cistrome via the direct and indirect actions of the transcription factor STAT6. Activation of STAT6 leads to chromatin remodeling and RXR recruitment to de novo enhancers. In addition, STAT6 triggers a secondary transcription factor wave, including PPARγ. PPARγ appears to be indispensable for the development of RXR-bound de novo enhancers, whose activities can be modulated in a very restricted manner by the ligands of the PPARγ:RXR heterodimer. Collectively, these data reveal the mechanisms leading to the dynamic extension of the RXR cistrome, identify the lipid-sensing enhancer set of alternatively polarized macrophages and suggest a pervasive ligand-independent mechanism of action of the receptors.

first: Laszlo


title: The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure

city: Washington

first: Zheng

last: Wang

state: DC

address: 4555 Overlook Ave. SW.

department: Center for Bio/Molecular Science and Engineering

institute: US Naval Research Laboratory

summary: The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses, and is used as a model for understanding the diverse roles of melanin in fungi. To further our understanding resistance mechanism of E. dermatitidis to acute γ-radiation exposure and whether melanin plays a role in this process, we performed RNA-seq on WT and the melanin deficient mutant Δpks1 cultures exposed to γ-radiation at the dose of 1000 Gy, which resulted in ~50% cell deaths in both strains. We observed a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation, and DNA repair, and is unaffected by the presence of melanin.

overall_design: Examine transcriptomic profiles of E. dermatitidis wild type and pks1 mutant and their exposues to 1000 Gy gamma radiaiton

first: Zachary

last: Schultzhaus

first: Seongwon

last: Kim


title: Transcriptional profiling of nutrient-balanced early trilineage differentiations derived from H9 hPSCs.

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Here, we show unexpected and crucial metabolic nodes through TCA flux and glutaminolysis that modulate germ layer specification. Previous reports have shown that sustained glycolytic flux though MYC regulation is required for ectoderm specification. Our data support the finding that the germ layers have distinct metabolic profiles, but through investigation into the role of OXPHOS in germ layer specification.

overall_design: Bulk RNA-Sequencing of H9-derived hPSCs differentiated to early trilineage (mesoderm, endoderm, and ectoderm) using a nutrient-balanced media formulation. Samples represent n = 5-7 of each lineage (hPSC, ME, EN, and EC).

first: Vivian

last: Lu

first: Michael

last: Teitell


title: A deep insight about the role of hydrogen cynamide in grape bud dormancy release by comparative transcriptomic and proteomic analysis

city: Nanjing

first: Muhammad

last: Khalil-Ur-Rehman

address: No.1 Weigang

institute: Nanjing Agricultural university

summary: Hydrogen cyanamide (HC) is an agrochemical compound frequently used to break bud dormancy in grapevine grown under mild winter conditions all over the world.   The present study was carried out to get a better understanding of the molecular mechanism associated with HC to release bud dormancy in grapevine using RNA-seq based transcriptomic and tandem mass tag (TMT) based proteomic analysis.

overall_design: Two samples (Control and Hydrogen cynamide treated at 50% bud break) of grapevine buds were selected, and  total RNA was extracted from these samples for further library construction.

last: Khalil-ur-Rehman

first: Jianmin

last: Tao


title: Expression of lncRNAs between buffalo and yellow cattle muscle

city: nanning

first: kongwei

last: huang

address: 100, Daxue Road Nanning,Guangxi P.R.CHINA

institute: Guangxi University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.

sample_organism:
Bos taurus
Bubalus kerabau

platform_organism:
Bos taurus
Bubalus kerabau

overall_design: Six longissimus muscle samples from Guangxi native cattles and swamp buffalo (adult, 12 M old) were collected from nanning meat factory abattoir, a local slaughterhouse of Nanning, P.R. China.

first: Kongwei

last: Huang

first: Pengcheng

first: Hui

first: Qingyou

last: Liu


title: The translatome of adult cortical axons is regulated by learning in vivo

city: Storrs

first: Linnaea

last: Ostroff

state: CT

address: 75 N Eagleville Rd. U-3156

institute: University of Connecticut

summary: Local protein synthesis has not been believed to occur in adult forebrain axons. We have used translating ribosome affinity purification (TRAP) to capture mRNA from the distal amygdaloid projections of auditory cortical axons.  An eYFP-tagged ribosomal protein (rpL10a) was expressed in the adult rat auditory cortex via a lentiviral vector, and rats were given Pavlovian fear conditioning or control training two hours before collection of auditory cortex and amygdala. The eYFP tag alone was used as an IP control.  Polysome extraction and eYFP immunoprecipitation were performed according to published protocols (Heiman et al., 2008 Cell 135:78; Kratz et al. 2014 Genome Res. 24:1396).

overall_design: Forty animals were injected with eYFP-L10a or eYFP virus (20 per virus). For each virus, half of the animals were given fear conditioning and half control training (10 per group), and cortex and amygdala were collected from each animal. Samples from five animals were pooled for sequencing, resulting in two biological replicates for each of eight samples (eYFP-L10a/eYFP-conditioned/control-cortex/amygdala). Total RNA was sequenced along with TRAPed RNA for a total of 32 samples.

first: Eric

last: Klann


title: Liver, Adipose Tissue, and Skeletal Muscle from adult male offspring of maternal nutrient restriction in mice

first: Victor

middle: KM

last: Han

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

summary: Pregnant CD-1 mice were fed control (ad libitum) and 70% total food (g) (MNR) diets from E6.5-birth. At birth, litters with 11-15 pups were cross-fostered to ad libitum-fed mothers. At weaning, males were kept for analysis and fed ad libitum until 6 months when they were euthanized by CO2 necropsis for quadriceps femoris, right medial liver lobe and perigonadal adipose tissue. Tissues were frozen in liquid nitrogen until total RNA isolations were done on whole-tissue homogenate. Libraries were made with polyA enrichment and sequenced. Differential expression between maternal nutrition or glucose tolerance groups (glucose intolerant MNR, tolerant MNR, MNR with a high fasting blood glucose [IFBG] and controls).

overall_design: Liver: control N=8 and MNR N= 19 (intolerant N=7, tolerant N=8, IMFB N=4), muscle: control N=8 and MNR N=21 (intolerant N=9, tolerant N=8, IMFB N=4), adipose tissue: control N=8 and MNR N=21 (intolerant N=9, tolerant N=8, IMFB=4)

first: Bethany

middle: N

last: Radford


title: MiRNA sequencing in raw and processed human breast milk

city: Lodz

first: Urszula

last: Smyczyńska

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: We report the application of miRNA next generation sequencing (NGS) for the analysis of impact of processing on miRNA in human breast milk, donated by 3 volunteers. MiRNA content of total and exosomal fraction was compared between unprocessed milk and sample subjected to either Holder (thermal) pasteurization (HoP) or elevated pressure processing (HPP). NGS reads were mapped to miRBase in order to obtain miRNA counts. Then, we analyzed differences in the miRNA abundance and function between raw and processed material. It was observed that both processing methods reduce number of miRNA reads and HoP is significantly more detrimental to miRNA than HPP.

overall_design: Mature breast milk in a volume of 150 ml was obtained from 3 donors at the 50th day of lactation. Each sample was immediately aliquoted into 3 equal volumes for further processing. 3 samples were subjected to HPP in 62.5°C for 30 minutes in Human Milk Pasteurizer S90 Eco (Sterifeed, Medicare Colgate Ltd, England, Cullompton), 3 to HoP using U 4000/65 apparatus (Unipress Equipment, Poland, Celestynow) and 3 were left untreated as control. Then, the samples were stored frozen at -20°C. Exosomes were isolated from 5 ml of milk using miRCURY Exosome Cell/Urine/CSF Kit (Qiagen, Hilden, Germany). MiRNA was isolated with a biofluid-tailored Serum/Plasma Advanced Kit (Qiagen). The cDNA sequencing libraries were prepared with use of QIAseq miRNA Library Kit (Qiagen), according to manufacturer’s protocol. Single-end sequencing was performed on NextSeq 500 sequencer (Illumina, USA, San Diego), according to standard manufacturer’s protocol.

last: Smyczynska

first: Marcin

last: Bartlomiejczyk

last: Stanczak

first: Paweł

last: Sztromwasser

first: Aleksandra

last: Wesołowska

first: Olga

last: Barbarska

first: Emilia

last: Pawlikowska

first: Wojciech

last: Fendler


title: PTEN is essential in the maintenance of normal transporter activity in the epididymal epithelium

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: A fully developed initial segment, the most proximal region of the epididymis, is important for male fertility. Conditional deletion of Pten from the initial segment from postnatal day 17 onwards resulted in de-differentiation of the initial segment. When spermatozoa progressed through the de-differentiated epididymal duct, they developed angled flagella, suggesting compromised sperm maturation, which eventually resulted in male infertility. To understand mechanisms that underlie this sperm maturation defect following loss of Pten, we compared transcriptome profile of the initial segment between controls and knockouts and revealed that the transporter activity was one of the top molecular and cellular functions altered following loss of Pten. Alteration in the protein levels and localization of several transporters following loss of Pten were also observed by immunofluorescence analysis. Epithelial cells of the initial segment from knockouts are more permeable to Fluorescein isothiocyanate-dextran (4000da) compared to controls. When analyzing GEO datasets with Pten deletion in the prostate and inner ear of mice, alteration in transporter activity was also found in these Pten knockout mouse models, suggesting it is a common phenomenon. PTEN regulates transporter activities probably through regulation of cell shape, size, and membrane property, which in turn regulates the intracellular and intercellular micro-environment.

overall_design: 2 groups: PTEN KO vs Control

first: Bingfang

last: Xu

first: Barry

last: Hinton


title: The mechanism of HHT in treating acute myeloid leukemia on RNA level.

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: Through the GSEA analysis, we identified the suppressed E2F targets, G2M checkpoints, and hyperactivated p53 pathway after HHT treatment.

overall_design: Two cell lines with PBS and two drug concentrations.

first: Chenying

last: Li

first: Lei

last: Dong

first: Rui

last: Su


title: mRNA sequencing from Arabidopsis mutants and transgenic plants in the Col-0 accession

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

country: France

institute: INRA

summary: We sequenced the mRNA of Arabidopsis mutants and transgenic plants with modified RTL genes

overall_design: Whole plants were grown in vitro, harvested 11 days after germination and grinded to extract total RNA with phenol/chloroform and ethanol precipitated. RNA samples were sent to GATC Biotech for size-selection, cloning and sequencing on HiSeq2000 platform.

first: Émilie

last: Elvira-Matelot

first: Mélanie

last: Hachet

first: Hervé

last: Vaucheret


title: Single-Cell RNA-seq of Skeletal Progenitors derived from Mesp1

city: Minneapolis

first: Sunny

last: Chan

state: MN

address: 2231 6th St SE

department: Pediatrics

institute: University of Minnesota

summary: We developed a differentiation protocol to create skeletal myogenic progenitors in vitro by the induction of Mesp1. The goal of this study is to study the heterogenity of Mesp1 derivatives.

overall_design: The Chromium Single Cell 3' technology was used to create library contructs for single cells. This was performed as recommended by 10X Genomics platform.

middle: S

first: Jacqueline

last: Penaloza


title: Sequential regulation of glutamatergic and subtype-specific projection neuron identities in the developing cerebral cortex

status: Public on Dec 18 2019

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
Purpose:To asses changes in gene expression profiles of cortices from the P0 wild type littermate controls and Tle4-/- null mutant mice.
Methords:Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed whicn perform P value <= 0.05
Results: Compared to controls, 306 genes were significantly down-regulated in the Tle4 null mutant mice, and 338 genes were significantly up-regulated in the Tle4 null mutant mice.

overall_design: Cortex RNA profiles of P0 Wild type mice brain, and Tle4-/- null mutant mice brain

first: David

last: Tastad

first: Jeremiah

last: Tsyporin

first: Thomas

last: Finn

first: Liora

last: Huebner

last: Roberts

first: Soloman

last: Katzman

first: Nenad

last: Sestan

first: Susan

last: McConnell

first: Zhengang

last: Yang

first: Shenfeng

last: Qiu

first: Bin


title: RNA Sequencing Analysis of Gene Expression Profiles in Control versus CIC Knockdown T47D Mammospheres

city: Pohang

first: Jeehyun

last: Yoe

state: Gyungbuk

address: 77 Cheongam-Ro. Nam-Gu

department: Life Science

country: South Korea

institute: POSTECH

summary:
Purpose: The goals of this study is to compare and examine the transcriptional profile in the secondary mammospheres of control versus CIC-deficient T47D cells by mRNA sequencing and to understand the molecular basis of the CIC regulation of CSC-like properties in luminal type of breast cancer cells.
Methods: DNA library for mRNA sequencing of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells was prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and their libraries sequenced on the NovaSeq sequencer accompanying the NovaSeq 6000 S4 Reagent Kit. The trimmed reads that passed quality filters were mapped to reference genome with HISAT2, followed by assembly of transcript with StringTie.
Results: A total of 20377 genes were differentially expressed (10438 upregulated and 9939 downregulated) in the CIC-deficient T47D mammospheres when compared with control mammospheres. Approximately 5% of the transcripts showed differential expression between the control and CIC-deficient secondary mammospheres, with a fold change ≥1.2 and p value <0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses revealed that CIC-deficient mammospheres differentially expressed genes that are involved in processes associated with cancer progression such as cell cycle, cell proliferation, cell growth, and apoptotic process, as well as autoimmunity.
Conclusions: Our results show the first comparative analysis of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells. The data reported here should also provide reference for expression profiles of CSC-like cells in ER+/PR+/HER2- luminal breast cancer cells. We conclude that CIC deficiency promotes CSC-like properties and thus breast cancer progression through controlling CSC-related pathways including focal adhesion and extracellular matrix (ECM)-receptor interactions, and may also regulate cell cycle, cell proliferation, and apoptosis.

overall_design: Secondary mammosphere mRNA profiles of control and CIC knockdown T47D breast cancer cells were generated by deep sequencing, in duplicate.

first: Yoontae

last: Lee


title: Identification of transcripts induced after treatment with protein disulfide isomerase inhibitor E64FC65 and panobinostat in PANC-1 cells

city: Omaha

first: Holly

last: Feser Stessman

state: NE

address: 2500 California Plaza

department: Pharmacology & Neuroscience

institute: Creighton University

summary: Protein disulfide isomerase and histone deacetylase inhibition induces a synergistic pro-apoptotic response. The goal of this RNA-Seq experiment is to (1) identify critical transcripts and pathways induced by the combination in PANC-1 cells that promote apoptosis and (2) conduct RNA-seq in parallel with ATF3 knockdown to identify ATF3-dependent target genes.

overall_design: Examination of transcripts in PANC-1 cell biological triplicates after (1) treatment with E64FC65, panobinostat, the combination, or DMSO and (2) treatment with DMSO or the combination in ATF3 knockdown and control cells.

first: Nathan

last: Dolloff

first: Ravyn

last: Duncan

last: Stessman


title: Transcriptome profiles of contrasting potato (Solanum tuberosum L.) genotypes under water stress

city: Santiago

first: macarena

middle: del pilar

last: Barra Jimenez

address: 1600 Tobalaba

country: Chile

institute: AAFC

summary: The potato is susceptible to water stress at all stages of development. We examined four clones of tetraploid potato, Cardinal, Desirée, Clone 37 FB and Mije, from the germplasm bank of the National Institute of Agricultural Research (INIA) in Chile. Water stress was applied by suspending irrigation at the beginning of tuberization. Stomatal conductance, tuber and plant fresh and dry weight was used to categorize water stress tolerance.  Cardinal had high susceptibility to water stress. Desirée was less suscepetible than Cardinal and had some characteristics of tolerance.  Mije had moderate and Clon 37 FB high tolerance. Differential gene expression in leaves from plants with and without water stress were examined using transcriptome sequencing.  Water stress susceptible Cardinal had the fewest differentially expressed genes at 101, compared to Desirée at 1867, Clon 37 FB at 1179 and Mije at 1010.  Water stress tolerance was associated with up-regulation of expression of transcription factor genes and genes involved in osmolyte and polyamine biosynthesis.  Increased expression of genes encoding late embryogenesis abundant (LEA) and dehydrin proteins along with decreased expression of genes involved in nitrate assimilation and amino acid metabolism were found for clones showing water stress tolerance.  The results also show that water deficit was associated with reduced biotic stress responses.  Additionally, heat shock protein genes were differentially expressed in all clones except for highly susceptible Cardinal.  Together the gene expression study demonstrates variation in the molecular pathways and biological processes in response to water stress contributing to tolerance and susceptibility.

overall_design: Comparison of the transcriptomic profile in 4 potato genotypes to drought stress in leaf samples

first: Macarena

first: Hellen

last: Tai


title: Transcriptional response of intestinal epithelial cells to type I and III IFN

city: Portland

first: Timothy

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: RNAseq of intestinal epithelial cell (IEC) organoids and treated with PBS, interferon beta (IFNB), or interferon lambda (IFNL). RNAseq of IECs sorted from neonatal mouse intestines following treatment with PBS, IFNB, or IFNL.

overall_design: Treatments were added to culture media (IEC organoids) or injected sub-cutaneously (neonatal mice). RNA was isolated four hours after treatments. Samples were collected in biological triplicate (IEC organoid) or quadruplicate (neonatal mice).

first: Jacob

last: Van Winkle


title: Expression data from EMT-derived NRK-52E cells before and after the AMPKα2 knockdown

city: Shenyang

first: Xiaoming

last: Yin

state: Liaoning

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary:
Recent studies have shown that AMPKα2 can regulate epithelial-mesenchymal transition(EMT) processes during kidney fibrosis. However, the underlying mechanisms for AMPKα2 changes in renal tubular EMT remain unclear.
TGF-β1 was used to induce epithelial-mesenchymal transition(EMT) in normal rat renal tubular epithelial (NRK-52E) cells. Gene microarray was used to analyze differential gene expression in EMT-derived NRK-52E cells before and after the AMPKα2 knockout

overall_design: TGF-β1 was used to induce epithelial-mesenchymal transition(EMT) in normal rat renal tubular epithelial (NRK-52E) cells. The shAMPKα2 lentivirus was used to interfere with AMPKα2 expression in EMT-derived NRK-52E cells. Cells of TGF-β1-treated+ shCtrl and TGF-β1-treated+shAMPKα2 knockdown groups were selected for RNA extraction and hybridization on Affymetrix microarrays.Gene microarray was used to analyze differential gene expression in EMT-derived NRK-52E cells before and after the AMPKα2 knockout.

first: Yi


title: HBO1 is required for the maintenance of leukaemia stem cells [ChIP-seq]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by transcriptional dysregulation resulting in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, with most showing modest efficacy due to an inability to effectively eradicate leukaemia stem cells (LSC). To specifically identify novel dependencies in LSC we screened a bespoke library of small hairpin RNAs (shRNAs) targeting chromatin regulators in a unique ex vivo model of LSC. We identified the MYST acetyltransferases HBO1 (KAT7) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance ex vivo and conditional ablation of HBO1 confirmed its requirement for LSC maintenance in vivo. CRISPR domain screening identified the histone acetyltransferases (HAT) domain of HBO1 as being essential to acetylate histone H3K14, which is required for the expression of the key genes including HOXA9 and HOXA10 that maintain the immature phenotype and self-renewal properties of LSC. To leverage this dependency therapeutically we developed highly potent small molecule inhibitors of HBO1 and provide structural data to demonstrate their mode of activity as competitive analogues of acetyl-CoA. These inhibitors phenocopy our genetic data and show efficacy in a broad range of human cell lines and primary patient samples encompassing the most common genetic subtypes of AML.

overall_design: ChIP-seq of BET inhibitor resistant leukaemic cells transduced with HBO1 sgRNA.

first: Laura

last: MacPherson

first: Miriam

last: Yeung


title: HBO1 is required for the maintenance of leukaemia stem cells [RNA-seq]

overall_design: RNA-seq of BET inhibitor resistant leukaemic cells transduced with HBO1 sgRNA.


title: HBO1 is required for the maintenance of leukaemia stem cells

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

overall_design: Refer to individual Series


title: Expression data from  AKR1C1 over-expression in Cal-27 cells or knockdown in HSC-2 cells, respectively

city: Taipei

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

summary: To exmaine the AKR1C1 controls transcriptome in HNSCC cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with empty vector or AKR1C1 expression vector in Cal-27 cells and shLuc control or shAKR1C1 in HSC-2 cells

overall_design: Total RNA was collected from empty vector or AKR1C1 expression in Cal-27 cells and shLuc or shAKR1C1-CDS in HSC-2 cells.

first: W

first: M

last: Hsiao


title: Transcription Factor p73 Regulates Th1 Differentiation

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street Hansen Life Sciences Bldg, HANS, 225

department: Biochemistry and Computer Science

institute: Purdue University

summary: T helper (Th) cells play critical functions in response to infectious, allergic, and autoimmune diseases. Upon exposure to a given infectious agent or stimulus, different individuals vary in their Th cell responses, influencing the final disease outcome. To investigate the genetic factors that contribute to such differential immune responses, we performed a haplotype-based computational genetic analysis based on the phenotypic profiles of in vitro differentiated Th1 cells from 16 inbred mouse strains. And we identified genes including that encoding the p53 family protein, p73, with SNP patterns that correlated with the quantitative difference in IFNγ expression. Overexpression of p73 inhibited Th1 differentiation, as evaluated by reduced IFNγ expression, whereas shRNA knockdown or knockout of the p73 gene augmented IFNγ production. An inhibitory effect of p73 on Th1 differentiation was also observed in Stat1-/- cells, indicating that the effect was at least partially independent of STAT1. The DNA-binding activity of p73 is required for its inhibitory effect on IFNγ expression, as deletion of p73 DNA binding domain abolished IFNγ inhibition. A global gene expression analysis showed that 206 genes are differentially expressed more than two-fold in response to p73 overexpression, and 55 of these are direct target genes of p73 in Th1 cells, based on ChIP-seq analysis. p73 binding peaks were identified at a range of genes, including at the Il12rb2, Il24, and Il2ra loci, and p73 was implicated for regulating these genes based on reporter constructs containing WT or mutant p73 binding sites. Furthermore, p73 deficient mice had reduced disease severity in MOG induced EAE, with increased IFNg production from spinal cord infiltrating cells. Thus, p73 is a novel regulator of IFNγ expression, revealing a previously unanticipated role for p73 in Th1 cell differentiation.

overall_design: mRNA expression and ChIP-Seq analysis.

first: Min

last: Ren

first: Ming

last: Zheng

first: Wei

last: Liao

first: Jessica

last: Li

first: Jonathan

last: Rajaseelan

first: Gary

last: Peltz

first: Warren

last: Leonard

first: Peng


title: Expression data from biopsies with chronic atrophic gastritis and gastric cancer

city: Ciudad de Mexico

first: Gonzalo

last: Castillo

state: Ciudad de Mexico

address: Av. Universidad 3000, Circuito Escolar s/n, Col. Universidad Nacional Autónoma de México-Copilco, Del. Coyoacán

department: Microbiologia y Parasitologia

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary:
Gastric cancer is an important health problem because it is difficult to diagnose and treat in advanced stage. This makes that the prognosis of gastric cancer patients remains scarce. Currently it is known that the cause of gastric cancer is attributed to chronic infection with Helicobacter pylori. Its persistent infection leads to development of chronic atrophic gastritis that is considered as a predecessor stage of intestinal-type gastric cancer. The understanding of the alteration of molecular mechanisms during the early stages of the development of gastric cancer, and the identification of their potential biomarkers can allow a rapid diagnosis that leads to an improvement diagnosis and increase the patient’s prognosis. We analyzed gene expression profiles of patients with chronic atrophic gastritis and gastric cancer through microarray analysis, functional enrichment analysis and validation of gene expression by quantitative PCR.
Gene expression profiles in patients with chronic atrophic gastritis showed molecular changes of the gastric mucosa, which leads to intestinal metaplasia and subsequently, gastric cancer. In gastric cancer the gene expression profile showed the stage of tumor progression, the product of these genes are potential biomarkers of early stages of cancer that can be potential therapeutic targets. Accordingly, the transcriptome analysis revealed several gene groups are related to development of chronic atrophic gastritis, some of which were inhibited in gastric cancer patients. The increased expression of CLDN1, CLDN7, OLFM4, c-Myc and MMP-9 genes in chronic atrophic gastritis and gastric cancer point outs to their use as promising biomarkers for the early diagnosis of gastric cancer.

overall_design: RNA from 11 biopsies from patients with follicular gastritis, chronic atrophic gastritis and gastric cancer were analized by microarrays. Gene Set Enrichment Analysis, and differential expression analysis with subsequent funtional annotation was performed for each group of histological lesions.

first: Claudia

middle: I

last: Rivas-Ortiz

first: Stephanie

middle: E

last: Morales-Guerrero

first: Sergio

middle: P

last: de León Rosales

first: Armando

last: Gamboa-Dominguez

last: Rangel-Escareño

first: Luis

middle: F

last: Uscanga-Dominguez

first: Germán

middle: R

last: Aguilar-Gutiérrez

first: David

last: Kershenobich-Stalnikowitz

first: Yolanda

last: López-Vidal

last: Castillo-Rojas


title: Next generation sequencing based transcriptomic analysis of bile stress response in Lactobacillus salivarius Ren

city: Beijing

first: Guohong

last: Wang

address: 17 Qing Hua East Road, Hai Dian District

institute: China Agricultural University

summary: Lactobacillus salivarius is a member of the indigenous microbiota of the human gastrointestinal tract (GIT). Tolerance to bile stress is crucial for intestinal lactobacilli to survive in the GIT and to exert their beneficial actions. In this work, the Next-Generation Sequencing platform Illumina HiSeq 2000 was used to investigate the global response to bile in L. salivarius Ren, a potential probiotic strain isolated from a healthy centenarian. In the presence of 0.75 g liter-1 oxgall, the transcription of nearly 200 genes was detected to be associated with bile stress, including genes involved in carbohydrate and amino acid metabolism, cell envelope and fatty acid biogenesis, transcription and translation. This study improves our understanding on bile stress response in L. salivarius Ren.

overall_design: Whole mRNA profiles of  L. salivarius Ren growing in the absence (CK) and presence (BS) of oxgall were generated using Illumina HiSeq 2000 platform and differentially expressed genes were anylyzed.

first: Yanling

last: Hao


title: Transcriptomic analysis of primary human hepatic stellate cells undergoing TGFb mediated activation and JQ1 mediated attenuation of activation

city: Cambridge

first: Ju

address: 610 Main Street

department: Inflammation & Immunology

institute: Pfizer Inc

summary: Comparison of longitudinal transcriptomic profiles of activated human primary hepatic stellate cells to activated human primary hepatic stellate cells that are treated with anti-fibrotic inhibitor reveals inflammatory signaling as a key pathway that is modulated during pro-fibrotic activation and repressed during attenuation of fibrotic response.

overall_design: Longitudinal examination of  TGFb treated or TGFb and JQ1 (inhibitor) treated hepatic stellate cells to model pro-fibrotic activation and anti-fibrotic attenuation by small molecule inhibitor

last: Min-DeBartolo

first: Robert

last: Martinez


title: HBO1 is required for the maintenance of leukaemia stem cells [shRNA screen]

first: Mark

last: Dawson

overall_design: shRNA screen of pooled BET inhibitor resistant and sensitive leukaemic cells.

first: Laura

last: MacPherson

first: Enid

middle: Y

last: Lam


title: Transcriptional profiling of pericytes in the cerebral cortex of a Gdnf-TRAP (ES2243) mouse line

status: Public on Dec 17 2019

city: New York

first: Eric

last: Schmidt

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in pericytes in the cerebral cortex of adult Gdnf-EGFP/Rpl10a (ES2243) mice

overall_design: TRAP-Seq of pericytes in the cerebral cortex of adult Gdnf-EGFP/Rpl10a (ES2243) mice

first: Cuidong

first: Nathaniel

last: Heintz


title: Transcriptional profiling of neurons in the subthalamic nucleus in a Cbln2-TRAP (NIDA176) mouse line

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the subthalamic nucleus of adult Cbln2-EGFP/Rpl10a (NIDA176) BAC transgenic mice.

overall_design: TRAP-Seq of neurons in the subthalamic nucleus of seven adult Cbln2-EGFP/Rpl10a (NIDA176) mice


title: Transcriptional profiling of neurons in the dentate gyrus in a Penk-TRAP (NIDA186) mouse line

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the dentate gyrus of adult Penk-EGFP/Rpl10a (NIDA186) mice.

overall_design: TRAP-Seq of neurons in the dentate gyrus of adult Penk-EGFP/Rpl10a (NIDA186) mice


title: Transcriptional profiling of cells in the dorsal striatum of Drd1-TRAP (CP73) mice: input data

summary: Using translational profiling we obtained RNA-Seq data from total RNA present in the dorsal striatum of Drd1-EGFP/Rpl10a (CP73) mice administed cocaine

overall_design: Long-access cocaine intravenous self-administration study; RNASeq of cells in the dorsal striatum of Drd1-TRAP (CP73) BAC transgenic mice

first: Erika

last: Andrade

first: Johana

last: Alvarez


title: ATF2 and ATF7 mediation of intestinal repair in murine colitis model

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

summary: AP1 transcription factor family members: activating transcription factor 2 (ATF2) and activating transcription factor 7 (ATF7) have highly redundant functions due to homology and hence overlapping DNA-binding sites. The role of these transcription factors in intestinal epithelial homeostasis and repair has not been critically examined. Here, by using an intestine-specific deletion of ATF2 combined with body wide deletion of ATF7 in mice we assess the role of these proteins during intestinal homeostasis and repair after inflammation.

overall_design: 12h treatment of WT and ATF2 KO/ATF7 fl/fl colon organoids with 50ng/ml of recombinant mouse TNF-alpha

first: Bart

last: Meijer

first: Vanesa

last: Muncan


title: Targeting Fibroblast growth factor-23 (FGF23)-responsive pathways in the control of phosphate and vitamin D metabolism

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W Walnut Street

department: Nephrology and Hypertension

institute: Indiana University School of Medicine

summary: Single cell RNA sequencing (scRNAseq) on wild type (WT) mouse kidneys showed overlapping HBEGF and EGFR expression in the proximal tubule (PT), and KL expression in PT and distal tubule (DT) segments.

overall_design: Wild type mouse kidneys were harvested and used for single cell RNAseq to examine baseline gene expression patterns

first: Danielle

last: Janosevic


title: Hippocampus miRNA profiles in chronic cerebral-hypoperfusion rats

first: Yu

last: Cao

state: Beijing

address: Xiyuan hospital, Haidian District, Beijing, China

department: Institute of Geriatrics

institute: Xiyuan Hospital

summary: Chronic cerebral hypoperfusion (CCH) is a well-known risk factor for vascular dementia and other neurodegenerative disease, for which there are currently no effective medications available. MicroRNA (miRNA) are noncoding RNAS mediating post-translational silencing of genes, and has been extensively studied for their involvement in neurodegenerative disease. However, little is known about their roles in vascular dementia (VaD). In this work, a bilateral common carotid arteries occlusion (2-VO) surgery in rats was employed to induced CCH related cognitive dysfunction. Four months later, the hippocampi were dissected from 2-VO and sham operated rats for high-throughput profiling of miRNAs. Twelve differentially expressed miRNAs were identified according to a cutoff of |log2(Fold Change)|≥1 and p＜0.05. GO analysis of target genes revealed that the most relevant biological processes included the regulatory region nucleic acid binding, histone acetyltransferase binding, organic acid transmembrane transporter activity, L-amino acid transmembrane transporter activity. The cellular structure mainly included histone deacetylation complexes, endosomes, Golgi membranes, etc. And the involved molecular processes mainly included axon development, organ morphogenesis, macromolecular modification, regulation of neuron projection development, neuron development. This study provides a framework for understanding the alternations in hippocampus miRNA profiles underwent hypoxia insult.

overall_design: miRNA profiles in the hippocampus of rats underwent bilateral common carotid  arteries occlusion

first: Zeihui

last: Li

first: Xuemei

last: Diao

first: Lina

last: Ma

first: Pei

last: Hui

first: Hao


title: Human miFinder miRNA PCR array of liver biospy specimen of chronic hepatitis C virus infected patients

city: Riyadh

first: Saira

last: Khalid

address: Amr Ibn Alaas street

country: Saudi Arabia

institute: King Saud University

summary: The miRNAs were purified from paraffin embedded liver biopsy samples of HCV and HCC patients, using an miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. First, 25mg of liver biopsy tissues was homogenized in 700μl QIAzol lysis reagent, mixed, and shaken with chloroform. After that, the phases were separated by centrifugation at 12000´g for 15 min. The upper aqueous phase was collected in a fresh tube and the remaining DNA and organic protein organic phases was stored at -70°C until required. The RNA aqueous phase was washed further on the column and finally RNA was eluted into DEPC water (Ambion). Purified miRNAs were reverse transcribed into first strand cDNA using a miRNA first strand kit. (Qiagen). The reaction was carried out at 37ºC for 2 hours followed by heating at 95ºC for 5 min.

overall_design: The liver biopsies classified as fibrosis stage F1 and F2 were grouped together and named as early HCV (E-HCV, n=4), while fibrosis stage F3 and F4 were grouped together and named as advanced fibrosis (A-HCV, n=5).


title: Zinc-dependent gene expression in neurons upon glutamate stimulation

city: Boulder

first: Lynn

last: Sanford

state: CO

address: UCB 596

institute: University of Colorado Boulder

summary: Zinc (Zn2+) has been increasingly recognized to function as an important neurotransmitter, although how it functions in the context of signaling cascades is as yet unknown. In dissociated rat hippocampal neuron cultures, we stimulated neurons with glutamate, with or without additional exogenous ZnCl2 or a cell-permeable zinc chelator TPA. We found considerable heterogeneity among biological replicates which complicated zinc-dependent gene expression analysis. In general, we saw upregulation of genes implicating ER stress in glutamate-stimulated neurons that experience a zinc signal.

overall_design: 5 replicates of each of 4 conditions (unstimulated control, glutamate treatment, glutamate/Zn treatment, glutamate/TPA treatment). Glutamate treatment was used as the reference condition for most comparisons. TPA = tris(2-pyridylmethyl)amine, a Zn2+ chelator.

first: Amy

last: Palmer


title: RNA sequencing analysis revealed a distinct motor cortex transcriptome in spontaneously-recovered mice after stroke

city: Palo Alto

first: Michelle

last: Cheng

address: 1201 Welch Rd., MSLS P352

department: Neurosurgery

institute: Stanford University

summary: The goal of this study is to elucidate the intrinsic changes in spontaneous recovery after stroke, by directly investigating the transcriptome of primary motor cortex in mice that naturally recovered after stroke.

overall_design: Examination of gene expression in the primary motor cortex of spontaneously recovered (3) versus non-recovered (5) stroke mice

first: Alex

middle: G

last: Lee

first: Gary

last: Steinberg


title: microRNA-335 promotes keratinocyte differentiation

city: Singapore

first: Prabha

last: Sampath

address: Novena

country: Singapore

institute: Skin Research Institute

summary: This study identifies genes differentially expressed upon the over expression miR-335 in N/TERT-1 keratinocytes

overall_design: N/TERT-1 cells were transfected with miR-335 mimics or control mimics at 30nM concentration and total RNA isolated at 48hr post transfection and subjected to microarray

first: Wen

last: Lew


title: Identification of GLYMA.13G317000 binding sites in soybean early maturation embryos.

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.13G317000 in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.13G317000 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq3000 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Leonardo

last: Jo

first: Min

last: Chen

first: Robert

middle: B

last: Golberg


title: Identification of GLYMA.06G314400 binding sites in soybean early maturation embryos.

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.06G314400 in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.06G314400 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.


title: An improved method of constructing degradome library suitable for Illumina high-throughput sequencing platform

city: Xinxiang

first: Miao

last: Zhao

state: Henan

address: Jianshe east road

department: Life sciences college

institute: Henan Normal University

summary: Post-transcriptional gene regulation is a critical layer of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA targets. The miRNA-guided cleavage on the mRNA targets can be confirmed by analyzing the sequenced degradome or PARE or GMUCT libraries. However, high-throughput sequencing of PARE or degradome libraries is not as straightforward as sequencing small RNA libraries. Moreover, the currently used degradome or PARE methods utilize Mme1 restriction site and the resulting fragments are only 20-nt long, which often poses difficulty in distinguishing between the family members of the same gene family. In this modified degradome protocol, EcoP15I recognition site is introduced to the 3' end of the 5’RNA adaptor of TruSeq small RNA library, the double strand DNA adaptor sequence is modified to suit with the ends generated by the EcoP15I. These modifications allow amplification of the degradome library by primer pairs used for small RNA library preparation. Therefore, degradome library generated using this protocol can be sequenced as easily as small RNA library, and the resulting tag length is ~27-nt, which is longer than previous methods (20-nt). The protocol allows sequencing small RNA and degradome libraries simultaneously.

overall_design: Examination of degraded polyA RNA with a monophospahate at 5’end. These RNA is ligated to an RNA adapter consisting Ecop15I recognition site at 3’end. After ligation and RT-PCR, the PCR product was digested with Ecop15I and then ligated to a double-stranded DNA oligo. The final degradome library is enriched by primer pairs used for small RNA library preparation. Therefore, the generated degradome library can be sequenced as easily as small RNA library using Illumina sequencing platform.

first: Yong-Fang

last: Li


title: MicroRNA  expression in Pancreatic Ductal Adenocarcinoma

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

summary:
Microarray was used to find out the differentially expressed miRNAs in Pancreatic Ductal Adenocarcinoma as compared to healthy control.
Resulting miRNAs could be further used to understand the disease as well as could act as secretory biomarker.

overall_design: Total 6 samples were used, 2 Pancreatic Ductal Adenocarcinoma samples and 4 healthy control samples were used

first: Srikanta

last: Goswami


title: Effect of Pirfenidone on NSCLC [A549 1.5 mg/ml Pirf 24hrs]

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

summary:
Investigating the effect of Pirfenidone on NSCLC cells
Although immune checkpoint and targeted therapies offer remarkable benefits for lung cancer treatment, some patients do not qualify for these regimens or do not exhibit consistent benefit. Provided that lung cancer appears to be driven by transforming growth factor beta signaling, we investigated the single drug potency of Pirfenidone, an approved drug for the treatment of lung fibrosis which is known to inhibit TGFB1 mRNA. Human A549 and H1975 lung adenocarcinoma cell lines were stimulated for 6h and 25h with 0.75 mg/ml or 1.5 mg/ml Pirfenidone or the respective volume of PBS as vehicle control. Total RNA was extracted and subjected to transcriptome analysis by microarrays.

overall_design: stimulation of A549 cell line with 1.5 mg/ml Pirfenidone or equal volume of PBS and incubation 24h (N=4 each)


title: Effect of Pirfenidone on NSCLC  [A549 1.5 mg/ml Pirf 6hrs]

overall_design: stimulation of A549 with 1.5 mg/ml Pirfenidone or equal volume of PBS and incubation for 6h


title: Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.

overall_design: Mouse Scc1 flfl and Scc1 CKO SN/NSN FGOs were collected from 2-3 month old Scc1fl/fl and Scc1fl/fl;Zp3-Cre mice separately as previously described (Flyamer et al., 2017). Single-nucleus Hi-C experiments were performed in these oocytes as previously described (Flyamer et al., 2017).

first: Johanna

last: Gassler

first: Sean

last: Powell

first: Kikuë

last: Tachibana


title: Effect of Pirfenidone on NSCLC

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

overall_design: Refer to individual Series


title: Gene expression alternations in Shenqi Jiangtang Granule-treated rats kidney

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary:
Diabetic rats changes gene exprssion in Shenqi Jiangtang Granule-treated rats kidney
Diabetic nephropathy (DN) is a major microvascular complication of diabetes. In addition to moderating hyperglycemia, Shenqi Jiangtang Granule (SJG) had a beneficial effect on kidney function in a clinical trial. However, the mechanism involved remains unclear. This study was conducted to identify the underlying molecular mechanisms. A diabetic rat model was generated by using a high-fat diet and streptozotocin (STZ) injection. Then, rats were given SJG at dosages of 800 mg/kg/d by gavage for 8 weeks.

overall_design: We performed microarray analyses of Shenqi Jiangtang Granule-treated rats kidney

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: Transcriptional profiling of Caenorhabditis elegans and Caenorhabditis briggsae before and after heat shock

city: La Jolla

first: Jacob

last: Garrigues

state: CA

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary: Transcriptional profiling of heat-shocked worms was compared to non-heat-shocked worms to determine genes that are induced upon heat shock in each species; heat-shock-induced genes in each species were compared

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design: 3 biological replicates were performed for both control (NHS) and heat-shocked (HS) worms of each species giving a total of 12 samples

middle: M

first: Amy

last: Pasquinelli


title: Gene expression profiling of multiple sclerosis brain samples

city: Roma

first: Eleonora

last: Arico'

state: RM

address: viale Regina Elena 299

country: Italy

institute: ISS

summary: Recent studies of cortical pathology in secondary progressive multiple sclerosis have shown that a more severe clinical course and the presence of extended subpial grey matter lesions with significant neuronal/glial loss and microglial activation are associated with meningeal inflammation, including the presence of lymphoid-like structures in the subarachnoid space in a proportion of cases.   To investigate the molecular consequences of pro-inflammatory and cytotoxic molecules diffusing from the meninges into the underlying grey matter, we carried out gene expression profiling analysis of the motor cortex from 20 post-mortem multiple sclerosis brains with and without substantial meningeal inflammation and 10 non-neurological controls.    Gene expression profiling of grey matter lesions and normal appearing grey matter not only confirmed the substantial pathological cell changes, which were greatest in multiple sclerosis cases with increased meningeal inflammation, but also demonstrated the upregulation of multiple genes/pathways associated with the inflammatory response. In particular, genes involved in tumour necrosis factor (TNF) signalling were significantly deregulated in MS cases compared to controls.

overall_design: Gene expression profiling analysis of the motor cortex from 20 post-mortem multiple sclerosis brains with and without substantial meningeal inflammation and 10 non-neurological controls

first: Roberta

last: Magliozzi

first: Pascal

last: Durrenberger

last: Aricò

first: Richard

last: Reynolds


title: Transcriptome profiling of prostate cancer cells on GLYATL1 knockdown

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

summary: The protein Glycine-N-Acyltransferase Like 1 (GLYATL1) is involved in detoxification of benzoate and other xenobiotics and is expressed in liver and kidney. Through In silico analysis of cancer gene expression profiling and transcriptome sequencing we revealed an overexpression of GLYATL1 in primary prostate cancer. Confirming these findings by immunohistochemistry we show that GLYATL1 is overexpressed in primary prostate cancer compared to metastatic prostate cancer and benign prostatic tissue. Low grade cancers had higher GLYATL1 expression compared to high grade prostate tumors. Our studies showed that GLYATL1 is upregulated upon androgen treatment in LNCaP prostate cancer cells which harbors ETV1 gene rearrangement.  Furthermore, ETV1 knockdown in LNCaP cells showed downregulation of GLYATL1 suggesting potential regulation of GLYATL1 by ETS transcription factor ETV1. Transcriptome sequencing using the GLYATL1 knockdown prostate cancer cell lines LNCaP showed regulation of multiple metabolic pathways.   In summary, our study characterizes the expression GLYATL1 in prostate cancer and explore its regulation mechanism. Future studies are needed to decipher the biological significance of these findings.

overall_design: RNA from prostate cancer cells (22Rv1 and LnCAP) treated with GLYATL1 shRNA and non-targeting shRNA were sequenced. RNA-seq experiment is intended to identify genes and pathways altered on GLYATL1 knockdown.

first: Marie-Lisa

last: Eich


title: Analysis of transcriptomic profile of iNKT cells

city: London

first: Patricia

last: Barral

address: Guy's Campus

department: Immunobiology

country: United Kingdom

institute: King's College London

summary: The maintenance of tissue homeostasis is critically dependent on the function of tissue-resident lymphocytes, including lipid-reactive invariant natural killer T (iNKT) cells. iNKT cells have unique properties according to their tissues of residency, but if and how the tissue environment shapes their antigen specificity remains unknown. By analysing iNKT cells from tissues of mice and humans we demonstrate that their T cell receptor (TCR) repertoire is highly diverse and is distinct for iNKT cells resident in individual tissues resulting in differential lipid-antigen recognition. Within peripheral tissues, the TCR repertoire of iNKT cell recent thymic emigrants is different from that of mature cells, indicating that the iNKT population is shaped after their arrival to the tissues. Accordingly, in homeostatic conditions the repertoire of iNKT cells is modulated by tissue-specific signals that control iNKT cell activation and proliferation resulting in differential clonal expansion found for cells resident in various organs. Moreover, the iNKT cell TCR repertoire changes in response to lipid immunization and is shaped by age and by environmental changes. Thus, post-thymic modification of the iNKT cell TCR repertoire underpins the distinct antigen specificity of iNKT cells residing in peripheral tissues

overall_design: iNKT cells were sort-purified from lymphoid tissues from 6-week old WT C57BL/6 mice (as CD1d-tetramer+TCR-b+B220-CD11b-CD11c-). Four biological replicates were performed. Tissues: spleen, thymus, mesenteric lymph node (mLN), inguinal lymph node (iLN)

first: Rebeca

last: Jimeno


title: Comparison of gene expression profiles obtained from whole blood and peripheral blood mononuclear cells (PBMCs)

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary: The goal of this study was to compare gene expression profiles between whole blood and PBMCs using the NanoString nCounter panCancer Immune Profiling Panel (730 endogenous genes)

overall_design: Whole blood and PBMCs were obtained from 5 subjects with mild allergic asthma and 5 healthy controls

first: Daniel

last: He


title: H3K9me2 protects lifespan against the transgenerational burden of germline transcription in C. elegans

city: Atlanta

first: David

middle: J.

last: Katz

state: GA

address: 615 Michael St.

department: Cell Biology

country: USA

institute: Emory University School of Medicine

summary: Chromatin state influences lifespan and may allow for the epigenetic inheritance of this complex trait. At sites of active transcription, the COMPASS complex methylates histone H3 at lysine 4 (H3K4me). In Caenorhabditis elegans, reductions in COMPASS extend lifespan, and wild-type descendants of COMPASS mutants inherit longevity for four generations. Here we show that the longevity of COMPASS mutants is itself a transgenerational trait caused by gradual changes in the repressive chromatin factor H3K9me2. H3K9me2 is required for longevity in COMPASS mutants and can confer longevity when increased in other chromatin modifier mutants. H3K9me2 levels also correlate with a transgenerational decline in wild-type lifespan after freezing or starvation. We propose that germline transcription-coupled H3K4me encroaches on H3K9me2 to limit lifespan. Loss of COMPASS complex alleviates the burden of H3K4me and therefore extends lifespan. This study suggests a causal role for a single heterochromatin factor in the establishment and inheritance of longevity.

overall_design: H3K9me2 ChIP-seq in early-, mid-, and late-gen wild-type and wdr-5 mutant populations and in early- and mid-gen wild-type and jhdm-1 mutant populations.

first: Teresa

middle: W

last: Lee

first: Heidi

last: David

first: Amanda

middle: K

last: Engstrom

first: Brandon

last: Carpenter


title: Axiom Sugarcane100K SNP array data for sugarcane mapping population

city: Gainesville

first: Jianping

last: Wang

state: Florida

address: 2033 Mowry Road

department: Agronomy

institute: University of Florida

summary: To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including one F1 population derived from cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.

overall_design: A total of 471 DNA samples were genotyped, including 305 F1 progeny derived from cross between Green German and IND81-146, 153 selfing population derived from CP80-1827, 11 diverse sugarcane accessions as controls and two parental DNA samples from F1 population were replicated for SNP array assay.

first: Qian

last: You

first: Xiping

last: Yang

first: Ze

last: Peng

first: M

last: Islam

first: Sushma

last: Sood

first: Ziliang

last: Luo

first: Jack

last: Comstock

first: Liping

last: Xu


title: Hepatic gene expression in male fetuses from maternal nutrient restriction in mice

first: Victor

last: Han

state: Ontario

address: 1151 Richmond St

department: Biochemistry

institute: University of Western Ontario

summary: The aim of this study was to identify fetal adaptations to gene expression in our mouse model of intrauterine growth restriction (IUGR). Starting at E6.5, pregnant CD-1 mice received either control (ad libitum) or 70% of ad libitum food (maternal nutrient restriction [MNR]). At E18.5, fetal right liver lobes were collected from 2 pups/litter in litters with 11-15 pups. Frozen liver was homogenized for RNA isolations. Isolated RNA was sequenced on a HiSeq2500 with an average read depth of 23M reads and a range of 17-31M reads per sample. Reads were aligned to the mm9 transcriptome with Bowtie2. Normalization and differential expression was done with DESeq2, ALDex2 and EdgeR, and genes were considered in the study if they were consistent in 2 or more tools (FDR <0.1).

overall_design: 10 control and 10 MNR samples were analyzed with (2 pups/ litter)

first: Bethany

last: Radford


title: A minimal DNA sequence within the ARF promoter represses p16INK4A expression via long-range chromatin interaction [Cut&Run ChiP-seq]

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

summary: Loss of function of CDKN2A/B, also known as INK4/ARF [encoding for p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)]), confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand molecular regulation of the locus, we knocked P2A-mCherry into the C-terminus of p16INK4A, and this construct faithfully recapitulated the endogenous transcription. Using this reporter cell line, we performed a noncoding tiling pooled screening targeting open chromatin regions spanning the approximately 500-kb region in the topological associated domain that includes p16INK4A. In both Cas9- and dCas9-KRAB–mediated screenings, we identified a 42-bp DNA sequence within exon 1β of the ARF gene, as the repressive element controlling p16INK4A expression. Chromatin conformation capture indicated that inactivating this element abolished the physical interaction between p15INK4B and ARF, thereby abolishing p16INK4A repression. This study has revealed a new mechanism of transcriptional regulation of p16INK4A by long-range chromatin interaction.

overall_design: CUT&RUN ChIP-seq was performed on p16mCherry/+;dCas9-KRAB cells infected with two sgRNAs targeting the ARF promoter and two sgRNAs targeting the CDKN2aINK4A promoter, using antibodies against dCas9 for a pulldown assay.

first: Yang

last: Zhang

first: Judith

last: Hyle

first: Shaela

last: Wright


title: Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Differentiation of neural retina in organoid cultures from human pluripotent stem cells (PSCs) is highly variable and requires an extended period of as many as 200 days. To provide objective assessment of different protocols and culture conditions, we performed transcriptome analysis and molecular staging using RNA-seq data from developing and adult human retina. Using a modified protocol with 9-cis retinal (9CRAL) instead of widely-used all-trans retinoic acid (ATRA) in the culture media, we show comparable differentiation of human embryonic and induced PSCs into a polarized, laminated architecture with all retinal cell types in retinal organoids. Transcriptome comparisons of multiple developing organoids to that of human fetal and adult retina have permitted molecular staging of the differentiation state and uncovered expedited rod photoreceptor maturation by 9CRAL. A direct comparison with the ATRA-organoid cultures revealed higher expression of rhodopsin and other rod genes in 9CRAL-organoids. Our studies thus provide a framework for transcriptome-based staging of retinal organoids to facilitate advances in human disease modeling and evaluation of therapies.

overall_design: Five cell lines, one ESC line (H9) and four iPSC lines (PEN8E, PEN8E_2, NEI377 and ESP) were cultured across two different institutions and four researchers. Samples were harvested at various time points during differentiation. Differentiation of H9, PENE8E, PENE8E_2, and NEI377-derived organoids followed similar protocols. ESP-derived organoids were differentiated via previously published protocols. Starting at day (D)63, H9 and PEN8E media was supplemented with 9-cis retinal (9CRAL), whereas PEN8E_2, NEI377 and ESP were supplemented with all-trans retinoic acid (ATRA). In addition, H9 experiments were performed a second time and direct comparisons performed at D90 and D120 with either ATRA or 9CRAL.

first: Koray

middle: D

last: Kaya

first: Holly

last: Chen

first: Ryan

last: Kelley

first: Hiroko

last: Shimada

first: Charles

middle: T

last: Drinnan

first: Linn

last: Gieser

first: Kamil

last: Kruczek

first: Slaven

last: Erceg

first: Tiansen

first: Dunja

last: Lukovic

first: Yogita

last: Adlakha

first: Emily

last: Welby

first: Anand

last: Swaroop


title: A minimal DNA sequence within the ARF promoter represses p16INK4A expression via long-range chromatin interaction [Capture-C]

first: Chunliang

last: Li

overall_design: To understand how certain DNA segments in the ARF promoter could regulate the p16INK4A promoter (which is located approximately 13 kb away in the genome) at the long-range chromatin interaction level, we deployed a recently developed multiplex assay of high-resolution chromatin conformation called Capture-C. When we used oligonucleotides to hybridize with the p16INK4A promoter in a 3C library, we detected strong enrichment of sequences at the bait site, confirming the efficiency of the capture. We then identified the ARF promoter as a strong cis-interaction region associated with the p16INK4A promoter by using two different oligonucleotides. Similarly, when we used oligonucleotides to hybridize with the p15INK4B promoter, we also detected strong interaction with the ARF promoter.

first: Yang


title: Transcriptome profiles of wild-type (AF293) and several mutants in Aspergillus fumigatus by RNA-Seq.

city: Daejeon

first: Sang-Cheol

last: Jun

address: 62 Daehak-ro, Dong-gu

institute: Daejeon University

summary: The mRNA profiles of [delta]rgsA, [delta]nopA, [delta]rgdA ([delta]swi4), [delta]mbpA ([delta]swi6) mutants and wild-type (AF293) of A. fumigatus.

overall_design: The construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit according to the manufacturer’s instructions. mRNA profiles of wild-type and mutants were generated by single-end 75 sequencing using Illumina NextSeq 500. Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools. The RT data were processed based on Quantile normalization method using EdgeR within R using Bioconductor. Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).

first: Kwang-Soo

last: Shin


title: A minimal DNA sequence within the ARF promoter represses p16INK4A expression via long-range chromatin interaction


title: Expression profiling of multiple Escherichia coli strains on glucose minimal media

city: San Diego

last: Sastry

address: 9500 Gilman Dr

department: Bioengineering

summary: RNA sequencing was performed on multiple E. coli strains grown on glucose minimal media

overall_design: Growth of E. coli with various supplements was performed with biological duplicates

middle: V

first: Ye

last: Gao

first: Richard

last: Szubin

first: Ying

last: Hefner

first: Sibei

last: Xu

first: Donghyuk

last: Kim


title: Expression profiling to identify independent regulatory signals in Escherichia coli

summary: RNA sequencing was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators


title: Expression profiling of E. coli K-12 MG1655

summary: Previously unpublished expression data from E. coli K-12 MG1655 involved in the creation of a large RNAseq database.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Mostly duplicate samples of MG1655 or BW25113 grown in M9 glucose minimal media. Includes gene knockouts of cbl, cra, fabR and fadR. Also includes WT strain grown without the presence of trace elements, and WT supplemented with glutamine.


title: Deconvoluting Independent Regulatory Signals in the Escherichia coli Transcriptome

institute: UCSD

summary: ChIPexo experiment was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators

overall_design: Identification of genome-wide bindings for transcripton factors MetJ and CysB


title: WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

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

overall_design: Refer to individual Series


title: WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway [RNA-seq CCL]

summary: The core subunit of the COMPASS-like complex, WD Repeat Domain 5 (WDR5) has a prominent role in reprogramming and Epithelial-to-Mesenchymal transition (EMT) in different tumor types. Our evidences support a model in which WDR5 is prominent for EMT and metastasis dissemination in breast cancer patient-derived xenografts and cell lines. Moreover, WDR5 silencing abrogates TGFB pathway activation and reverts mesenchymal into epithelial phenotype, by inhibiting transcription of main master regulators of EMT (CDH2, TWIST1, SNAI1, SNAI2 and ZEB1).  Our data suggest that WDR5 inhibition may be a successful approach to prevent progression of metastatic BC.

overall_design: Total RNA from MCF10DCIS.com human breast cancer cell line was processed for multiparallel sequencing. Experiments were carried out in shLuc (control) and WDR5 silenced cells

first: Simona

last: Punzi

first: Luisa

last: Lanfrancone


title: WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway [RNA-seq PDX]

overall_design: Total RNA from human breast cancer metastatic patient-derived xenografts (PDXs) line was processed for multiparallel sequencing. Experiments were carried out in shLuc (control) and WDR5 silenced cells


title: A maple syrup extract alters lipid metabolism in obese type 2 diabetic model mice [adipose]

city: Gunma

first: Tsudoi

last: Toyoda

address: 54 Nakaorui-machi, Takasaki-shi

country: Japan

institute: Tkasaki University of Health and Welfare

summary: Some polyphenols are known to improve the symptoms of diabetes. In the present study, we investigated the effects of a polyphenol-rich extract of maple syrup (MSx) on a diabetic mouse model. KK-Ay mice were fed a normal or 0.05% MSx-supplemented diet for 42 days. Body weight, food intake, serum biochemical parameters, and fecal total bile acid were measured. Gene expression of liver and epididymal white adipose tissue (WAT) and cecal microbiota were analyzed. Data were analyzed with an unpaired two-tailed Student’s t test or Welch’s t test according to the results of the F test. Serum low-density lipoprotein cholesterol levels were significantly reduced in mice that consumed MSx. Hepatic genes related to fatty acid degradation and cholesterol catabolism were upregulated in mice that consumed MSx. In contrast, the expression of genes related to lipid metabolism in WAT was unaffected by the intake of MSx. There were no significant differences between the two groups in terms of total bile acid level in the feces and the relative abundance of bacteria in the cecum. Our results primarily indicate that MSx can help alleviate one of the symptoms of dyslipidemia.

overall_design: Male KK-Ay mice 4 weeks of age were purchased from CLEA Japan (Tokyo, Japan). The mice were individually housed in a room maintained at a temperature ranging from 21 to 23 °C with 50–70% relative humidity and a 12:12-h light/dark cycle. Normal and 0.05% MSx-supplemented diets were prepared based on the AIN-93G formula by Oriental Yeast Co. (Tokyo, Japan). After 4 days of acclimation, the mice were divided into two groups (n = 8 each) with approximately equal mean body weights. Mice were fed the normal or MSx diet for 42 days and were allowed free access to the diet and ultrapure water during this period. Body weight and food intake were measured every 2 days. Feces were collected on days 36–38 of the testing period and were stored at − 80 °C until use. After 16 h of food deprivation, mice were sacrificed under sodium pentobarbital anesthesia.

first: Asuka

last: Kamei

first: Tomoko

last: Ishijima

first: Keiko

last: Abe

first: Shinji

last: Okada


title: A maple syrup extract alters lipid metabolism in obese type 2 diabetic model mice [liver]


title: Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos

city: Beijing

first: Zhenhai

last: Du

country: China

summary: In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.

overall_design: Mouse primordial germ cells (PGCs) are collected by FACs with OG2 mice. WT mouse oocytes were collected from C57BL/6N mice. And WT preimplantation embryos were obtained from crosses of C57BL/6N and PWK/PhJ. Ring1 KO Rnf2 flfl and  Ring1 Rnf2 dKO FGOs were collected from Ring1-/-Rnf2flox/flox and Ring1-/-Rnf2 flox/flox; Zp3-Cre mice. Eed flfl and Eed CKO oocytes were collected from Eed flox/flox and Eed flox/flox; Gdf9-Cre mice. Eed flwt late 2cell were obtained from crosses of Eed flox/flox females and PWK/PhJ males.  Eed mNull late 2cell were obtained from crosses of Eed flox/flox; Gdf9-Cre  females and PWK?PhJ males. Hi-C experiments were performed in these PGCs, oocytes and embryos at various stages. CUT&RUN experiments were performed in Eed flfl and Eed CKO oocytes. RNA-seq experiments were performed in  Ring1 KO Rnf2 flfl, Ring1 Rnf2 dKO FGOs, Eed flfl and Eed CKO FGOs.

first: Hui

last: Zheng

first: Yumiko

last: Kawamura

first: Ke

last: Zhang

first: Antoine

last: Peters

first: Wei

last: Xie


title: Comparative Transcriptome analysis of hESCs- and iPSCs-derived lentoid body

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary:
Purpose: To investigate the transcriptomes of H9 human embryonic stem cells (hESCs)- and peripheral blood mononuclear cells (PBMC) originated induced pluripotent stem cells (iPSCs)-derived early stage lentoid bodies at day 24 through RNA-Seq based whole transcriptome sequencing.
Methods:  The PBMC obtained from a healthy donor were subjected to generate iPSCs using Sendai-virus delivery system Cytotune 2.0 whereas the H9 hESCs were obtained commercially. Both hESCs and iPSCs were differentiated into lentoid bodies using “fried egg” method with feeder-free conditions as described previously. The differentiating lentoid bodies were examined for the expression of lens-specific and pluripotency markers at days 0, 6, 10, 15 and 24 by quantitative real-time PCR (qRT-PCR). Briefly, four biological replicates for each hESCs- and iPSC-derived lentoid bodies at day 24 were used for the RNA-Seq library preparation followed by sequencing on a single lane of HiSeq 2500. The raw reads were processed and analyzed using Lasergene Genomics Suite and the expression profiles were examined for differential expression using Spotfire DecisionSite with Functional Genomics.
Results: The differentiating lentoid bodies at day 24 revealed transparent lens like morphological features with an increased expression of lens-specific markers including CRYGC. A total of 193.41, and 170.00 million reads were obtained for hESCs- and iPSCs-derived lentoid bodies, respectively. Of these, >96% reads aligned to the human reference genome resulting in >200x sequence coverage for both hESCs- and iPSCs-derived lentoid bodies. Additional analysis identified expression (≥ 0.659 RPKM) of 13,991 and 14,018 genes in hESCs- and iPSCs-derived lentoid bodies, respectively, representing ~70% of the total human protein-coding transcriptome expressed in lentoid bodies. Finally, a comparative analysis of both hESCs- and iPSCs-derived lentoid bodies transcriptomes identified >96% similarity at the gene level.
Conclusion: The transcriptome analysis revealed an overall similar transcriptional profile in both hESCs- and iPSCs-derived lentoid bodies during differentiation at day 24.

overall_design: The hESCs and iPSCs were differentiated into lentoid bodies using “fried egg” method. Subsequently, RNA-Seq based whole transcriptome profiling was performed for a comparative analysis of hESCs and iPSCs-derived lentoid bodies.

first: Muhammad

last: Ali

first: Firoz

last: Kabir

first: C

middle: C

last: Talbot

first: Shahid

last: Khan

first: S

middle: A