title: Transcriptome sequencing of isolated MNT-1cells after 72 h coculturing with KRT5 downregulation HaCaT cells

city: Nanjing

first: Weixue

last: Jia

state: Jiangsu

address: 12 Jiangwangmiao St., Nanjing, P.R. China.

institute: Hospital for Skin Diseases (Institute of Dermatology), Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To investigate the effect of KRT5-KD Hecat cells on cocultured melanocytes

overall_design: MNT-1 cells were obtained from American Type Culture Collection (Manassas, VA, USA), and cultured according to standard procedures. MNT-1 cells were seeded at a density of 2×10^4 cells/ml and cultured for 24 h. Lentivirus-infected HaCaT cells were then seeded at a density of 4×104 cells/ml in high-glucose DMEM containing 20% fetal bovine serum for 72 h. The cells were digested with trypsin, and GFP-negative cells were isolated by flow cytometry, and total mRNA was extracted.

first: Jia

last: Weixue

first: Li

last: Chengrang


title: RNA-seq analysis of the effect of surgical treatment on secretory eutopic endometrium of patients with endometriosis

status: Public on Dec 31 2023

city: Guangzhou

first: Rui

last: Xiang

state: Guangdong

address: the 26th Yuancun Erheng Road

country: China

institute: the sixth affiliated hospital of Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was conducted for RNA expression profiling from secretory eutopic endometrium of 6 patients with endometriosis who didn't receive surgery and 12 patients with endometriosis who received surgery in less than 24 months. The differential expression of RNAs was generated.

first: Peigen

last: Chen

first: Zhi

last: Zeng

first: Huijun

last: Liu

first: Juan

last: Zhou

first: Chuanchuan

first: Jintao

last: Peng

first: Haitao


title: Expression profiles of circRNAs in goat skeletal muscle development

city: nanjign

first: yi

middle: xuan

last: fan

address: No 1 weigang

institute: nanjing agricultural university

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore functional circRNAs during goat muscle development, we systematically investigated the circRNAs profiles using high throughput transcriptome sequencing technology (RNA-seq) at key developmental stages of fetus and Kid in Haimen goat.

overall_design: CircRNA profiles of   goat skeletal muscle were generated by sequencing at key development stages（75 d fetus and 1 d Kid ), three skeletal samples for each developmental.

first: Yixuan

last: Fan


title: Effects of AKT/WEE1 inhibitors or ALDH inhibitor combined with PD-1 antibody on melanoma

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

country: USA

institute: Penn State University

summary: The effects of AKT/WEE1 inhibitors or ALDH inhibitor combined with PD-1 antibody on melanoma were examined.  Mouse B16F10 melanoma cells were subcutaneously injected into C57/B6 mice.  When tumors were well-vascularized, mice were treated with  anti-PD-1, AKT I (AZD5363)+WEE1 I (MK1775), AZD5363+MK1775+anti-PD-1, ALDH I (KS100), KS100+ anti-PD-1 daily.  Mice were sacrificed when tumors in the control group (DMSO treated) reached 2000 mm3 and tumors were removed.  RNA was extracted from tumor samples and gene expression was analized using RNAseq analysis.

overall_design: Total 6 samples were analyzed; tumors for each treatment group were pooled before RNA extraction and RNAseq analysis.

first: Saketh

middle: S

last: Dinavahi

first: Gavin

middle: P

last: Robertson


title: Ribo-seq analysis in HEK293A cells with or without IRE1a knockdown

city: DALLAS

first: Zhao

middle: V.

last: Wang

state: TX

address: 6000 Harry Hines Blvd

institute: UT southwestern medical center

summary: We conducted RNA-seq and Ribo-seq for the same samples. IRE1a was knockde down by siRNA. There are two replicates for each group.

overall_design: HEK293A cells were transfected with Control and IRE1a siRNA, then were treated FBS to induce protein synthesis. At last Ribo-seq was conducted.

first: Chao

last: Li

middle: V


title: Next generation RNA sequencing elucidates the antitumor effects of Zelnorm via immune microenvironment regulation using DU145 tumor model

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

summary: Prostate cancer DU145 tumors were subcutaneously established in male nude mice. In nude mice, Zelnorm were orally administrated. Tumor volume and body weight were assessed (tumor volume=1/2 (length×width2)). Tumors were excised and weighted. Tumor samples were profiled by RNA-seq analysis. Respectively, to differentiate the gene expression originated from human (cancer cells) or mouse (tumor TME part), data were mapped against human (GRCh38) and mouse (GRCm38) genomes separately.

overall_design: control group (NC), Zelnorm group (MBZ)

first: Qiaoling

last: Song

first: Chenyang

last: Zhao

first: Jinbo

last: Yang

first: Lijuan

last: Wu


title: Single-cell RNA profiling of living cells with LC-seq

summary: Our study reports a new technique, named ‘Live cell sequencing LC-seq’, by which RNAs can be profiled from single live cells with minimal deleterious cellular effects using a conventional electrophysiology rig. We show that subsequent physiological monitoring on the same cells is doable. Furthermore, benchmarking against single whole-cell sequencing WC-seq confirmed the validity of the LC-seq method. We also applied LC-seq to reveal the molecular changes caused by chemical treatment of a cancer cell line and molecular characteristics of neuronal subtypes in the brain.

sample_organism:
Homo sapiens
Mus musculus
blank sample

platform_organism:
Homo sapiens
Mus musculus
blank sample

overall_design: Single-cell RNA profiling of living cancer cells in vitro and cortical neurons in mouse brain coronal slices with LC-seq and WC-seq

first: Kazue

last: Hashimoto-Torii

first: Payal

last: Banerjee

first: Toru

last: Sasaki


title: The RNA-seq analysis of RNAi-GLAD fruit flies

city: Shanghai

first: Yanshan

last: Fang

address: 100 Haike Rd, Building 13

institute: Interdisciplinary Research Center on Biology and Chemistry

summary: In our research, we identified GLAD as a regulator gene of longevity and glia-associated neurodegeneration. This is the RNA-seq data of RNAi-GLAD fruit flies and the control (RNAi-GFP).

overall_design: RNA samples are collected from heads of the adult TubGS>RNAi-GLAD and the TubGS>RNAi-GFP flies are collected on Day 7 after RU486 induction.

first: Shunpan

last: Shu

first: Mingsheng

last: Jiang

first: Xue

last: Deng

first: Hao

last: He

first: Kun

last: Qu


title: Intrinsic innate immunostimulation by small circRNA vaccines [tumor]

city: Richmond

first: Guizhi

last: Zhu

state: VA

address: 410 N 12th St

institute: Virginia Commonwealth University

summary: Various RNAs have been shown to elicit innate immunity by activating endosomal PRRs such as Toll-like receptors 3/7/8 (TLR3/7/8), and cytosolic PRRs (e.g., retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated protein 5 (MDA5)). Such innate immunity provides cytokines and co-stimulation signals that are essential for adaptive immunomodulation.

overall_design: We further employed RNA-seq genome-wide transcriptome analysis for the comprehensive understanding of the immunomodulation mechanisms by small circRNA vaccines in BMDCs or tumor tissues.

first: Yu

last: Zhang

first: Jinze

last: Liu

first: Katarzyna

middle: M

last: Tyc


title: Next generation RNA sequencing elucidates the antitumor effects of Zelnorm via immune microenvironment regulation

first: qiaoling

last: song

summary: Syngeneic B16F10 tumors were subcutaneously established in female C57BL/6J mice. Zelnorm (1.25 mg/kg) were orally administrated once every two days. Tumor volume and body weight were assessed (tumor volume=1/2 (length×width2)). Tumors were excised and weighted. Tumor samples were profiled by RNA-seq analysis.

first: Qiaoling

last: Song


title: RNA expression profiling of CD13/CD33-positive and CD13/CD33-negative B-ALL patients

city: Chengdu

first: Hongli

last: Lai

state: Sichuan

address: No. 37, Guoxue Alley

institute: West China Hospital, Sichuan University

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

overall_design: Refer to individual Series


title: RNA expression profiling of CD13/CD33-positive and CD13/CD33-negative B-ALL patients [miRNA expression]

summary: To study the effect of expression of CD13/CD33 on the pathogenesis of B-cell acute lymphoblastic (B-ALL), we collected samples from 4 CD13/CD33-positive and 4 CD13/CD33-negative B-ALL patients and performed RNA-seq.

overall_design: RNA profiles of CD13/CD33-positive and CD13/CD33-negative B-ALL cells

first: Hongyan

last: Liao

first: Jiao

last: Chen

first: Qin

last: Zheng


title: High throughput gene expression data from H520 human lung squamous carcinoma cell lines with BLU9931 and palbociclib treatment

city: shanghai

first: Yanshuang

state: China

address: 1954 Huashan Road, Shanghai Jiao Tong University, Shanghai 200030, PR China

institute: Shanghai Jiao Tong University

summary: The combination treatment of BLU9931 andpalbociclib potentiated the growth inhibition and arrested cells in G1 phase.

overall_design: LUSC cell line H520 was treated with BLU9931 (1 μM), palbociclib (1 μM) or their combination for 72 h

first: Tingyu

last: Wu

first: Weiliang

last: Xia


title: Transcriptomics analysis of NOP16-regulated genes in MDA-MB231 cells [RNA-seq]

city: Palo Alto

first: Eric

middle: Lieberman

last: Greer

state: CA

address: Alway M314 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: The goal of RNA-seq is to identify the global transcriptional alteration by NOP16 overexpression or deletion in triple negative breast cancer cell line MDA-MB231 cells. Three (or Two) biological replicates were assigned for each group and in total 6 groups were prepared for these RNA seq libraries. We mapped about 20 million reads per sample to hg38 human reference genome, and counted and normalized each reads number and identified the differentially expressed genes.

overall_design: (1) RNA-seq analysis using MDA-MB231-NOP16 stably overexpression(OE1 or OE4) and empty vector control(E.V.)  (2) RNA-seq analysis using MDA-MB231-NOP16 bulk KO (KO1 or KO4) and control line(no guide RNA control: n.g.)  Total RNA was extracted from each cell lines, and cDNA libraries were generated for NGS sequencing in biological triplicate (or partially duplicate), and sequenced by NovaSeq 6000.  (2) RNA-seq analysis using MDA-MB231-NOP16 bulk KO (KO1 or KO4) and control line(no guide RNA control: n.g.)  Total RNA was extracted from each cell lines, and cDNA libraries were generated for NGS sequencing in biological triplicate (or partially duplicate), and sequenced by NovaSeq 6000.

first: Ken

last: Takashima

first: Meeta

last: Mistry


title: RNA expression profiling of CD13/CD33-positive and CD13/CD33-negative B-ALL patients [mRNA expression]

overall_design:
RNA profiles of CD13/CD33-positive and CD13/CD33-negative B-ALL cells

**Raw data not provided due to patient privacy concerns**


title: CUT&RUN analysis for NOP16-mediated H3K27me3 alteration in MDA-MB231 cells [CUT&RUN-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of CUT&RUN-seq is to identify the global alteration of H3K27me3 levels by NOP16 overexpression or deletion in triple negative breast cancer cell line MDA-MB231 cells. Three (or Two) biological replicates were assigned for each group and in total 6 groups were prepared for these CUT&RUN-seq libraries. We mapped about 20 million reads per sample to hg38 human reference genome, and counted and normalized each reads number and identified H3K27me3 distribution.

overall_design: (1) CUT&RUN-seq analysis using MDA-MB231-NOP16 stably overexpression(OE1 or OE4) and empty vector control(E.V.)  (2) CUT&RUN-seq analysis using MDA-MB231-NOP16 bulk KO (KO1 or KO4) and control line(no guide RNA control: n.g.)  1.5x105 nuclei extracted from each cell lines were used for CUT&RUN reaction (Skene, P. J. & Henikoff, S, eLife, 2017). CUT&RUN library were generated for NGS sequencing in biological triplicate (or partially duplicate), and sequenced by Illumina NextSeq 500.


title: Glutaminase (GLS) was a target gene downstream of lithocholic acid inhibiting gallbladder cancer

first: Weijian

last: Li

state: Shanghai

address: NO. 160, Pujian Road, Pudong New District, Shanghai, China

institute: Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary:
Purpose:To further explore the molecular mechanisms of LCA treatment underlying its tumor suppressive functions.
Methods:For the NOZ cells cultures, there were two different conditions performed in biological triplicates: (I) mock (DMSO), (II) 150 μM LCA for 24 h. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Paired t-test was used to normalize and statistically analyze the data. The threshold we set to screen for upregulated and downregulated genes with a fold change >0 and a padj-value < 0.05. Hierarchical clustering was performed and a heat map was constructed with edgeR R package (3.18.1) to visualize differential mRNA   expression. Gene set enrichment analysis was conducted with the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp.
Results: By means of RNA-seq and subsequent data analysis with volcano plot and hierarchical clustering, we found that LCA treatment led to a different gene expression profile with the upregulation of 3607 genes and the downregulation of 3501genes compared with those in cells treated with mock. Gene Set Enrichment Analysis (GSEA) suggested that alanine, aspartate, and glutamate metabolism pathways were top-listed in the inhibitory regulation of LCA, and the heatmap plots showed that the pathways involved a set of 35genes. In addition, qRT-PCR was used to confirm the expression of several metabolism genes including GLS, ASS1, CPS1, ASNS, ABAT, and ADSSL. We were particularly interested in the commonly downregulated GLS in both NOZ and EH-GB1 cells, which mediates glutamate and glutamine metabolism. As the result, protein levels of GLS were dramatically inhibited by LCA in NOZ and EH-GB1 cells in a time-dependent manner as compared with the untreated cancer cells,
Conclusion: GLS was a downstream effector of LCA treatment in gallbladder cancer.

overall_design: mRNA profiles of LCA treated gallbladder cancer cell line


title: Inhibition of the IL-17A axis Protects against Immune-related Adverse Events while Supporting Checkpoint Inhibitor Anti-tumor Efficacy [RNA-seq (human)]

city: Los Angeles

first: Melissa

middle: G

last: Lechner

address: 10833 Le Conte Ave, CHS 57-154

department: Div of Endocrinology, Diabetes, and Metabolism

institute: UCLA Geffen School of Medicine

summary: Checkpoint inhibitor (ICI) immunotherapy leverages the body’s own immune system to attack cancer cells but leads to unwanted autoimmune side effects in up to 60% of patients. Such immune related adverse events (IrAE) lead to treatment interruption, permanent organ dysfunction, hospitalization and premature death. Thyroiditis is one of the most common IrAE, but the cause of thyroid IrAE remains unknown. Here we present a novel mouse model in which checkpoint inhibitor therapy leads to multi-organ autoimmune infiltrates and show that activation and infiltration of Type 3 immune cells including IL17A+ RORt+ CD4+ (T helper 17 or Th17) and gamma delta 17 (T17) T cells promote thyroid IrAE development. In parallel, Th17 and T17 cells were similarly expanded in cancer patients treated with ICI. Furthermore, antibody-based inhibition of IL-17A, a clinically available therapy, significantly reduced thyroid IrAE development in ICI-treated mice. Finally, combination of IL-17A neutralization with ICI treatment in a mouse tumor model did not reduce ICI anti-tumor efficacy and indeed showed a trend toward enhancement. These studies suggest that targeting Th17 and 17 function may reduce IrAE without impairing ICI anti-tumor efficacy and may be a generalizable strategy to address IL17-mediated IrAE.

overall_design: This dataset contains scRNAseq data for CD45+ immune cells isolated from human thyroid fine needle aspirate specimens. Specimens are derived from patients with spontaneous thyroid autoimmunity (Hashimoto's thyroiditis) or immune checkpoint inhibtor (ICI)-associated thyroiditis.

first: Anushi

middle: Y

last: Patel

first: Willy

last: Hugo

first: Trevor

middle: E

last: Angell

first: Mandy

middle: I

last: Cheng

first: Marissa

last: Pioso

first: Aline

middle: T

last: Hoang

first: Natalie

last: Yakobian

first: Ethan

middle: C

last: McCarthy

first: Ho-Chung

first: Eduardo

middle: D

last: Rodriguez

first: Lily

last: Guo

first: Michael

last: Astourian

first: Alexandra

last: Drakaki

first: Pouyan

last: Famini

first: Antoni

last: Ribas

first: Maureen

middle: A

last: Su


title: Identification of TBX3 and shared HAND2-TBX3 target gene in early mouse limb buds [RNA-seq]

city: Basel

first: Aimee

last: Zuniga

address: Mattenstrasse, 28 4058

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: ChIP-seq is combined with RNA-seq analysis to identify the TBX3 and HAND2 target genes during mouse limb bud development. This analysis identifies the DEGs and direct transcriptional targets of HAND2 and TBX3 during the early determinative period critical to establishment of limb axis polarity and the SHH signaling center in the posterior limb bud mesenchyme. In particular, bioinformatics analysis identifies the target gene networks that are co-regulated by both TBX3 and HAND2 transcription factors in the limb bud mesenchyme. A significant fraction of the target genes identified are required for normal limb bud development and their spatio-temporal expression patterns are changed in mutant limb buds at early stages. This project was supported by SNSF Grant 310030_184734 to Rolf Zeller (project partner: Aimée Zuniga).

overall_design: RNA-seq analysis of a) Hand2-deficient and b) Tbx3-deficient mouse forelimb buds

first: Shalu

last: Jhanwar

first: Ausra

last: Girdziusaite

first: Rolf

last: Zeller


title: Identification of TBX3 and shared HAND2-TBX3 target genes in early mouse limb buds [ChIP-seq]

overall_design: Identification of the genomic regions enriched in TBX3 chromatin complexes in mouse limb buds using ChIP-seq

first: Rushikesh

last: Sheth


title: Identification of TBX3 and shared HAND2-TBX3 target genes in early mouse limb buds


title: ChIP-seq analysis of COUP-TFI enrichment in neural retina.

first: Ran

last: Wang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: The genome-wide binding sites of COUP-TFI in neural retina.

overall_design: Examination of COUP-TFI enrichment distributions in neural retina.

first: Xianfa

last: Yang

first: Su

last: Feng

first: Naihe

last: Jing

first: Ke

last: Tang


title: Global gene expression prolife of primary cultured murine stress erythroid progenitors.

city: University Pk

first: Robert

last: Paulson

address: 115 Henning Building, Penn State University

department: Veterinary and Biomedical Sciences

summary: Inflammation inhibits steady state erythropoiesis, while at the same time it induces stress erythropoiesis to maintain erythroid homeostasis. Stress erythropoiesis relies on the rapid expansion of early progenitors that do not differentiate until the increase in serum Epo promotes a transition in progenitors to enable their synchronous differentiation. RNA-seq analysis allows us to identify an inflammatory transcriptome signature in early progenitors that induces iNOS-derived NO production. The accumulation of NO establishes a metabolism that promotes cell proliferation while inhibiting the differentiation of early progenitors. In contrast, the transition of progenitors to differentiation is marked by the suppressed inflammatory responses and a consequent decrease of iNOS-derived NO. We show that Epo initiates this transition response by altering progenitor metabolism to support itaconate production, resulting in the activation of Nrf2 that suppresses the inflammatory responses, which in turn alleviates the NO-mediated inhibition of erythroid program. Consequent differentiation of stress erythroid progenitors generates a bolus of new erythrocytes to maintain erythroid homeostasis until steady state erythropoiesis can resume.

overall_design: mRNA profiles of primary cultured stress erythroid progenitors in five conditions: WT expansion cultures treated with vehicle or 1400w, WT differentiation cultures treated with vehicle or 1400w, and Nrf2-/- differentiation cultures treated with vehicle.

first: Baiye

last: Ruan


title: Transcriptome analysis of gene expression in Lasiodiplodia theobromae

city: Beijing

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

summary: Botryosphaeriaceae is an important fungal family that can colonize a wide range of woody hosts including economically important plants and cause serious diseases worldwide. To uncover the virulence variation in Lasiodiplodia theobromae, we sequenced the transcriptome of Las1 in L. theobromae inoculated with the stems of V.vinifera using dual-RNAseq method. We found a lot of expanded genes were induced after inoculated with grapevine compared with the transcriptome of Las1 that was maintained in PDA under the same condition.

overall_design: The L. theobromae strain Las1 was selected for inoculation tests on detached Vitis vinifera cv. ‘Summer Black’ branches. Briefly, wounds of green grapevine shoots were inoculated with mycelium plugs (5 mm in diameter) cut with a cork borer and then maintained under an alternating dark/light cycle inside a growth chamber with constant humidity and a temperature of 25 °C. All the inoculated grapevine tissues were collected at 24 h post-inoculation, and fungal mycelia collected from PDA at 24 h post-culturing at 25 °C were used for subsequent RNA-seq analyses. Total RNA was extracted and processed following Novogene Company methodologies for preparing Illumina RNA-seq libraries. Paired-end sequencing was performed on an Illumina HiSeq 4000 platform to generate 150-bp paired-end reads. RNA-seq was performed on three independent biological replicates.

first: Jiye

last: Yan


title: Microsatellite stable Left Colon Cancer distinct in Indigenous African patients versus other ethnic groups

city: Braamfontein

first: Michelle

middle: Lynn

last: McCabe

state: Gauteng

address: National Health Laboratory Services, Corner Hospital and De Korte street

department: Human Genetics

country: South Africa

institute: NHLS

summary:
A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease.
This study revealed distinct histopathological features for Left Colon Cancer (LCC), and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients.

overall_design: qPCR gene expression profiling.  RNA from FFPE tumour tissue from 3-4 CRC tumour samples were pooled according to their molecular subgroup status: 1) MSI-L LCC, 2) MSI-L RCC, 3) MSS LCC and 4) MSS RCC. Equal amount total RNA from each sample was pooled prior to gene expression analysis.

middle: L

first: Clement

last: Penny

first: Pumza

last: Magangane

first: Sheefa

last: Mirza

first: Yvonne

last: Perner


title: RNA-Seq analysis of recombinant articulatin B chain treated murine bone marrow-derived dendritic cells

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: We performed RNA-seq analysis using primary murine bone marrow derived dendritic cells (BM-DCs) for recombinant articulatin B chain (rATB) treatment. We reported that rATB regulates immunological related genes in BM-DCs. rATB  induces CD4 T cell type I driven  and maturation genes in BM-DCs.

overall_design: Examination of mRNA profile of  primary murine bone marrow derived dendritic cells under rATB treatment.

first: Tzu-Li

last: Lu

first: Yuh-Pyng

last: Sher

first: Hui-Chen

last: Chen

first: Ling-Heng

last: Hsu

first: Chen-Chen

last: Lee


title: Nutritional geometry framework on sleep in Drosophila

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

institute: School of Pharmaceutical Sciences (Shenzhen)

summary: Sleep is a fundamental physiological function and is essential for all animals, including humans. Sleep has been reported to be affected by diet compositions including protein (P) and carbohydrates (C), but there has not been a systematic investigation of the effect of dietary macronutrient balance on sleep. Here, we used the nutritional geometry framework (NGF) to explore the interactive effects on sleep of protein (P) and carbohydrate (C) in the model organism Drosophila. Our results showed that the combination of low protein and moderate carbohydrate prolonged sleep time and sleep quality, with fewer sleep episodes and longer sleep duration. We further found that the effects of macronutrients on sleep mirrored levels of haemolymph glucose and whole-body glycogen. Moreover, transcriptome analyses revealed that high protein, low carbohydrate diet elevated the gene expression of amino acid metabolic pathways when compared to a diet lacking protein, with the glycine, serine, threonine metabolism pathway being most strongly regulated. However, sleep was not decreased in flies fed on a protein-deficient diet with added glycine, serine and threonine. In summary, our results demonstrate that sleep is affected by the balance of protein and carbohydrates in the diet and that reduced protein coupled with moderate carbohydrate promote sleep duration and quality.

overall_design: Brain mRNA profiles of 4-7-day old flies treated with low protein and high carbohydrates diet（P:C=0:1,180g/L) that caused longest sleep time and high protein and low carbohydrates diet（P:C=1:1,180g/L) that induced shortest sleep time.

first: Meiling

last: Lai

first: Anqi

last: Li

first: Alistair

last: Senior

first: G

last: Neely

first: Stephen

middle: J

last: Simpson

first: Qiao-Ping

last: Wang


title: Transcriptomic analysis of Francisella tularensis infected lungs from human AT-1 receptor expressing mice II

city: Valhalla

first: Sudhir

last: Jain

state: New York

address: 15 Dana Rd

department: Pathology, Microbiology and Immunology

institute: New York Medical Collage

summary: Human angiotensin-II receptor type-I (hAT1R) over-expression may cause adverse pathological outcomes due to renin-angiotensin system overactivity. We have shown that transgenic (TG) mice containing Hap-I (hypertensive genotype) of hAT1R gene are more prone to develop metabolic syndrome (MetS) disorders as compared to the TG mice with Hap-II (normotensive genotype). Aging together with an increased risk of hypertension, can affect multiple organ systems, including increased susceptibility to various pathogenic infections. The current study, therefore, was designed to examine the potential role of aging and hypertension on lung pathology and altered transcriptome, in our TG mice, in response to Francisella tularensis live vaccine strain (LVS) intranasal infection. Our results showed that in comparison to Hap-II, aged Hap-I TG mice had a significantly higher mortality post-infection; elevated lung pathology; and altered gene expression profile. Consistent with worsened phenotype in aged Hap-I mice post LVS infection, RNA-seq data from their lungs revealed that >1400 genes (p <0.005) were significantly altered. Bioinformatics analysis identified major alterations in canonical pathways related to immune responses including interferon signaling, antigen presentation, agranulocyte adhesion and dendritic cell maturation. These alterations in turn resulted in disorders including, lung infection, inflammation, and immunological diseases. Importantly, IFNG, STAT1, STAT3 and TNF were among the top upstream regulators significantly affected by LVS infection. Overall, these results provide a deeper insight in molecular signaling associated with hypertension associated lung infections in aged subjects.

overall_design: overall 6 samples were analysed by RNA seq. These samples were devided into two groups in triplicate. These groups are #1 Hap-II aged; #2 Hap-II aged+LVS

first: Harshada

last: Ketkar

first: Weihua

last: Huang


title: Effect Of Western Diet On Renal Transcriptome Of Hypertensive Mice Overexpressing Human Angiotensin Receptor Type 1 II

summary: Over-expression of human angiotensin-II receptor type1 (hAT1R) may cause pathological outcomes due to overactivation of renin-angiotensin system. Transgenic (TG) mice containing Hap-I (hypertensive genotype) of human hAT1R gene are more prone to develop metabolic syndrome disorders as compared to TG mice with Hap-II (normotensive genotype). This gene variant associated risk of hypertension together with Western diet and aging may lead to renal disorders. However, mechanisms underlying this process are not well examined. For this purpose, we studied the renal gene expression alterations in aged TG mice containing either Hap-I or Hap-II of hAT1R gene. Aged mice (20-24 months of age) were maintained on a regular diet or high fat diet with 2% NaCl (Western diet, WD) for 16 weeks. On a regular diet, aged Hap-I mice presented higher (~9 mmHg) systolic blood pressure with respect to age-matched Hap-II animals. Following administration of Western diet, blood pressure increased in both groups of mice, but to a larger extent in Hap-I animals (~15 mmHg in comparison to ~7 mmHg in Hap-II). Aged Hap-I mice on Western diet showed increased renal fibrosis. RNA-seq data from renal tissue of Hap-I aged mice revealed that WD significantly altered the expression of >400 genes (p-adj. <0.05). Bioinformatics analysis (Qiagen IPA software) identified major alterations in main canonical pathways involved in renal function and oxidative damage. These changes in turn resulted in kidney failure, renal tubular injury, and renal proliferation. In addition, post WD treatment, RNA seq. analysis from Hap-I and Hap-II kidneys also reveals haplotype specific regulation of genes associated with blood pressure regulation and kidney disorders. Overall, these results indicate that Western diet promotes hypertension and fibrosis in the kidneys of aged mice. These alterations are paralleled by perturbation of renal transcriptional profile. Overall, these studies will assist in the identification of novel mechanisms and molecules involved in hypertension and associated kidney pathophysiology.

overall_design: overall 8 samples were analysed by RNA seq. These samples were devided into two groups (4 ANIMALS EACH GROUP). These groups are #1 Hap-II adults+WD (western diet); #2  Hap-II aged+WD


title: Effect Of Western Diet On Renal Transcriptome Of Hypertensive Mice Overexpressing Human Angiotensin Receptor Type 1 I

overall_design: overall 24 samples were analysed by RNA seq. These samples were devided into six groups (4 ANIMALS EACH GROUP). These groups are #1 Hap-I adults+WD (western diet); #2  Hap-I aged+WD; #3 Hap-II adult+WD ; #4 Hap-I adult; #5 Hap-I aged; #6 C57 adults


title: Pathogenesis And Altered Cardiac Transcriptomic Landscape In Western Diet Treated Aged Mice Overexpressing Human Angiotensin Type 1 Receptor II

summary: Overexpression of human angiotensin II type 1 receptor (hAT1R) may lead to pathophysiological outcomes due to overactivation of the renin angiotensin system. We have shown that transgenic (TG) mice containing Hap-I (hypertensive genotype) of human AT1R gene are more prone to develop metabolic syndrome (MetS) as compared to TG mice with Hap-II (normotensive genotype). The increased risk of MetS, especially in hypertension, compounded by the effects of aging and Western diet (WD), which may lead to cardiac complications. However, the underlying mechanisms are not well examined. For this purpose, we studied the pathophysiological changes and gene expression profile alterations in the heart of aged Hap-I and Hap-II TG mice following exposure to WD. Aged mice (20-24 months of age) were maintained on a regular diet or high fat diet with 2% NaCl (WD) for 16 weeks. On regular diet, aged Hap-I mice presented higher (~9 mmHg) systolic blood pressure with respect to age-matched Hap-II animals. Following administration of WD, blood pressure increased in both groups of mice, but to a larger extent in Hap-I animals (~15 mmHg), in comparison to Hap-II (~7 mmHg). With respect to Hap-II, aged Hap-I mice on regular diet tended to have larger heart weight-to-body weight ratio and higher levels of fibrosis. Western Diet treatment exacerbated these differences. RNA sequencing data from cardiac tissue of WD treated Hap-I aged mice (compared to control diet treated age-matched mice) revealed that WD significantly altered the expression of >500 genes (p-adj. <0.05). Bioinformatics analysis, using Qiagen IPA software, identified major alterations in main canonical pathways involved in cardiac function, inflammation, and oxidative damage. Top hits in the disease and biological function category included arrhythmia, chamber enlargement, and cell death. Importantly, IRF3, IRF7, IFNG and STAT1 were among the top upstream regulators significantly affected by WD. Overall, these results indicate that Western diet promotes hypertension, hypertrophy, and fibrosis in the heart of aged mice. Results from these studies will assist in the identification of novel molecules and mechanisms involved in hypertension and associated cardiac pathophysiology.

overall_design: overall 8 samples were analysed by RNA seq. These samples were devided into two  groups (n=4). These groups are #1 Hap-II aged; #2 Hap-II aged+WD (western diet)


title: Transcriptome analysis of Aoswi6 in nematode-trapping fungus Arthrobotrys oligospora

city: Yunnan Kunming

first: xie

middle: mei

last: hua

state: Yunnan

address: 121 street

institute: Yunnan university

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aoswi6 were involved in DNA replication, repair, and recombination during trap formation.

overall_design: The WT and ΔAoswi6 mutant strains were cultured in PD shaking at 28 °C, 180 rpm for 5 days. Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2). The mycelium was divided and induced with about 600 nematodes for 0, 12, 24, and 36 h, respectively. Three replicates were performed for each sample.

first: meihua

last: xie

first: ni

last: ma

last: bai

first: jingkui

last: yang


title: Pathogenesis And Altered Cardiac Transcriptomic Landscape In Western Diet Treated Aged Mice Overexpressing Human Angiotensin Type 1 Receptor I

overall_design: Overall 16 samples were analysed by RNA seq. These samples were devided into four groups (3-5 ANIMALS EACH GROUP). These groups are #1 C57 adults; #2  Hap-I aged; #3 Hap-I aged+WD (western diet); #4 Hap-I adult


title: The fibroblast-centered cellular crosstalk in HBV-positive liver cancer revealed by single cell sequencing

first: Yao

last: He

state: Haidian District

address: Room 307A, Intergrated Science Building 2, Peking University,, No.5 Yiheyuan Road

institute: BIOPIC

summary: Here, we generated full-length single cell transcriptome data for ~9,000 cells from clinical samples of 11 liver cancer patients to delineate cellular relationships of diverse malignant, immune and stromal cells. We identified an immunomodulatory fibroblast population, FAP+CCL19+CCL21+ CAFs, that expressed signatures of fibroblastic reticular cells and was associated with favorable prognosis in hepatocellular carcinoma (HCC). These CAFs exhibited the potential to recruit NK cells and regulate tumor-associated macrophages, and appeared to be regulated by CXCL12+ endothelial cells in tumors through specific ligand-receptor interaction. Further, we uncovered clonal HBV integration events enriched in tumor cells, and trajectory analysis on tumor cells with clonal HBV integration events revealed that hepatoblast-like cells differentiated into a terminal state with high expression of an immune-resistance program. The intercellular crosstalks between CAFs and cancer cells, macrophages, and NK cells, combined with HBV-based lineage tracing, provide a better understanding for functional roles of CAFs in the HCC microenvironment, and the relationship between HBV integration and liver malignancies.

overall_design:
Here, we utilized Smart-seq2 protocol to obtain full-length transcriptional profiles of CD45+ and CD45− cells for 11 liver cancer patients  from PBMC, adjacent liver and tumor sites.
>>> Due to patient privacy concerns, raw sequence data access provided at China Genomic Sequence Archive (GSA) under accession HRA001595 (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001595) <<<

first: Qiming

last: Zhang

first: Zemin


title: Gene expression profiling of drought-sensitive (IR64) and tolerant (N22) rice cultivars

city: New Delhi

first: Mukesh

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: We generated the global transcriptome profile of the two rice genotypes under control and drought conditions. More than 80 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control condittons for each cultivar.

overall_design: We collected 21-day-old seedlings of the drought sensitive (IR64) and tolerant (N22) rice cultivars under drought and control conditions. The RNA-seq libraries were prepared for sequencing using standard Illumina protocols and sequencing was performed on the Illumina HiSeq platform by a commercial sequencing service provider. The raw reads were filtered using NGSQC Toolkit (v2.3.3) at default parameters . Rice genome downloaded from RGAP (v7.0) was indexed using bowtie (v2.3.3.0) and filtered reads were mapped against the rice genome using Tophat (v2.1.1) at default parameters. Reference-based transcriptome assembly was performed using cufflinks (v2.2.1). The FPKM for each transcript was calculated using cufflinks by fragments per kilobase of transcript per million mapped fragments.  Transcripts ID identified in at least two of three biological replicates were selected and the missing value for one replicate was imputed by random forest imputation using the missForest R package. Differential gene expression (log2 fold change ± 1 and FDR ≤ 0.05) analysis was performed using edgeR.

first: Anuj

middle: K

last: Dwivedi


title: Single-cell RNA-Seq of Foxe1KO mouse ESC-derived cells

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary: Functional thyroid follicles generation in vitro is obtained at high efficiency by doxycycline-mediated expression of Nkx2-1 and Pax8, two proteins involved in early specification of thyroid lineage. Although those factors are sufficient to induce thyroid specification in vitro, other players, such as Foxe1, are also present in early thyroid primordium and its loss-of-function is responsible for thyroid congenital defects in mice and humans. Here we show that Foxe1KO mESCs can be induced to differentiate towards thyroid lineage but the efficiency of thyroid follicular cells generated is drastically low. Moreover, correct expression of maturation genes and capacity to produce thyroid hormone in vitro are completely disrupted.  On the other hand, Nkx2-1 expressing cells derived from Foxe1KO have an unexpected ability to deviate to a lung epithelium differentiation program and form organoids containing multiple lung cell types. These findings demonstrate that Foxe1 is required to reinforce thyroid cell fate in vitro and to promote terminal maturation of thyroid follicles.

overall_design: At day22 of differentiation protocol, cell populations derived from Foxe1KO/Nkx2-1-T2a-mKO2 reporter mESC lines were isolated for scRNAseq profiling. GFP+, mKO2+ and mKO2- cells were sorted at different proportions (15%, 50%, 35%, respectively). Sorted cells were collected in PBS at a density of 800cells/ul and diluted accordingly to kit’s instruction (10x Genomics Chromium Single Cell 3’ v3). 12000 cells were loaded onto a channel of the Chromium Single Cell 3′ microfluidic chip and barcoded with a 10X Chromium controller. Subsequently, RNA was reverse transcribed and amplified according to manufacturer’s recommendations (10X Genomics). Library preparation (e.g. fragmentation, dA tailing, adapter ligation, indexing PCR) was performed based on 10x Genomics guidelines. Libraries were sequenced on a Illumina NovaSeq 6000 system.


title: The Fzr1-mediated early embryo stress response impairs fetal growth and metabolic reprogramming of offspring

first: ping

middle: Yan

last: Jia

address: 1239 siping road

department: School of Life Sciences and Technology

institute: Tongji University

type: Methylation profiling by high throughput sequencing

summary: Stressors during early embryogenesis influence embryo developmental trajectories and have long-term metabolic effect on offspring, but the underlying mechanism remains elusive. We performed RNA-Seq to identify transcriptional differences among control and IVF embryos. Results revealed that DNA damage and the resulting activation of Fzr1 play a central role in early embryo stress responses and subsequently affect metabolic reprogramming in offspring. To investigate the underlying molecular mechanism by which Fzr1 affected embryo development and adult metabolism. We performed RNA-Seq and H3K9me3 ChIP-seq experiments to identify transcriptional and histone modification differences among control and Fzr1-OE blastocysts. To explore the underlying mechanisms of Fzr1 activation-induced metabolic disorder, we performed RNA-Seq on the subcutaneous fat tissues of 4-month-old control and Fzr1-OE mice. We further performed reduced-representation bisulfite sequencing (RRBS) of subcutaneous fat tissues to identify possible DNA methylation alterations that could potentially mediate the intergenerational transmission of the obesity phenotype.  Our findings therefore provide a new perspective on the mechanisms underlying transgenerational metabolic reprogramming and will help improve offspring health.

overall_design: mRNA profiles of WT and IVF embryos, and mRNA and H3K9 histone modification profiles of Fzr1-OE and control embryos, as well as mRNA and DNA methylation profiles of fat tissues from Fzr1-OE, IVF and WT mice

first: Yanping

first: Yalin

first: Xiaoming

last: Teng

first: Miaoxin

last: Chen


title: Bulk RNA-Seq of Foxe1KO and control Nkx2-1/mKO2+ mouse ESC-derived cells

overall_design: Foxe1KO and control cells from Nkx2-1 reporter line were cultured following the differentiation protocol. 10000 Nkx2-1+ (mKO2+) cells per condition were sorted (FACS Aria; BD Bioscience) at day10 and day22 time points of the differentiation protocol. Cells were collected directly into Qiazol lysis reagent (Qiagen) and RNA isolation performed with miRNeasy micro kit (Qiagen) following manufacturer’s indications.Ovarion Solo RNA-seq Systems (NuGen) was employed, as indicated by the manufacturer. Multiplexed libraries (10ρM) were loaded onto flow cells and sequenced on the HiSeq 1500 system (Illumina) in high-output mode using the HiSeq Cluster Kit v4 (Illumina).


title: Whole-genome transcriptomic analysis from stem internodes in Sorghum bicolor variety ICSV12012

first: Manoj

middle: K.

last: Sharma

state: Delhi

summary: We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

overall_design: Examination of middle internode tissues from four development stages and three soil moisture readings representing proSSessive drought stress in sweet sorghum variety ICSV12012

first: Supriya

last: Mathur

first: Madan

last: Pal Singh


title: Bulk ATAC-seq of Foxe1KO and control Nkx2-1/mKO2+ mouse ESC-derived cells

overall_design: Biological replicates were obtained from control and Foxe1KO cells (Nkx2-1 reporter line), at different time points of the differentiation protocol. 50000 Nkx2-1(mKO2+) cells were collected using FACS from both lines at day 10, day17 and day22. Cells derived from embryoid bodies before (day 4) and after  doxycycline treatment (day7) were also collected. Samples were prepared based on Omni-ATAC protocol (Corces et al 2017). Briefly, cell pellets were resuspended in 50µl of an ice-cold cell lysis buffer (0.1% Igepal, 0.1% Tween20 and 0.01% Digitonin in Omni-ATAC Resuspension buffer). After 3 min, samples were  centrifuged for 15min at 800g and subsequently, nuclei were resuspended in 50µl of reaction buffer (2.5μl Tn5 transposase, 22.5μl TD buffer, both from Nextera DNA sample preparation kit, Illumina; 16.5μl PBS, 0.5μl 1%Digitonin, 0.5μl 10% Tween20 and 5μl H20). Tagmentation reaction was performed for 30min at 37°C in a rocking plate (1000 rpm). DNA  was purified using the MiniElute purification kit (QIAGEN) following the manufacturer’s indications.Barcoded libraries were PCR amplified in 11 cycles (Nextera DNA Sample Preparation Kit,Illumina). Libraries were sequenced on Ilumina HiSeq1500 system.


title: RNAseq Analysis Identifies Pathways Associated with Uptake of 18F-Fluciclovine in Breast Cancer Patients

city: Atlanta

first: Carlos

middle: Sanchez

last: Moreno

state: GA

address: 101 Woodruff Circle NE, Room 2309

department: Pathology and Laboratory Medicine

institute: Emory University

summary: We report RNAseq analysis of 12 breast cancer patients treated with the ratiotracer 18F-Fluciclovine and the associated radiotracer uptake data. FFPE samples from 12 tumor and 7 benign tissue were sequenced. In addition, tissue samples from 6 normal breast reduction cases were sequenced for a total of 25 samples.

overall_design:
Comparison of tumor vs benign samples and correlation of radiotracer uptake to gene expression

**Due to patient privacy concerns, raw data were not provided**

middle: S

first: David

middle: M

last: Schuster


title: Ah receptor activation coordinates intestinal epithelial cell programing

city: State College

first: Gary

middle: H.

last: Perdew

address: 309A Life Sciences Building

institute: The Pennsylvania State University

summary: The intestinal epithelium undergoes differentiation into multiple cell types and undergoes rapid cellular turnover. The Aryl hydrocarbon receptor (AHR) is a sensor of small molecules found either in the diet or due to microbiota metabolism. Ahr and Cyp1a1 exhibits the highest expression in the duodenum. Germ-free mice display similar levels of Cyp1a1 expression suggesting that in mice diet is the primary source of AHR activation potential. The lack of AHR expression alters; the rate of transit down the small intestine, barrier function, and proliferative index. In Ahr-/- mouse duodenum there is also a decrease in goblet cells, mucin levels and expression of gene expression linked to epithelial cell differentiation. AHR activation with indolo[3,2b]carbazole or broccoli; increases expression of differentiation markers, decreases epithelial proliferative index and increases goblet cell number. Math1 and Klf4 are AHR target genes that are linked to development of the secretory cell linkage. Collectively, our study indicates that dietary activation of the AHR leads to altered epithelial programing leading to increased goblet cells and decreased cell shedding.

overall_design: Transcriptomic profiling across the mouse small intestine epithelial crypt-villus axis in response to 12 h exposure to the diet-derived potent AHR agonist indolo[3,2b] carbazole (ICZ). Triplicate biological replicates for both control and ICZ exposure

middle: H

first: Molly

last: Hall

first: Iain

last: Murray

first: Denise

last: Coslo

first: Xiaoliang

last: Zhou

first: Carolyn

last: Ton

first: Debopriya

last: Chakraborty

first: Zoe

last: Kehs

first: Andrew

last: Patterson

first: Jiayan


title: scRNA-seq of tailbud development in zebrafish

city: Irvine

first: Thomas

middle: F

last: Schilling

address: 4462 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California Irvine

summary: We have performed single-cell RNA-seq of whole tailbuds in WT zebrafish at 16 hours post fertilization (hpf).

overall_design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.

last: Tatarakis

first: Julia

last: Horsfield

first: Benjamin

last: Martin


title: Sequencing in transcriptomes in Ovarian cancer cell line SKOV3 and bevacizumab-treated SKOV3

city: Jinan

first: cheng

middle: cheng

last: Li

state: Shandong

address: Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, No.107 Wenhuaxi Road, Jinan, Shandong, China

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital of Shandong University

summary: To investigate the possible mechanism of bevacizumab resistance in ovarian cancer ,we examined the changes in gene expression of SKOV3 before and after bevacizumab intervention. Results provide insight into molecular mechanisms of acquired resistance to bevacizumab in ovarian cancer.

overall_design: We treated SKOV3 cells with condition medium(control group) and 150ug/ml bevacizumab in condition medium (experimental group) in vitro. The cells were collected 24 hours after treatment and used for RNA-sequencing

first: Chengcheng

first: Jin

last: Peng

first: Kun

last: Song


title: Identification of hub genes and key miRNAs associated with oxidative stress in radiation-induced lung injury via RNA sequencing and bioinformatics analysis

city: Nanning

first: Lin

last: Deng

state: Guangxi

address: No.6 Shuangyong Road

department: Department of Radiation Oncology

institute: The First Affiliated Hospital of Guangxi Medical University

summary: In this study, through X-ray irradiation and RNA sequencing of human bronchial epithelial BEAS-2B cells, central genes and enrichment pathways related to oxidative stress of radiation lung injury were found, and the potential molecular mechanism of RILI was elucidated.The GO function annotation and KEGG pathway enrichment analysis of candidate genes were performed using David database.The STRING database and Cytoscape platform were used to construct PPI network diagram.The result was 421 DEGs.The candidate genes (158 up-regulated genes and 101 down-regulated genes) enriched 289 GO terms and 38 KEGG pathways.The top 10 pivot genes and the top 3 key miRNAs were found by constructing the network map.In summary, we identified central genes, key miRNAs and enrichment pathways related to oxidative stress, as well as the potential molecular mechanisms of RILI.These results provide new ideas for elucidating the potential molecular mechanism of RILI and identifying new targets and new approaches for prevention and control of RILI.

overall_design: Examination of mRNA-seq in NC and radiation group beas-2b cells

first: Liuyin

last: Chen

first: Rensheng

last: Wang

first: Kai

last: Hu


title: Control of macrophage response to TNF by the sst1 locus

city: Dublin

first: Vadim

last: Zhernovkov

address: Belfield

country: Ireland

institute: University College Dublin

summary: We studied effects of the mouse sst1 locus that controls susceptibility to intracellular bacteria, on macrophage response to TNF.

overall_design: Bone marrow-derived macrophages were isolated from the B6 wild type and the sst1 congenic  B.Sst1S mice and differentiated in vitro in the presence of CSF1. Cells were stimulated with 10 ng/ml of TNF for 12 hours prior to RNA isolation.

first: Igor

last: Kramnik

first: Alexander

last: Gimelbrant


title: mRNA expression profile of peripheral blood samples from ovarian cancer patients before and after bevacizumab treatment

summary: we performed transcriptome sequencing and microarray analysis of peripheral blood samples from two ovarian cancer patients (A and B) before and after two times bevacizumab treatment to analyze the expression of mRNA and explore pathway enrichment and  their correlation with drug-resistance and tumor microenvironment changes.

overall_design: we selected advanced ovarian cancer patients who receive bevacizumab treatment,collected blood samples before and after bevacizumab treatment,1ml blood was mixed with 3ml Trizol and storaged at -80℃ for RNA-Sequencing.


title: Maternal vitamin D deficiency impairs heart formation in mouse offspring through a change in 3D-chromatin structure

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

summary: The origins of congenital heart diseases, the most common congenital diseases are still largely unknown. Environmental factors are now emerging as major causes of these diseases. Vitamin D deficiency has become a public health burden, notably for childbearing age, pregnant and breastfeeding women. Since maternal 25-hydroxyvitamin D (25(OH)D) determined fetal and neonatal 25(OH)D status, foetuses exposed to insufficient levels of vitamin D, may feature developmental defects.Herein, we investigated the effects of maternal vitamin D deficiency on cardiovascular defects in early and later life of offsprings as well as the molecular mechanisms underlying vitamin D effect.Eight weeks before and during pregnancy, C57BL/6JRj female mice received a sufficient or vitamin D deficient diet ((1.0 IU/g in control vs 0.0 IU/g in Vitamin D Deficient (VDD) group). E16.5 Embryos of maternal VDD diet featured hypertrophic heart revealed by a thicker left ventricular (LV) wall and septum. RNAseq analysis of LV revealed 1555 transcripts differentially expressed in the VDD group and among them cardiac transcription factors and constitutive cardiac genes (tbx5, gata4, myl2). Anti-Vitamin D receptor (VDR) Chip-seq from chromatin of E16.5 LV uncovered different targeting of tbx5 and tbx3 loci by VDR in the VDD vs control embryos. Anti-CTCF ChIP-loop experiments focusing on the Tbx3 and Tbx5 loci uncovered a change in the Topology Associated Domains associated with these loci.  Herein, we investigated the effects of maternal vitamin D deficiency on cardiovascular defects in early and later life of offsprings as well as the molecular mechanisms underlying vitamin D effect.Eight weeks before and during pregnancy, C57BL/6JRj female mice received a sufficient or vitamin D deficient diet ((1.0 IU/g in control vs 0.0 IU/g in Vitamin D Deficient (VDD) group). E16.5 Embryos of maternal VDD diet featured hypertrophic heart revealed by a thicker left ventricular (LV) wall and septum. RNAseq analysis of LV revealed 1555 transcripts differentially expressed in the VDD group and among them cardiac transcription factors and constitutive cardiac genes (tbx5, gata4, myl2). Anti-Vitamin D receptor (VDR) Chip-seq from chromatin of E16.5 LV uncovered different targeting of tbx5 and tbx3 loci by VDR in the VDD vs control embryos. Anti-CTCF ChIP-loop experiments focusing on the Tbx3 and Tbx5 loci uncovered a change in the Topology Associated Domains associated with these loci.

overall_design: Left ventricles of E16.5 mouse embryos from mother fed with normal or vitamin D deficient diet were collected and used to prepare chromatin; the vitamin D receptor (VDR) was immunoprecipitated and the DNA bound to it sequenced

first: Eva

last: Seipelt

first: Paul

last: Besadoun

first: Michel

last: Puceat


title: Chromatin-enriched RNA sequencing of HL-1 mouse cardiomyocytes

city: Chicago

first: Johnathon

last: Hall

state: IL

address: 920 E 58th St

department: Molecular Genetics & Cell Biology

institute: University of Chicago

summary: Biochemical fractionation of HL-1 mouse cardiomyocyte nuclei and RNA-seq of chromatin-enriched and soluble-nuclear RNA

overall_design: Three biological replicates of HL-1 cell nuclei were subjected to biochemical fractionation. ERCC spike-in RNA standards were added to each fraction prior to RNA extraction. RNA from three chromatin pellet and three soluble nuclear fractions were converted to cDNA using NEBNext Ultra II Directional RNA library peparation and sequenced on the Illumina HiSeq4000.

last: Ruthenburg


title: Stem transcriptome of sweet sorghum hybrid CSH22SS during development and in response to water limiting conditions.

first: Manoj

last: Sharma

summary: We report transcriptome profiling from three developing stages of middle internode in Hybrid sweet sorghum. Samples were harvested at Booting, milky stages and physiological maturity.

overall_design: Examination of 3 different stages of middle internode development inHybrid sweet Sorghum variety CSH22SS

first: Neeraj

last: Kumar

first: A

middle: V

last: Umakanth

first: Rita


title: Gene regulation by m6A demethylase ALKBH5 in U2OS osteosarcoma

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: To identify target genes regulated by ALKBH5 in osteosarcoma,  we silenced the expression of ALKBH5 in osteosarcoma cell line-U2OS and tested its effect on U2OS transcriptome.

overall_design: U2OS cells were were transfected with either scrambled-siRNA or ALKBH5-siRNAs (Sigma-Aldrich) for 48 hours. Transfection was carried out using the RNAiMAX Reagent (Thermofisher) according to the manufacturer’s protocol. After 48 hours, cells were harvested and total RNA extraction was done using RNeasy Mini Kit (Qiagen).For whole-genome transcriptome profiling, four libraries (3 replicates each for knockdown and control) were generated from total RNA from scrambled-siRNA- and ALKBH5-siRNA-transfected U2OS cells, using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Pooja

last: Yadav

first: Manjeet

last: Rao

first: Zhao

last: Lai


title: Gene expression after low dose irradiation in pluripotent stem cells developing to retinal ganglion cells

city: Tsukuba

first: Tomohiro

last: Ito

address: 16-2, Onogawa

country: Japan

institute: National Institute for Environmental Studies

summary: The effects of low dose irradiation on the gene expression on the neural cell development using human induced pluripotent stem cells (hiPS cells).

overall_design: We irradiated 30 and 180 mGy of radiation on hiPS cells between day 4 and 5 of differentiation to determine alteration of genome-wide gene expressions on day 6, 10, 17 and 35 of development. Activated and inactivated canonical pathways were identified by ingenuity pathway analysis and upstream molecules, diseases and functions were predicted.

first: Mari

last: Katsura

first: Urade

last: Yoshihiro

first: Hiroko

last: Nansai

first: Mika

last: Kobayashi

first: Akashi

last: Taguchi

first: Yukiko

last: Ishikawa

first: Hisako

last: Fukunaga

first: Hideto

last: Tozawa

first: Yoko

last: Chikaoka

first: Ryo

last: Nakaki

first: Akinobu

last: Echigo

first: Takahide

last: Kohro

first: Hideko

last: Sone

first: Youichirou

last: Wada


title: Bump-finder: identification of causal codons to the stalling of ribosomes

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

summary: Stalling of the ribosomes on the mRNA has been linked to myriad of molecular and biological functions. While a multitude of algorithms predict codon-usage in ribosome profiling data, no tool exists to predict the context-specific stalling of ribosomes on transcripts. Combining these two features can reveal unprecedented insights in the ribosomal function and their usage across cells and conditions. To overcome this lack of tools to comprehensively analyze these features, we created Bumpfinder, a web-server, that provides comprehensive analytical details on differences in total ribosome occupancy on transcripts, ribosomal occupancy across codons, ribosome-stalling and the underlying causal amino-acids/codons, as well as collisions. Employing Bumpfinder on generated and publicly available ribosome-profiling datasets, we studied the response of various cell types to amino-acid starvation conditions. We observed interesting patterns in response to the biological effects, suggesting the impact of quality control mechanisms of protein synthesis. Complimentary analysis of collided ribosomes demonstrated phased ribosome stalling on the identified sites. Thus, by deciphering context-specific ribosome distribution, Bumpfinder provides unprecedented molecular insights in the ribosome function and mRNA translation during stress response conditions.

overall_design: ribosome profiling to measure mRNA levels and mRNA translation

first: Pierre-René

first: Julien

last: Champagne

first: Remco

last: Nagel

first: Naomi

last: Blommaert

first: Abhijjeet

last: Pataskar

first: Reuven

last: Agami


title: Single cell gene expression profiling of adult WT and ipRGC-ablated prefrontal and motor cortices

city: Bethesda

first: Samer

last: Hattar

state: MD

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

summary: The ventromedial prefrontal cortex (vmPFC) is a part of the limbic system engaged in higher-order functions ranging from behavioral flexibility to social cognition characteristically impaired in schizophrenia and autism. Intrinsically photosensitive retinal ganglion cells (ipRGCs) are a major source of indirect input to this area by way of the recently discovered perihabenular nucleus (PHb). Here, we demonstrate that the integrity of the vmPFC is dependent on ipRGC input: Its loss in mice causes dendritic degeneration, dysregulation of genes involved in synaptic plasticity, and depressed neuronal activity in the vmPFC. These alterations are reflected in a profound inability to suppress emotional interference in behavior.

overall_design: Single cell gene expression profiling of prefrontal cortex and motor cortex tissue collected from ipRGC-ablated ("DTA") and ipRGC-intact, ("CTRL") mice using the 10X Genomics 3' single cell gene expression V2 system. A total of 24383 prefrontal cortex cells (11815 CTRL, 12568 DTA) and 8602 motor cortex cells (6229 CTRL, 2373 DTA) were collected and analyzed.

first: Michael

middle: B

last: Thomsen

first: Jesse

last: Zhan

first: Lorenzo

last: Ospri


title: Single cell sequencing of human nucleus pulposus

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: In order to discover the cell type in nucleus pulposus and find the cell type specific genetic change during intervertebral disc degeneration, we applied single cell RNA sequencing of nucleus pulposus tissue from degenerated and non-degenerated disc.

overall_design: Nucleus pulposus cells are extracted from the tissue immediately after acquire the tissue from surgery. The tissue are then digested using Collagenase for 3 hours. The cell viability are tested and viable sample are send to sequencing.

first: Huajiang

last: Chen

first: Wen

last: Yuan


title: Examination of effect of LPS on chromatin accessibility and the role of Lamin-A [ATAC-Seq]

city: Zürich

first: Jain

last: Nikhil

address: Vladimir-Prelog-Weg 1/5-10

department: Health Science and Technology

institute: ETH Zürich

summary: We report here the ATAC-Seq data for Control, Control LPS treated, Lamin-A-KO and Lamin-A-KO LPS treated

overall_design: Examination of effect of LPS on chromatin accessibility and the role of Lamin-A/C

first: Johanna

last: Mehl

first: Nikhil

last: Jain


title: Proteomics of centromere repeat in distinct chromatin states reveals pathways to heterochromatin nucleation and transmission

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

summary: Heritable heterochromatin domain formation is initiated by dynamic changes in the proteome on specialized loci, leading to chromatin modifier recruitment, heterochromatin assembly and propagation. Here we characterize the proteomes associated with a defined heterochromatin nucleation region in three distinct chromatin states: before de novo H3K9 methylation nucleation, following heterochromatin assembly and upon heterochromatin disassembly. Our analyses separate sequence-dependent from sequence-independent processes, providing a systematic examination of the template-driven nucleation and epigenetic wiring underlying heterochromatin transmission. We identify functional interactions that reveal an integral role for the conserved nucleolytic Grc3 complex, and its associated network, as pioneer factors in heterochromatin assembly. More broadly, we demonstrate the power of quantitative proteomics-based strategies for the unbiased scrutiny of the single regions assembled in distinct chromatin states.

overall_design: wt-phet & wt_pcontrol H3K9me2 ChIP-seq

first: Tanya

last: Auchynnikava

first: Sharon

middle: A

last: White

first: Sito

last: Torres-Garcia

first: Pin

last: Tong


title: Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology

city: Guangzhou

first: Wei

last: Luo

state: Guangdong

address: Wushan Road

department: The College of Animal Science

institute: South China Agricultural University

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

summary:
Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype.
After conducting a genome-wide association study (GWAS), a 36.5-kb candidate genomic region (chromosome 19:757,754-794,200) related to the Antler-comb phenotype was identified, which wholly and partially encompassed heat shock factor 5 (HSF5) and ring finger protein 43 (RNF43), respectively. HSF5 was ectopically expressed and RNF43 was up-regulated in Antler-comb chickens at embryo ages 7 and 9 (E7 and E9). We further genotyped the most significant single-nucleotide polymorphism (SNP) site, Chr19:794200, across 222 chickens of 16 breeds. We found that the major allele G in Antler-comb chickens remained highly significant across different breeds, and each Antler-comb chicken harbored an allele G. Whole-genome re-sequencing (WGS) involving 10 Hetian Antler-comb and 10 Wildtype-comb chickens reaffirmed the 36.5-kb candidate genomic region, and revealed a genomic duplication, which was 15.7 kb in length and pertained to the 5’-untranslated region and 5’-flanking region of HSF5 (Chr19:784,335-800,034), suggesting its possible role in inducing ectopic expression of HSF5 and altering expression of RNF43 during comb development (E7 and E9). The present study furthers our understanding of this novel chicken comb phenotype, and likely gives another example regarding interactions between genetic variation and phenotype.

overall_design: 24 female chickens with Antler-comb phenotype and 12 female chickens with Wildtype-comb chickens, for which all 36 chickens were from a same farm in Guangdong, were genotyped with Affymatrix 600K Axiom® Genome-Wide Chicken Genotyping Array. Based on case-control model, Plink version 1.9 was employed to perfrom genome-wide analysis, aiming for identifying candidate genomic regions concerning Antler-comb phenotype. Meanwhile, we whole-genome resequenced another 6 male Antler-comb chickens from Fujian province, 4 female Antler-comb chickens from Guangdong province, and 10 Wildtype-comb chicken from above GWAS population to interrogate the results from GWAS, and search for variations in terms of InDel or CNV inside the candidate genomic regions from GWAS. Additionally, qPCR was further performed across the genes encompassing above candidate genomic region.

first: We


title: MAP Kinase inhibition depletes tumor-infiltrating macrophages in mouse pancreatic cancer

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

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

overall_design: Refer to individual Series


title: MAP Kinase inhibition depletes tumor-infiltrating macrophages in mouse pancreatic cancer [Essen]

summary: The MAP Kinase pathway is the index oncogenic signaling towards which many compounds have been developed for the treatment of KRAS-driven cancers, including pancreatic ductal adenocarcinoma (PDA). How targeted MEK1/2 inhibition (MEKi) alters the tumor-microenvironment (TME) of PDA is poorly understood. Here, we showed that transcriptional signatures of MAP Kinase activation are enriched in aggressive human PDA subtype, while short term MEKi treatment in mouse PDA induced subtype switching. Moreover, MEKi induced depletion of tumor-infiltrating macrophages, while augmenting infiltration by neutrophils. Depletion of macrophages is observed early during in vivo treatment and is at least partially due to their higher sensitivity to MEKi. Since tumor-associated macrophages are consistently reported to interfere with gemcitabine uptake by PDA cells, we tested a sequential combination of MEKi and gemcitabine, which showed superior antitumor activity in vivo. These findings suggest that MEKi-induced TME remodeling might be exploited to increase therapeutic responses in PDA.

overall_design: We screened RNA from mice pancreas freshly isolated tissues (isograft) from 7 mice in total; 4 controls and 3 MEKi (Trametinib) treated for 2 days (48h) at 1mg/kg.

first: Christian

last: Neander

first: Dea

last: Filippini

first: Sabrina

last: D'Agosto

first: Caterina

last: Vicentini

first: Elena

last: Fiorini

first: Francesca

last: Lupo

first: Claudia

first: Borislav

last: Rusev

first: Gael

middle: D

last: Temgue Tane

first: Francesco

last: De Sanctis

first: Michele

last: Simbolo

first: Stefano

last: Ugel

first: Vincenzo

last: Bronte

first: Matteo

last: Fassan

first: Rita

middle: T

last: Lawlor

first: Federico

last: Boschi

last: Barbi

first: Aldo

last: Scarpa

first: Phyllis

last: Cheung

first: Jens

last: Siveke

last: Corbo


title: MAP Kinase inhibition depletes tumor-infiltrating macrophages in mouse pancreatic cancer [Verona]

first: Pietro

last: Delfino

overall_design: We screened RNA from mice pancreas freshly isolated tissues (isograft) from 13 mice in total; 5 controls, 4 MEKi (Trametinib) treated for 7 days and 4 MEKi (Trametinib) treated for 14 days at 1mg/kg.

first: Christian

last: Neander

first: Dea

last: Filippini

first: Sabrina

last: D'Agosto

last: Vicentini


title: tRNA pool analysis of S. cerevisiae using tRNA-HySeq

city: Hyderabad

first: Purnima

last: Bhargava

state: Telangana

address: Habsiguda X road

institute: CSIR-Centre for Cellular and Molecular Biology

summary:
For a typical RNA polymerase (pol) II transcribed budding yeast gene, the 5' -end is characterized by a nucleosome-free region (NFR) immediate upstream of the transcription start site (TSS), flanked by two well-positioned nucleosomes (-1 and +1) containing H2A.Z. A similar arrangement of nucleosomes  containing H2A.Z is found on the genes transcribed by pol III, which reside in the NFR actively maintained by the chromatin remodeling complexes. We did genome-wide MNase-seq and ChIP-seq experiments to study the nucleosome arrangement near pol III transcribed genes.
We also measured the levels of different tRNAs in the tRNA pool of the wild type and Spt16 mutant (*spt16-197*) cells using tRNA-HySeq method. Although, it is difficult to measure the primary transcripts of tRNA due to their quick processing and the sequence degeneracy of the tRNA isogenes; a comparison of the wild type and Spt16 mutant showed both increase or decrease of tRNA transcripts. The result suggest that Spt16 may not be necessary for the transcription per se of tRNA genes.

overall_design:
tRNAs isolated from log phase yeast cells were hydrolyzed, followed by adapter ligation and sequencing.
Single end RNA sequencing on Illumina Next-seq 500.

first: G

last: Arimbasseri


title: MAP Kinase inhibition depletes tumor-infiltrating macrophages in mouse pancreatic cancer [RNA-Seq]

overall_design: We screened RNA from mice pancreas freshly isolated tissues (isograft) from 8 mice in total; 4 controls and 4 MEKi (Trametinib) treated for 7 days.

first: Caterina

first: Elena

last: Fiorini

first: Francesca

last: Lupo

first: Claudia

first: Borislav

last: Rusev

first: Gael

last: Temgue Tane

last: De Sanctis

last: Simbolo

last: Ugel


title: Transcriptome of U251 cells knocking down RPL13

city: Kunming

first: Yong-Gang

last: Yao

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

summary: RPL13 was identified to be downregulated in brain of Alzheimer's disease (AD). To explore the involved pathways in response to RPL13 reduction, we knockdownRPL13 using siRNA in U251 cell line with a stably expressed mutant APP (K670N/M671L, U251-APP cells). RNA-seq (by IlluminaHiseq 4000) and following analyses were then performed to detect genes whose expression were influenced by RPL13 knockdown.

overall_design: RPL13 inteference were performed in U251 cell with a stable expression of mutant APP 128 (M671L) (U251-APP cells) with biological triplicates for each condition (siNC, and RPL13).  Differential expression genes were obtained by comparing gene expression levels in RPL13 knockdown (si-RPL13) with control cells (siNC).

first: Min

last: Xu

first: Deng-Feng

last: Zhang


title: Expression data from endothelial cells isolated from IL-33 knock-out and wildtype rats

city: Oslo

first: Monika

last: Szymanska

address: Songsvannsveien 20

department: Pathology

country: Norway

institute: Oslo University Hospital

summary:
Endothelial cells form the innermost layer of vessel walls and their activation is important for the recruitment of white blood cells to inflammatory lesions and for the formation of new blood vessels. Endothelial expression of IL-33 is prominent in human, guinea pig and rat, while is almost absent in the mouse. We have therefore generated IL-33-deficient rats, a more suitable animal model than the commonly laboratory mouse, to  address a knowledge gap in the IL-33 research field by providing an in vivo model system that closely reflects the IL-33 expression in human.
We performed here gene-level expression profiling of the endothelial cells isolated from IL-33 knock-out rat dermal blood vessesl and looked for the role of endogenous IL-33 in regulating the endothelial cell phenotype.

overall_design: Endothelial cells from three IL-33 knock-out and three wildtype rats were isolated for RNA extraction and hybridization on Affymetrix microarray. We sought to obtain pure, single cell population of blood vessel endothelial cells by magnetic activated cell sorting-based method (MACS), with sequential depletion of CD45 positive and Lyve-1 positive cells, and positive isolation of CD31 positive cells.

first: Astrid

last: Haaskjold Lossius

first: Katarzyna

last: Marciniak

last: Gatti

first: Clara

last: Hammarström

first: Olav

last: Sudnes

first: Johanna

last: Hol

first: Guttorm

last: Haraldsen


title: Understanding the early vegetative stage drought tolerance mechanism in rice

city: Cuttack

first: Koushik

last: Chakraborty

address: Bidyadharpur

institute: ICAR-National Rice Research Institute

summary: In this project we are investigating the mechanism of drought tolerance in rice at early vegetative stage by looking into expression profile of DEGs and uniquely expressed genes

overall_design: Plants of differing genotypes were investigated to understand their behavior under drought stress

first: Padmini

last: Swain


title: Lineage-Specific TOP2A Cleavage Landscape in Leukemia Cell

first: Xiang

last: Yu

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: Topoisomerases II (TOP2) play role in relief of torsional stress during DNA replication and gene transcription, and TOP2 is also a target of anticancer agents which cause secondary leukemia. To address cell lineage-specific TOP2A cleavage relative to leukemia, here we profile genome-wide TOP2A cleavage in human acute lymphoblastic leukemia (ALL) cell line CEM, and compare to TOP2A cleavage landscape of chronic myelogenous leukemia (CML) cell line K562. We find that TOP2A cleavage activity are correlated with chromosome length, suggesting that TOP2A cleavage is critical for segregation or supercoil relaxation of long chromosomes. Meanwhile, we find that  evolutionally  conserved TOP2A cleavage cluster regions (CCRs) are depleted in gene promoter and enriched in introns and 3’ UTR, and TOP2A cleavage genes tend to be highly expressed, indicating the conserved function of TOP2A cleavage in promoting transcription elongation and activation. In addition, we found that the oncogenic transcription factor complex TAL1, GATA3 and RUNX1 can further promote the activation of TOP2A cleavage genes by binding to their promoters. Further analysis reveal that native TOP2A cleavage are lineage-specific, which play role in cell commitment and leukemia development , while drug-enhanced TOP2A cleavage promote apoptosis of cancer cells in both ALL and CML.Taken together, our findings suggest that native TOP2A cleavage function in long chromosome segregation and transcription activation, and together with the transcriptional regulatory factors shape the commitment of leukemia cell.

overall_design: Global TOP2A-cleavage cluster region in human CEM cell tread with different TOP2 poisons.

first: James

middle: W

last: Davenport

first: Carolyn

last: Felix

first: Brian

last: Gregory


title: RNA-seq based transcriptional profiling of petroleum sludge-derived Pseudomonas aeruginosa ZS1 strain in response to alteration of growth conditions

city: Zhoushan

first: Jianhua

last: Liu

address: 1 Zheda Road, Lin-cheng street

institute: Ocean College, Zhejiang University

summary: We show that ZS1 in the medium supplemented with YE (YE-medium) produces more cell biomass but less rhamnolipid than it does in Glc-medium. To elucidate the transcriptional regulation of genes that are involved in biosynthesis of rhamnolipids and its precursors, RNA-seq-based transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-media is performed. Based on the assembly of ZS1 transcriptome using the reference PAO1 genome, we show that genes involved in energy metabolic pathways in ZS1 strain are highly transcribed in YE medium but not in Glc-medium, in agreement with their cell mass production. Similarly, transcription of quorum sensing systems genes lasI-lasR, rhlI-rhlR, and pqsH-mvfR are downregulated in Glc-medium. On the other hand, we show that two of the three enzymes RhlB and RhlC essential for rhamnolipid biosynthesis are transcriptionally upregulated, independent of quorum sensing signals. Notably, three of the four enzymes involved in dTDP-L-rhamnose, a precursor for the rhamnolipid biosynthesis, are downregulated in Glc except for RmlD that catalyzes the last reaction in the pathway. Together, our results indicate that increased rhamnolipid production in ZS1 cells is independent of quorum sensing signals. We propose that quorum sensing-independent rhamnolipid production in ZS1 Glc-culture is achieved by transcriptional re-programming of the minimum number of genes involved in rhamnolipid biosynthesis.

overall_design: Examination of transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-medium.

first: Liu

last: Jianhua

first: Zhang

last: Xiaolin

first: Wen

last: Fang


title: Genome-wide mapping of uncapped and cleaved transcripts (GMUCT) and transcriptome of DCLs

summary: Absence of miRNA in dcl1 mutant activates global translation-independent 5’->3’ exonucleolytic decay to maintain robust mRNA abundance of miRNA target genes.

overall_design: polyA-selected RNA-seq, and polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana.

first: Lee

middle: E

last: Vandivier


title: mRNA and miRNA profiling of patients infected with Ebola virus compared with healthy adult

city: Beijing

first: xiong

last: liu

state: Beijing

address: No.20，Dongdajie Street，Fengtai District

institute: State Key Laboratory of Pathogen and Biosecurity


title: Expression data of 20 Arabidopsis thaliana accessions at dusk, dawn and after an extension of the night

city: Potsdam

first: Eva-Theresa

last: Pyl

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

summary:
Large-scale identification of transcripts with large cross-genotype differences in abundance provides a genome-wide approach to identify natural variation in gene function.
Transcript profiling was performed in 20 Arabidopsis accessions at dusk, dawn and after a 6h extension of the night. Individual genes with a high variance in transcript abundances across accessions were identified by inspection at each individual time point and by ANOVA across all three time points. Up to 40% of genes show significant changes in transcript abundance between accessions, with over-enrichment for biotic resistance, including pathogenesis resistance proteins and glucosinolate metabolism, cell wall modification, minor carbohydrate metabolism, amino acid degradation, brassinosteroid metabolism, redox and abiotic stress and underrepresentation of photosynthesis, DNA synthesis, RNA processing, regulation of transcription, protein synthesis and protein targeting. Some functional classes were enriched at all three time points. Genes related to carbon starvation-responses were enriched specifically at dawn, when their transcript abundance varied independently of carbohydrate levels, pointing to genetic variation in the sensitivity with which low carbon is sensed. Cross-accession correlation networks were generated at each time point to identify sets of genes whose transcripts show coordinated change in abundance between accessions. A cluster that was highly enriched for cold-response genes was found at dusk and after an extension of the night. Another cluster found at all three time points was highly enriched for glucosinolate biosynthesis, and correlated with glucosinolate content. We conclude that genes involved in stress and defense related processes show especially large and coordinated natural variation in transcript abundance.

overall_design: 20 A.th. accessions were harvested at the end of the day (ED), the end of the night (EN), and 6h into an extended night (XN) with two biological replicates per line and time point (exception: Cvi at EN only one replicate) for RNA extraction and hybridization on Affymetrix microarrays.

first: Björn

last: Usadel

first: Takayuki

last: Tohge

first: Alisdair

middle: R

last: Fernie

first: Ronan

last: Sulpice

first: Mark

last: Stitt


title: Induced Endothelial Cell Cycle Arrest Prevents Arterio-venous Malformations in Hereditary Hemorrhagic Telangiectasia

status: Public on Dec 30 2023

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: Endothelial cell late G1 arrest induced by Palbociclib modulates the expression of genes regulating arterio-venous identity and prevents AVM development induced by Alk1 genetic deletion.

overall_design: We isolated retinal endothelial cells (ECs) from P5 Alk1fl/fl mice, Alk1fl/fl treated with CDK4/6i, Alk1ECiKO, and Alk1ECiKO treated with CDK4/6i, mice. After retinal tissue dissociation, we FACS-isolated ECs (CD31+CD45-) and performed scRNA-seq analysis.

first: Gael

last: Genet

first: Nafiisha

first: Umadevi

first: Karen

last: Hirschi


title: Transcriptome analysis of zebrafish exposed to neomycin and/or tacrine

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

summary: Aminoglycosides remain in current use because of the benefits, including the broad-spectrum, inexpensiveness to produce, and a relatively small incidence of allergic reactions. However, aminoglycosides may induce irreversible hearing loss. Recently, tacrine, an acetylcholineesterase inhibitor originally developed to treat Alzheimer’s disease, was found to be protective to neomycin-induced hair cell damage in zebrafish and mouse. However, the protection mechanism remain to be largely unknown. In this study, we revealed that tacrine significantly suppressed the expression of tnf mRNA and ROS production induced by neomycin. Reduction of tnf expression by the antisense morpholino or transcription activator-like effectors nuclease significantly suppressed the hair cell damage but not ROS production induced by neomycin. In zebrafish treated with an antagonist of NMDA receptor MK-801 or a mitochondrial ROS inhibitor acetyl-L-carnitine, ROS production, tnf expression, and hair cell damage induced by neomycin were also significantly reduced. These levels of suppression were not significantly different from those of co-treatment of tacrine and MK-801 or acetyl-L-carnitine. These findings suggest that activation of NMDA receptor followed by ROS production and subsequent tnf expression are involved in neomycin-induced hair cell damage and that tacrine ameliorate neomycin-induced hair cell damage through inhibition of the signaling pathway.

overall_design: Gene expression regulated by neomycin and/or tacrine in zebrafish at 5 dpf was measured. Three independent experiments were performed for each group.

first: Takanori

last: Kondo

first: Toshio

last: Tanaka


title: bnsdp1 impaired seedling growth, especially in yellowed seedlings

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

summary: impaired seedling growth, especially in yellowed seedlings, was not fully rescued in medium supplemented with exogenous sucrose.

overall_design: To understand the global effects of cotyledons disturbed lipid metabolism during the seedling stage, WT and bnsdp1#CR88 cotyledons, from the seedling growth on medium supplemented sucrose in dark for 4D and transferred to normal condition for 6 h, were used for RNA-seq.


title: miRNA profiling in the blood of patitents infected with Ebola virus

summary: Ebola virus can cause a severe and often fatal hemorrhagic fever in humans and other mammals, known as Ebola virus disease (EVD),the mechanism of how this pathogenesis comes about is not well understood, It is assumed that miRNA may have important roles in virus infection response. To better understand the function of miRNA in EBOV infection disease, we undertook a miRNA profiling analysis using the whole blood of EBOV infection patients.

overall_design: Human blood mRNA profiles of 12 EBOV infection patients and 3 healthy adults were generated by deep sequencing, using Illumina Hiseq 2500 platform

first: Hui

last: Wang

first: Tao

last: Li


title: IL-22 promotes cell proliferation to combat virus infection in human intestinal epithelial cells

city: Gainesville

first: Megan

last: Stanifer

state: FL

address: 1200 Newell Dr

institute: University of Florida

summary: Interferon lambdas (IFN-λs) are crucial to control virus infections at mucosal surfaces. Interleukin-22 (IL-22) was reported to help IFN-λ control rotavirus infection in mice either by aiding in the induction of interferon stimulated genes (ISGs) or by increasing cell proliferation thereby clearing virally infected cells. We investigated whether IL-22 and IFN-λs exhibited similar synergistic effects in human intestinal epithelial cells models. Our results showed that co-treatment of IL-22 and IFN-λ induced more phosphorylation of STAT1 than either cytokine used alone. However, this increased STAT1 activation did not translate to increased ISG production or antiviral protection. Transcriptomics analysis revealed that despite sharing a receptor and activating the similar STATs, the signaling generated by IL-22 and IFN-λs is independent where IFN-λs signaling induces ISGs and IL-22 signaling induces cell proliferation genes. Using human intestinal organoids, we confirmed that IL-22 increased the size of the organoids due to increased cell proliferation and increasing the stem cell marker (OLFM4). These findings suggest that in human intestinal cells, IFN-λs and IL-22 act independently to clear virus infections. IFN-λs induce ISGs to control virus replication and spread while IL-22 increases cell proliferation to eliminate infected cells and repair the damage epithelium. Although, these two cytokines do not increase each other’s function, they each play a key role in protecting human intestinal epithelium cells.

overall_design: To investigate whether IL-22 or IFN-λ induce distinct or unique genes, human colon carcinoma cells (T84) cells were mock treated or treated with 100ng/ml of each IFN-λ1,2,and 3; 100ng/mL IL-22 or a combination of 100ng/mL of IFN-λ1-3+ 100ng/mL IL-22. 3 biological replicates for each condition were collected at 3, 6, 12, and 24 hours post-treatment. Samples were analyzed for the gene upregulation as compared to mock treated.

first: Cuncai

last: Guo

first: Ashwini

middle: K

last: Sharma

first: José

last: Guzmán

first: Carl

last: Herrmann

first: Steeve

last: Boulant


title: mRNA profiling of patients infected with Ebola virus compared with healthy adult

first: xiong

last: liu

summary: Ebola virus can cause a severe and often fatal hemorrhagic fever in humans and other mammals, known as Ebola virus disease (EVD),the mechanism of how this pathogenesis comes about is not well understood, but it is well accepted that pathogenesis is significantly driven by a hyperactive immune response. To better understand the overall response to Ebola virus challenge, we undertook a transcriptomic analysis using the whole blood of EBOV infection patients.

overall_design: Human blood mRNA profiles of 22 EBOV infection patients and 10 healthy adults were generated by deep sequencing, using Illumina Hiseq 4000 platform


title: PTHrP regulates fatty acid metabolism via novel lncRNA in breast cancer initiation and progression models

city: Montreal

first: Jiannis

last: Ragoussis

state: Quebec

address: 740, Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

summary: The 5-year survival rate for women with metastatic breast cancer is 29%. Potential biomarkers identification is important for new therapeutic treatment in affected patients. Previous studies have shown that Parathyroid hormone-related peptide (PTHrP) plays a critical role in breast cancer growth and metastasis. The aim of our study was to use a genetically modified breast cancer mouse model to precisely examine the role of PTHrP from early primary breast cancer initiation to late progression. We identified a novel lncRNA, a new target for fatty acid metabolism that can be regulated by PTHrP in our unique mouse breast cancer model. We confirmed that a potential human lncRNA, OLMALINC, plays a similar role in fatty acid metabolism that can be regulated by PTHrP. Therefore, we validated our mouse finding in the human breast cancer cell lines. Genetically engineered mouse models provide valuable tools to study the molecular progression for breast cancer metastasis.

overall_design: Here we generated Pthrpflox/flox; Cre+ mT/mG and Pthrpwt/wt; Cre+ mT/mG tumor and tumor-free mice to examine the signaling pathways under the control of PTHrP from early to late stage of tumorigenesis. GFP+ mammary epithelial cells were further enriched for subsequent RNA sequencing (RNAseq) analyses.

first: Rui

last: Zhang

first: Jiarong

first: Dunarel

last: Badescu

first: Andrew

middle: C

last: Karaplis

first: Richard

last: Kremer


title: Extracellular Matrix Disorganization Caused by ADAMTS16 Deficiency Leads to Bicuspid Aortic Valve with Raphe Formation

city: Hangzhou

first: Ying

middle: Ying

last: Lin

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology

institute: Zhejiang University

summary:
BACKGROUND: A better understanding of the molecular mechanism of aortic valve development and bicuspid aortic valve (BAV) formation would significantly improve and optimize the therapeutic strategy for treating BAV patients. Over the past decade, the genes involved in aortic valve development and BAV formation has been increasingly recognized. On the other hand, ADAMTS gene family members have been reported to be able to modulate cardiovascular development and diseases. The present study aimed to further investigate the roles of ADAMTS family members in aortic valve development and BAV formation.  METHODS: Morpholino-based ADAMTS family gene-targeted screening for zebrafish heart outflow tract phenotypes combined with DNA sequencing in a 304 cohort BAV patient registry study was initially carried out to identify potentially related genes. Both ADAMTS gene-specific fluorescence in situ hybridization assay and genetic tracing experiments were then performed to evaluate the expression pattern in the aortic valve Accordingly, related genetic mouse models (both knock-out and knock-in) were generated using the CRISPR/Cas9 method to further study the roles of ADAMTS family genes. The lineage tracing technique was used again to evaluate how the cellular activity of specific progenitor cells was regulated by ADAMTS genes. Bulk RNA sequencing was used to investigate the signaling pathways involved. Both inducible pluripotent stem cells (iPSC) derived from BAV patients and genetic mouse tissue were used to study the molecular mechanism of the gene. Immunohistochemistry using different antibodies was performed to describe the phenotype of cardiac valve anomalies, especially in the ECM components.  RESULTS: ADAMTS genes targeted phenotype screening in zebrafish and targeted DNA sequencing on a cohort of BAV patients identified ADAMTS16 as a BAV-causing gene and found the ADAMTS16 p.H357Q variant in an inherited BAV family. In addition, both in situ hybridization and genetic tracing studies described a unique spatiotemporal pattern of ADAMTS16 expression during aortic valve development. Adamts16+/- and Adamts16+/H355Q mouse models both exhibited an R-NC-type BAV phenotype, with progressive aortic valve thickening associated with raphe formation (fusion of the commissure). Conditional Adamts16 mutant mouse models further demonstrated that Adamts16 deficiency mainly in endothelial lineage cells recapitulated the BAV phenotype. This was confirmed in lineage tracing mouse models in which Adamts16 deficiency affected endothelial and second heart field cells, not the neural crest cells. Accordingly, the changes were mainly detected in the noncoronary and right coronary leaflets. Bulk RNA sequencing using iPSC-induced endothelial cells (iPSC-ECs) and genetic mouse embryonic heart tissue unveiled enhanced FAK signaling, which was accompanied by elevated fibronectin levels. Both in vitro iPSC-ECs culture and ex vivo embryonic outflow tract explant studies validated the altered FAK signaling.  CONCLUSIONS: Our present study identified a novel BAV-causing ADAMTS16 p. H357Q variant. ADAMTS16 deficiency led to BAV formation.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 15 different tissues of different genetic mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, Adamts16 mutant and Adamts16 knockoout mice.

first: Jian'an