title: mRNA transcriptome sequencing of colon tissues from Usp25+/+ and Usp25-/- mice treated with 2.5% DSS for 5 five days followed by two-day normal water.

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

summary: Female Usp25+/+ and Usp25-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days. The colons were flushed with PBS to clear feces and slit open longitudinally. The distal colon tissues (0.5 cm in length, about 0.5 cm away from the anus) were washed in PBS and homogenized in 2 ml TRIzol (Invitrogen). Total RNAs were prepared and the qualities of RNAs were determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently puriﬁed from 10 ng total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. The first strand cDNA was synthesized with NEBNext® RNA First Strand Synthesis Module. NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first strand cDNA. The resulted double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep Kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 100 bp paired-end reads strategy (Novogene Co. Ltd, Beijing). Quality control of mRNA-seq data was performed by using Fatsqc and low-quality bases were trimmed by Cutadapt. All RNA-seq data were mapped to the mouse genome (mm9) by TopHat (version 2.1.1) and allow maximum 2 mismatch per read. Gene expression level was calculated by Cufflinks with default parameters and normalized by FPKM.

overall_design: Two Usp25+/+ mice and two Usp25-/- mice were used.

first: Xiao-Meng

last: Wang

first: Bo

last: Zhong


title: Sexually dimorphic role of constitutive androstane receptor in the regulation of endocrine and metabolic homeostasis

status: Public on Jan 02 2020

city: Toulouse

first: Céline

last: Lukowicz

address: 180 chemin de tournefeuille

department: ToxAlim

country: France

institute: INRA UMR1331

summary: The constitutive androstane receptor (CAR) is a transcription factor involved in detoxification through regulating expression of xenobiotic-metabolizing enzymes. Highly expressed in the liver, it is important in protecting the organism against exogenous and endogenous toxic molecules such as bile acids and bilirubin and in the catabolism of thyroid and steroid hormones. A role has also been assigned to CAR in the regulation of energy metabolism, although related mechanisms have been studied primarily in males and in physiopathological conditions. Here, we compared the impact of CAR deficiency on energy homeostasis regulation between male and female mice in a normal physiological context. Large-scale gene expression analysis in 16-week-old animals revealed significant sexual dimorphism in the hepatic transcriptome of CAR-/- mice.

overall_design: Thirty-six WT or CAR-/- males and 36 WT or CAR-/- females were housed in the laboratory animal room (23 ± 2 ºC) and segregated in 2 groupes each including 18 mice. One groupe of WT and CAR-/- males and females was sacrified at the age of 16 weeks. An other group containing the same animals was  followed for 68 weeks. Body weight was monitored throughout the experiment, and glucose tolerance and insulin sensitivity tests were performed. At death, blood, liver, epididymal adipose tissue (WAT) were collected and serum biochemical parameters were measured. Liver were analyzed for fatty acid content, histology. Hepatic gene expression studies were performed on the 16 week-old mice  by microarray . Gene expression profiles were performed on 6 liver samples per group at the GeT‐TRiX facility (GénoToul, Génopole Toulouse Midi-Pyrénées) using Agilent Sureprint G3 Mouse GE v2 microarrays (8x60K, design 074809) following the manufacturer's instructions. For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium). 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions. Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software and fluorescence signal extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters. Microarray data were analyzed using R (www.r-project.org, R v. 3.1.2), using Bioconductor packages (www.bioconductor.org, v 3.0, as described in GEO accession GSE. Raw data (median signal intensity) were filtered, log2 transformed and normalized using quantile method3

first: Sandrine

last: Ellero-Simatos

first: Fabiana

last: Oliviero

first: Arnaud

last: Polizzi

first: Claire

last: Naylies

first: Yannick

last: Lippi

first: Herve

last: Guillou

first: Laila

last: Mselli-Lakhal


title: RNA-Seq of CircHomer1a shRNA Knockdown vs. scrambled shRNA Control Mouse Orbital Frontal Cortex

status: Public on Jan 01 2020

city: Albuquerque

first: Nikolaos

last: Mellios

state: NM

address: 915 Camino De Salud NE

department: Neuroscience

country: USA

institute: University of New Mexico

type: Expression profiling by high throughput sequencing

summary: We report the application of RNA-sequencing to profile gene expression changes associated with shRN- mediated knockdown of circHomer1a RNA in mouse orbital frontal cortex

overall_design: Examination of circHomer1a knockdown vs control OFC gene expression changes

first: Mellios

last: Nikolaos


title: Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 grown on ribose

city: Ann Arbor

first: Eric

middle: C

last: Martens

state: MI

address: 1150 West Medical Center Drive, 6751 Medical Science BLDG II

department: Microbiology and Immunology

institute: University of Michigan

summary:
Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 grown on ribose to look at global changes in regulation in vitro on the defined monosaccharide, ribose as a sole carbon source.
Methods: Bacteroides thetaiotaomicron was grown on 5 mg/ml ribose or glucose as a sole carbon source in vitro. Fold change was calculated as ribose over glucose with n=3 biological replicates.  Once cells reached an optical density corresponding to mid-log phase growth  (absorbance between 0.6-0.8), RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) using RPKM normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average RPKM expression level in either glucose or ribose, and a p-value < 0.05 (t test with Benjamini-Hochberg correction)
Results: We identified 81 genes differentially expressed at a 5-fold cutoff when grown in ribose over the reference glucose condition, many of which are involved in other metabolic processes important for seemingly unrealted nutrients.

overall_design: rRNA-depleted, mRNA profiles of Bacteroides thetaiotaomicron VPI-5482 grown in vitro on ribose compared to glucose as a reference in biological triplicate  run on Illumina Hi-Seq platform.

first: Robert

middle: W

last: Glowacki


title: Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (ChIP-seq)

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

country: China

institute: School of Basic Medicine, Peking Union Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Function and number of muscle stem cells (satellite cells, SCs) declines with muscle aging. Although SCs are heterogeneous and different subpopulations have been identified, it remains unknown if a specific subpopulation of muscle SCs selectively decreases during aging. Here, we find Pax7Hi cells are dramatically reduced in aged mice and this aged-dependent loss of Pax7Hi cells is metabolically mediated by myofiber-secreted granulocyte-colony stimulating factor G-CSF as the Pax7Hi SCs are replenished by exercise-induced G-CSF in aged mice. Mechanistically, we show that transcription of G-CSF (Csf3) gene in myofibers is regulated by MyoD in a metabolism-dependent manner and the myofibers-secreted G-CSF acts as a metabolic niche factor required for establishing and maintaining the Pax7Hi SC subpopulation in adult and physiological aged mice by promoting the asymmetric division of Pax7Hi and Pax7Mi SCs. Together, our findings uncover a metabolic niche role of muscle metabolism in regulating Pax7 SC heterogeneity in mice.

overall_design: MyoD ChIP-seq on differentiated myotubes cultured in the presence or absence of pyruvate

first: Hu

last: Li

first: Qian

last: Chen

first: Changyin

first: Ran

first: Yixia

last: Zhao

first: Qianying

first: Weimin

last: Tong

first: Dahai

last: Zhu


title: Transcriptomic analysis of Arthrobacter sp. CGMCC 3584 responding to pde gene knockout

city: Nanjing

first: Huanqing

last: Niu

state: Jiangsu

address: No.30, Puzhu South Road

institute: Nanjing Tech University

summary: Arthrobacter sp. CGMCC 3584 are able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. Comparative transcriptomic analysis revealed that arpde inactivation had two major effects on metabolism: inhibition of glycolysis, PP pathway, and amino acid metabolism; promotion of the purine metabolism and carbon flux from the precursor PRPP, which benefited cAMP production.

platform_organism:
Clostridium acetobutylicum
Arthrobacter sp.

overall_design: Samples (two biological replicates) of Arthrobacter sp. CGMCC 3584 and arpde knockout mutant were respectively collected at 18h and 36h for DNA microarray analysis. Genes expression level log (mutant/wild strain)  ratios≥ 1 or ≤ -1 were considered to be significantly regulated.

first: Dong

last: Liu

first: Hanjie

last: Ying

first: Chenjie


title: Next Generation Sequencing Facilitates Quantitative Analysis of the control and H2O2-treated IMR90 cells Transcriptomes

city: Changchun

first: Cong

last: Lin

state: Jilin

address: Renmin Street

institute: Northeast Normal University

summary: We generated 6 Gb of high-quality sequencing data (per sample) and catalogued the expression profiles of annotated genes in each sample. The analysis showed differences of transcriptomes between the control and H2O2 treatment as well as revealed that H2O2 treatment induced genes expression changes. We identified numerous differentially expressed genes that known or potential roles in cellular senescence.Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to cellular senescence

overall_design: IMR90 cells mRNA profiles of the control and H2O2 treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.


title: Cell cycle-dependent YTHDF2 promotes mitotic entry by repressing WEE1

city: Chicago

first: Qili

last: Fei

state: Illinois

address: 929 E 57th Ave

institute: University of Chicago

summary: The m6A modification regulates mRNA stability and translation. Here we show that transcriptomic m6A modification is dynamic and the m6A reader protein YTHDF2 promotes mRNA decay during the cell cycle. Depletion of YTHDF2 leads to the delay of mitotic entry due to overaccumulation of WEE1, a negative regulator of CDK1. We demonstrate that WEE1 transcripts contain m6A modification, which promotes their decay through the m6A reader YTHDF2. Moreover, we found that YTHDF2 protein stability is dependent on CDK1 activity. Thus, CDK1, YTHDF2, and WEE1 form a feedforward regulatory loop to promote mitotic entry. We further identified CUL1, CUL4A, DDB1, and SKP2 as components of E3 ubiquitin ligase complexes that mediate YTHDF2 proteolysis. Our study provides insights into how cell cycle mediators modulate transcriptomic m6A modification, which in turn regulates the cell cycle.

overall_design: Illumina TruSeq stranded mRNA libraries prepared for m6A-seq, RIP-seq and RNA-seq in two replicates by Illumina HiSseq 4000 platform.

first: Chuan

last: He


title: RNA-seq analysis of Rfx expressing neurons of the Drosophila larval brain.

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: We report the mRNA profile of Drosophilaearly third instar larval brain neurons that specifically express the transcription factor Rfx1b isoform and compare the profile between control and Rfx1b mutant brains.

overall_design: mRNA profiles of Rfx expressing cells sorted by FACS from Drosophila third early instar larval brains. RNA profile were establisehd by Illumina RNA sequencing

first: Bénedicte

last: Durand


title: Cell-to-cell adhesion and neurogenesis in human cortical development: a study comparing 2D monolayers with 3D organoid cultures

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

summary: Organoids (ORG) are increasingly used as models of cerebral cortical development. Here we compared transcriptome and cellular phenotypes between ORG and monolayers (MON) generated in parallel from three biologically distinct iPSC lines. Multiple read-outs revealed increased proliferation in MON, which was caused by increased integrin signaling. MON also exhibited altered radial glia polarity, global suppression of Notch signaling and impaired generation of intermediate progenitors (INP), outer radial glia (oRG) and cortical neurons, which  were all partially reversed by reaggregation of dissociated cells into organoids. Network analyses revealed co-clustering of cell adhesion, Notch- related transcripts their transcriptional regulators in a module strongly downregulated in MON. The data suggest that cortical ORG, with respect to MON, initiates more efficient Notch signaling in ventricular radial glia owing to preserved cell adhesion, resulting in subsequent generation of INP and oRG, in a sequence that better recapitulates the evolution of the cortical ontogenetic process.

overall_design: Examination of 3 cell lines at 3 differentiation time points

first: G

first: F

last: Vaccarino

first: V

last: Cimini

middle: G

last: Altobelli

first: S

last: Scuderi


title: Transcriptome analysis of adipocyte differentiation (3T3-L1 WT and MIGA2 perturbed/overexpressed)

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: RNA-Seq of 3T3-L1 WT and MIGA2 perturbed/overexpressed adipocyte differentiation

overall_design: RNA was extracted at different time points (0 and 6 days) during an adipocyte differentiation time course from WT and MIGA2 depleted cells. Furthermore, differentiated adipocytes (6 days) with overexpressed MIGA2-GFP were analysed. RNA-Seq was performed to study the transcriptomic changes during the differentiation.

first: Pascal

last: Rauher

first: Robin

last: Klemm


title: Genome-wide analysis of mesenchymal stem cell gene expression upon Mycobacterium tuberculosis infection

city: New Delhi

first: Dhiraj

last: Kumar

state: New Delhi

address: Aruna Asaf Ali Marg

department: Cellular Immunology

country: India

institute: ICGEB, New Delhi

summary: Analysis of mesenchymal stell cell gene expression level upon Mycobacterium tuberculosis infection. Transcriptome landscape provide important information of the response of stem cell infetion with Mycobacterium tuberculosis such as antibacterial pathways and specific anabolic/catabolic cellular functions.

overall_design: Total RNA obtained from Mycobacterium tuberculosis infected mesenchymal stem cells and compared with that of uninfected mesenchymal stem cells.

first: Jain

last: Neharika

first: Kalam

last: Haroon

first: Kumar

last: Dhiraj


title: Chronic Arsenic Exposurre Impairs Adaptive Thermogenesis in Male C57BL/6J Mice

city: Berkeley

first: Felicia

last: Castriota

state: CA

address: 188 Li Ka Shing Center, Room 375E

institute: UC Berkeley

summary:
Purpose: To determine the effects of sodium arsenite in male mice on adaptive thermogenesis.
Methods: Male C57BL/6J mice were exposed to sodium arsenite in drinking water at 300 parts per billion (ppb) for 9 weeks
Findings: Arsenic-treated mice experienced significantly decreased metabolic heat production when acclimated to chronic cold tolerance testing, as evidenced by indirect calorimetry, despite no change in physical activity. Arsenic exposure increased total fat mass, and unilocular lipid droplet size in both subcutaneous inguinal white adipose tissue (iWAT) and brown adipose tissue (BAT).
Conclusion: Chronic arsenic exposure impacts the mitochondria of thermogenic tissues involved in energy expenditure and glucose regulation, providing novel mechanistic evidence for arsenic’s role in metabolic pathologies.

overall_design: Inguinal WAT RNA profiles were generated for C57BL/6J male mice treated with either 300 ppb sodium arsenite or dH20, for a duration of 9 weeks

first: Michele

middle: A

last: La Merrill


title: DIS3L2 promotes progression of hepatocellular carcinoma via hnRNP U-mediated alternative splicing

city: Hefei

first: Songge

last: Xing

state: An Hui

address: No.443, Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: DIS3-like 3'-5' exoribonuclease 2 (DIS3L2) degrades aberrant RNAs, however, its function in tumorigenesis remains largely unexplored.hnRNP U regulates the alternative splicing of pre-mRNA, and our results also showed that RNA promoted the interaction between DIS3L2 and hnRNP U, suggesting that DIS3L2 may be involved in splicing regulation. Thus, we next performed RNA-Seq to investigate whether DIS3L2 regulated pre-mRNA alternative splicing in cancer cells.

overall_design: Human hepatocellular carcinoma PLC cells were transfected with Dis3l2 shRNAs, hnRNP U shRNAs or non-targeting control shRNA followed by RNA extraction and sequenced on Illumina Novaseq (Homo sapiens).

first: songge

first: WenHao

last: Ma

first: Shenqi

last: Shen

first: Huafeng

last: Zhang

first: Ping

last: Gao


title: The Dynamics of Cytoplasmic mRNA Metabolism

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

summary: For all but a few mRNAs, the dynamics of metabolism are unknown. Here, we developed an experimental and analytical framework for examining these dynamics for mRNAs from thousands of genes. mRNAs of mouse fibroblasts exit the nucleus with diverse intragenic and intergenic poly(A)-tail lengths. Once in the cytoplasm, they have a broad (1000-fold) range of deadenylation rates, which correspond to cytoplasmic lifetimes. Indeed, degradation appears to occur primarily through deadenylation-linked mechanisms, with little contribution from endonucleolytic cleavage or deadenylation-independent decapping. Most mRNA molecules degrade only after their tail lengths fall below 25 nt. Decay rates of short-tailed mRNAs vary broadly (1000-fold) and are more rapid for short-tailed mRNAs that had previously undergone more rapid deadenylation. This coupling helps clear rapidly deadenylated mRNAs, enabling the large range in deadenylation rates to impart a similarly large range in stabilities.

overall_design: The experiments consist of ribosome profiling libraries (small RNA-seq and RPF reads) from two microRNA-inducible 3T3 cell lines (miR-1 and miR-155) with or without microRNA induction. These samples were prepared for 5 and 6 metabolic-labeling time points for the miR-1 and miR-155 lines, respectively. In addition, a metabolic labeling/transcriptional shutoff experiment was performed which generated 12 sequences samples made with the NEXTflex RNA-seq kit. Finally, 38 PAL-seq samples from these time courses are also included to measure poly(A)-tail lengths.

first: Stephen

last: Eichhorn

first: Alexander

middle: O

last: Subtelny

first: Kathy

middle: S

last: Lin

first: Sean

middle: E

last: McGeary

first: Sumeet

last: Gupta

first: David

middle: P

last: Bartel


title: Identification of long non-coding RNA and circular RNA in mice after intra-tracheal instillation with fine particulate matter

first: Guangfa

last: Wang

address: No.8 Xishiku street

department: Respiratory and Critical care medicine

institute: Peking University First Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Intra-tracheal instillation of saline or PM2.5 was performed in BALB/c Mice once a week for consecutive eight weeks. Genomewide transcriptome profiling of coding genes, long non-coding RNAs (lncRNA), and circular RNAs (circRNA) in mice lung were done by ribosomal RNA-depleted RNA sequencing.

overall_design: Lung RNA profiles of saline or PM2.5 exposed mice were generated by deep sequencing, in triplicate, using Illumina.

first: Yijue

last: Zhong


title: Sexual dimorphism in transcriptomic response to fluocinolone acetonide (FA) in murine epidermis

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

summary:
Topical application of glucocorticoid fluocinolone acetonide (FA) induces sexually dimorphic transcriptomic response in murine epidermis
NULL

overall_design: Wild-type B6129 male and female mice were  treated with glucocorticoid fluocinolone acetonide (FA) or vehicle (acetone) as a control, with 2 animals per an experimental condition.

first: Irina

last: Budunova

first: Gleb

last: Baida


title: Short-chain fatty acids improve post-stroke recovery via immunological mechanisms.

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

summary: This transcriptomic study investigates the effect of therapeutic short-chain fatty acids (SCFA) administration on post-stroke recovery.

overall_design: The transcriptomic profiles of 15 weeks old C57BL/6 mice 14 days after stroke were compared according to their treatment with +/- SCFA (n = 3/3).

first: Rebecca

last: Sadler

middle: H

first: Lesca

middle: M

last: Holdt

first: Arthur

last: Liesz


title: RNA-seq in pancreatic cancer PANC1 cells

city: Tianjin

first: Xiaodong

last: Zhang

address: 94 Weijin Road

institute: Nankai University

summary: We report the the effect of PGAM1 succinylation on gene expression profiling.

overall_design: RNA-seq was performed in the PANC1 cells depleted endogenous PGAM1 and reconstituted expression of PGAM1 or PGAM1 mutant (K99R)

first: Guang

last: Yang


title: ChIP-seq in liver cancer HepG2 cells

summary: We report the the chromatin occupancy of histone H3K122 succinylation and its correlation with HAT1 by using ChIP-seq.

overall_design: ChIP-seq was performed in the HepG2 cells by using the antibody of histone H3K122 succinylation and HAT1


title: Screening on Platelet Non-coding RNA Expression Profiles Discloses Its Correlations with Low Residual Platelet Reactivity

city: Chengdu

first: Mao

last: Chen

address: 37 Guoxue Street

institute: West China Hospital

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

summary: Double anti-platelet therapy (DAPT) has wide inter-individual variabilities in coronary heart disease (CHD) patients’ responses, which undermines the prognosis effect in clinical practice. Noncoding RNAs are present in platelets, albeit their potential roles in platelet responses to DAPT largely remains in the realm of the unknown. This study aims to screen differential noncoding RNAs responsible for low residual platelet reactivities under DAPT. We enrolled 144 CHD patients that received DAPT and assigned them to high platelet reactivity (HPR) group and baseline group according to their residual platelet reactivities. Through microarray analysis, we detected a total of 22,424 kinds of co-expressed lncRNAs in three pairs of the patients between the HPR and baseline groups.

overall_design: 3 pairs of patients were randomly selected from the high residual and baseline platelet reactivity group from the recruited CHD patients. Their platelet were mixed to stand respectively.

first: Shao-Di

last: Yan

first: Xiao-Jing

last: Liu

first: Xiao

last: Ke

first: Jun-Li

last: Li

first: Zhan-Chao

last: Xian

first: Chang-Nong

last: Peng


title: De novo genome sequencing and comparative stage-specific transcriptome analysis of Dirofilaria repens

first: giancarlo

last: russo

summary: The zoonotic mosquito-borne filarial nematode Dirofilaria repens causes subcutaneous and ocular infections in dogs, cats and humans. Microfilariae (mf) are taken up by mosquitoes from infected vertebrate hosts which develop in the mosquito to the infectious third stage larvae (L3). These are transmitted to new vertebrate hosts and develop over two further moults to adult worms. The aims of the project were 1) the de novo sequencing and annotation of the D. repens genome and 2) comparative transcriptome analyses of the developmental stages mf and L3 as we hypothesized remarkable differences in gene expression between the different developmental stages. Genomic DNA was obtained from adult male D. repens. RNA was extracted from microfilariae from naturally infected dogs and from L3 produced in Aedes aegypti mosquitoes fed on blood spiked with microfi-lariae. The 99.59 MB genome was around 17% larger than that of the related species D. immitis (dog heartworm) and contained 8.9% fewer predicted genes (10,357). Around 1.8% of identified proteins (206/11,262) could not be mapped to D. immitis. Out of these, 6 (2.9 %) presented an ortholog in all other considered filarial nematodes (e.g. Loa loa) and Caenorhabditis elegans. A sig-nificantly higher number of D. repens proteins as compared to D. immitis mapped to the filarial nem-atode L. loa, reflecting the similarity in biology of D. repens and L. loa. A total of 876 genes were differentially expressed, of which 591 could be annotated in UniProtKB/Swiss-Prot. In particular, 155 genes with a UniProtKB/Swiss-Prot annotation to C. elegans and filarial nematodes were upregulat-ed in the L3 and 57 in the mf stage, respectively. Fifteen GO BP (Gene Ontology Biological Pro-cesses) were significantly enriched for the L3 group and 12 for the mf. These data provide first in-sight into the differential gene expression profiles of this filarial nematode and can serve for future investigations of metabolic processes and stage-specific diagnostics.

overall_design: 6 samples, 2 groups (mf, L3). Three biological replicates per group.


title: Sex-specific small RNA profiling and target gene expression in dioecious and monoecious Pistacia chinensis

first: Qian

last: Bai

address: 35 East Qinghua Road

department: College of Forestry

institute: Beijing Forestry University

summary: Pistacia chinensis Bunge is known as dioecious, but we have found wild monoecious individuals. In order to screen the candidate genes which may influence the sex expression or floral phenotypic differences of P. chinensis, the inflorescence buds for different sex types associated with the sex differentiation were selected and tested for small RNA sequencing. Sex-specific differentially expressed small RNA were discovered, combined with real-time PCR data, the regulation patterns of various sex types were first revealed. Our study represents the first detailed analysis of small RNA sequencing, providing more clues for understanding the mechanism of sex determination on P. chinensis.

overall_design: The inflorescence buds of four sex types (female, male, monoecious female and bisexual) during two sex differentiation stages were selected for small RNA sequencing.

first: Shuchai

last: Su


title: Transcriptomic analysis of Arabidopsis wild-type (Col-0), phyb-9, jaz10 and jaz10phyB-9 plants to methyl jasmonate (MeJA)

city: Buenos Aires

first: Carlos

middle: Daniel

last: Crocco

state: Buenos Aires

address: Av. San Martín 4453

country: Argentina

institute: University of Buenos Aires - IFEVA - CONICET

summary:
We used Affymetrix 1.0 ST arrays to compare the transcriptome of 4 weeks‐day‐old plants sprayed with 250uM of MeJA or mock (control). For the experiments we used wild-type (Col-0), phyB-9 and jaz10 single mutants and jaz10phyb double mutant. Samples were harvested after 3hours of induction with MeJA or mock.
We performed a first analysis with the transcriptomes of wild‐type (Col-0) to identify those group of genes that are up‐ and down‐regulated by MeJA treatment (2 fold-changes). We founded 719 genes whose expression was statistically significantly different between the two treatments. To gain knowledge into the regulation of phyB over these set of 719 genes, we contrasted their expression levels against phyB transcriptome. By cluster analysis, we identified five major groups of genes, where in two of them the transcript levels increased in presence of MeJA  (clusters 1 and 2) and three whose expression decrease after MeJA treatment (Cluster 3, 4 and 5).

overall_design: We used a factorial experimental design comprising four genotypes (Col-0, phyb-9, jaz10 and jaz10phyb-9) and two treatments (MeJA or mock). 4 weeks‐day‐old plants were sprayed with MeJA (250μM) or mock solution and harvested 3hs later. Two replicates per treatment were performed for col and tree replicates for phyb-9. RNA was extracted using The Spectrum Plant Total RNA Kit (Sygma), prepared, labelled and hybridized to the arrays in accordance with the manufacturer’s instructions for the GeneChip Arabidopsis Gene 1.0 ST Array (Affymetrix). Raw microarray data were processed and analyzed using Affymetrix Expression Console® software. Genes with ‘absent’ calls and a signal of <50 units in all replicate experiments were filtered out. Significantly differentially expressed genes were identified by performing profile analysis using Significance Analysis of Microarrays with a p-value <0.05. A test filter was performed to work only with those genes for which the ratio of expression showed at least a 2‐fold change between “col mock” vs “col MeJA”.

last: Ballaré

middle: D


title: Genetic dissection of gene silencing mediated by H3K27 methylation

city: Corvallis

first: Kristina

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

summary: We are intereted in changes in transcriptome in putative polycomb mutants generated by exposure to UV light. We included polycomb mutants made by reverse genetics and other WT strains with different genetic backgrounds used as parents for bulk segregant analysis.

overall_design: RNA-seq for 68 samples, each from a different strain of Fusarium graminearum.

first: Lanelle

middle: R

last: Connolly

middle: L

last: Chang

first: Phuong

last: Pham

first: Rodrigo

last: Gonçalves

first: Brett

last: Pierce

first: Corinne

last: Fargo

first: Brian

last: Josephson

first: Zackary

last: Bango

first: Madison

last: Esposito

first: Lye

last: Markillie

first: Galya

last: Orr

first: Michael

last: Freitag


title: ANILLIN REGULATES BREAST CANCER CELL MIGRATION, GROWTH AND METASTASIS BY NON-CANONICAL MECHANISMS INVOLVING CONTROL OF CELL STEMNESS AND DIFFERENTIATION

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Breast cancer metastasis is driven by profound remodeling of the intracellular cytoskeleton enabling efficient cell migration. Anillin is a unique cytoskeletal scaffolding protein that regulates actin filaments, microtubules, septin polymers and Rho GTPases. Anillin is markedly overexpressed in breast cancer and other solid cancer, however its functions in cancer cells remain poorly understood. This study aims at investigating the roles of anillin in regulating breast cancer cell migration, invasion and metastasis. CRISPR/Cas9 technology was used to deplete anillin in highly metastatic MDA-MB-231and BT549 cells and to overexpress it in poorly invasive MCF10AneoT cells. These loss-of-function and gain-of-function studies demonstrated that anillin is necessary and sufficient to accelerate migration, invasion and anchorage-independent growth of breast cancer cells in vitro. Furthermore, loss of anillin markedly attenuated both primary tumor growth and metastasis of breast cancer in vivo. In breast cancer cells, anillin was localized in the nucleus, however anillin knockout affected the cytoplasmic/cortical events such as the organization of actin cytoskeleton and cell-matrix adhesions. This was accompanied by a global transcriptional reprogramming of anillin-depleted breast cancer cells that resulted in suppression of their stemness and induction of the mesenchymal to epithelial trans-differentiation. Such trans-differentiation was manifested by upregulation of basal keratins along with increased expression of E-cadherin and P-cadherin. Knockdown of E-cadherin reversed attenuated migration and invasion of anillin-deficient cells. Our study provides the first evidence that anillin plays causal roles in breast cancer development and metastasis in vitro and in vivo and unravels novel functions of anillin in regulating breast cancer stemness and differentiation.

overall_design: Examination of the effect of ANLN KO in MCF-231 breast cancer cells using two CRISPR probes

first: Dongdong

last: Wang

first: Nayden

last: Naydenov

first: Jennifer

last: Koblinski

first: Andrei

middle: I

last: Ivanov


title: Mutating Zta(N182) to S, Q, T, I, and V changes sequence specific DNA binding to four types of DNA (32k data set)

city: Bethesda

first: Charles

last: Vinson

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: The Epstein-Barr virus (EBV) bZIP transcription factor (TF) Zta is a sequence-specific DNA binding protein that recognizes both unmethylated and methylated double stranded DNA (dsDNA).  To study the contribution to sequence specific dsDNA binding of the conserved asparagine in the DNA binding region (Zta(N182)), we replaced it with five other amino acids:  serine (S), glutamine (Q), threonine (T), isoleucine (I), or valine (V).  We used protein binding microarrays (PBMs) to evaluate sequence-specific DNA binding to four types of dsDNA: 1) DNA with cytosine in both strands (DNA(C|C), 2) DNA with 5-methylcytosine (5mC, M) in one strand and cytosine in the second strand (DNA(5mC|C)), 3) DNA with 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand (DNA(5hmC|C)), and 4) DNA with methylated cytosine in both strands in all CG dinucleotides (DNA(5mCG)).  With unmethylated DNA, Zta binds the consensus TRE motif, also known as the AP1 motif (T-4G-3A-2G/C0T2C3A4).  Zta(N182S) binds the variants andwhere C3 is replaced with G3 in one (T-4G-3A-2G/CT2G3A4) or both T-4C-3A-2G/CT2G3A4 half sites.  Zta(N182S) also binds stronger to DNA containing modified cytosines compared to wildtype. Zta(N182Q) binds new sequences containing G0T2A3A4 with DNA(C|C), DNA(5mC|C) and DNA(5hmC|C) where C3 is replaced with A3 only on one half site.  Zta(N182I) and Zta(N182V) bind sequence specifically to DNA(5mC|C), and weakly with all other types of DNA examined.  Zta(N182T) DNA binding is weaker to all types of DNA examined.  Our data highlights that mutation of Zta(N182) with the hydrophilic amino acids serine and glutamine alters Zta sequence specific DNA binding, while mutation with hydrophobic amino acids (I and V) increases binding to DNA(5mC|C).

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of Zta, Zta(N182S), Zta(N182Q), Zta(N182I), Zta(N182V), and Zta(N182T).  Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines.  We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine.  Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.

first: Assad

last: Nima


title: Deep sequencing of WNV isolates collected in Harris County, TX 2013-2016

city: Galveston

first: Daniele

last: Swetnam

state: TX

address: 301 University Blvd

department: Experimental Pathology

institute: University of Texas Medical Branch

summary: Harris County, Texas experienced its largest outbreak of West Nile (WNV) disease in 2014. Characterization WNV isolates from the outbreak using next generation sequencing approaches, phylogeny, and animal studies revealed a novel genotype characterized by selection of an amino acid substitution, NS2A-R188K. Retrospective analysis of Genbank showed this genotype was first identified in New York and Connecticut in 2008 and then in Texas subsequently. Thus, we have termed this the Northeast 2008 (NE/WN08) genotype. Emergence of this genotype in Texas likely involved the displacement of the SW/WN03 genotype. Quasispecies diversity revealed significant variation occurred among viral isolates, but no phenotypic changes were observed in terms of temperature sensitivity and mouse virulence, suggesting that despite WNV being in North America for 15 years there are strong mutational robustness among naturally occurring WNV isolates. Examination of Genbank showed that convergent evolution of NS2A-R188K was also taking place worldwide.

overall_design: Mosquito pools and dead birds in Harris County, TX were collected by the Harris County Public Health, Mosquito & Vector Control Division (HCPHMVCD) in Houston, TX, USA. The brain homogenate of twenty nine WNV-positive birds and a single WNV-positive mosquito pool was passaged once or twice in Vero cells, and virus was collected from the supernatant of infected Vero cells when CPE was apparent. WNV RNA was extracted using the QIAamp Viral RNA Mini kit according to the manufacturer’s recommendations. Libraries were generated with a TruSeq RNA v2 kit (Illumina) and samples were sequenced on an Illumina HiSeq 1500 platform.

first: Alan

last: Barrett


title: Mutating Zta(N182) to S, Q, T, I, and V changes sequence specific DNA binding to four types of DNA

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

overall_design: Refer to individual Series


title: icSHAPE from GM12878 (ENCSR052BBY)

status: Public on Jan 06 2020

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
icSHAPE control (DMSO) on GM12878 immortalized cell line

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mutating Zta(N182) to S, Q, T, I, and V changes sequence specific DNA binding to four types of DNA (65k data set)


title: Gene expression and whole-transcriptome analysis of heart tissue isolated from mutant transgenic mice after 16 weeks of treatment with AAV9-M7.8L shRNA

city: San Diego, California

first: Kathia

last: Zaleta-Rivera

address: 9500 Gilman Drive, MC 0412

institute: UCSD

summary:
Purpose: Assess the effects of the myocardial transcriptional program and off-target delivery or endogenous RNA interference pathways by AAV9-M7.8L shRNA
Results: RNA sequencing including small RNA profiling was used to assess i) the presence of delivered therapeutic, ii) effects on the mutant and wild type alleles, iii) gene expression network effects of disease and silencing, and iv) disruption of the native small RNA processing apparatus and microRNA function. Transcriptome analysis showed that M7.8L shRNA and CFP was highly expressed in the hearts of humanized mutant transgenic mice treated at 3 days old of age and allele specific silencing  27% of the human MYL2-47K (RLC-47K) mutation without affecting the mouse endogenous myl2 gene.  miRNA profiling showed a pathological signature in untreated and control RLC-47K mice, with the upregulation of mir208a, and mir208b and downregulation of mir-499, which is a common response to cardiac injury, however no significant changes were observed for mir208a and mir-499 in the M7.8L treated group compared to the untreated and control groups. On the other hand, the expression of  mir208b was significantly downregulated in the treated group, which was consistent with a positive therapeutic benefit. This emphasizes the complexity of cardiac remodeling and the time-dependent nature of the changes in different signaling networks. To assess downstream broader transcriptional effects of the treatment, we adopted a network approach similar to those we have previously published.We obtained the top 30 differentially expressed genes between treated and control groups and extracted interacting genes and relationships from the STRING database. We then plotted the resulting interaction network with each gene's expression fold change . This visualization revealed reversal of the stress/remodeling myocardial gene program and related markers (including Myh7, Nppa, Nppb, Acta1) as well as up-regulation of gene networks that included acetyl-CoA transferases (Ech1, Ecl1, Acaa1), indicating a wide, systemic, transcriptional effect of the treatment in reverting the disease gene expression program. We also observed minimal impact of off-target delivery or endogenous RNA interference pathways. Thus, we assessed the expression level of the enzymes argonaute and dicer and found a slight increase of argonaute and no significant changes in the expression of dicer in the 3 days old treated mutant transgenic mice as compared to the untreated and control animals suggesting that shRNA/miRNA-shared pathways were modestly affected during four months of constitutive expression of M7.8L shRNA in the hearts of adult mice. These effects and the lack of in vivo cytotoxicity in RLC-4K treated mice are consistent with the effects of the H1 promoter that drives M7.8L shRNA expression in a more restrained manner than the U6 promoter. Similar findings have been observed in mouse liver after knockdown of hepatitis B virus with shRNA driven by weak promoters.
Conclusions: in vivo allele-knockdown of MYL2-47K at 4 months was 27% by RNA sequencing. This sustained but modest reduction appeared sufficient to revert the disease phenotype during four months of observation without affecting the normal allele. In addition, we observed that shRNA expression declined after four months of treatment, however this course of treatment was sufficient to ameliorate the disease with minimal off-target effects, while efficacy when mice were treated at older age was reduced. In humans, there is often progression of disease seen during adolescence. Based on this observation it would seem that RNAi therapies should target early disease.

overall_design:
Methods: RLC transgenic mice were injected via the jugular vein at three days old of age with AAV9 H1-M7.8L RSVp-Cerulean. For the neonatal group, 25ul of virus were injected (3x10^11 viral particles). Echocardiography and treadmill studies were done at 2 and 3.5 months of age. At 4 months of age, animals were sacrificed and hearts were isolated for hyperttophic biomarker quatification, collagene deposited and microRNAseq and mRNAseq. Two illumina RNA libraries were prepared: one Small RNA library ran in MiSeq Rapid Mode 50 nt-single end and an Poly A library  in HiSeq Rapid mode 100 nt -pair end
Heart_wtTg= Heart tissue isolated from wild type transgenic mice (wtTg) carrying the normal human allele of the MYL2 gene.
Heart_mutTg=Heart tissue isolated from mutant transgenic mice (mutTg) carrying the mutated human allele of the MYL2 gene.
Control virus= AAV9 virus non-expressing M7.8L shRNA.


title: Genome-wide analysis of murine white adipose tissue gene expression in response to an overexpression of mitochondrial ferritin

city: Dallas

first: Philipp

last: Scherer

state: Texas

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center, Internal Medicine

institute: The University of Texas Southwestern Medical Center

summary:
Analysis of mitochondrial matrix iron overload in white adipose tissue at the gene expression level. The hypothesis tested in the present study was that iron overload in mitochondria of white adipose tissue will cause a unique mitochondrial perturbation in white fat.
Results should provide information regarding the critical compensatory mechanisms by which the adipocyte repsonses to mitochondrial dysfunction; locally and at the whole-body level, such as the key genes up- and downregulation in response to mitochondrial iron overload.

overall_design: Total RNA obtained from murine white adipose tissue following feeding control and fat-speciifc mitochondrial ferrritin transgenic mice (FtMT-Adip) with Dox-HFD for 3-weeks

first: Christine

last: Kusminski


title: Loss of the nucleolar DUB USP36 impairs Parkin dependent mitophagy via downregulation of autophagic components

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: The Parkin dependent final elimination of defective mitochondria is halted by loss of the nucleolar DUB USP36. The authors suggest a general failure in autophagy induction due to a decline in Beclin-1 and ATG14 levels. Reduction of the epigenetic mark histone 2B lysine 120 ubiquitination possibly contributes to the observed phenotype.

overall_design: comparison of mRNA expression levels from control siRNA and USP36 siRNA transient transfected HeLa cells of five independent experiments

first: Sven

last: Geisler

first: Lea

last: Jäger

first: Sonia

last: Golombek

first: Etsuro

last: Nakanishi

first: Friederike

last: Hans

first: Caren

last: Linnemann

first: Nicolas

last: Casadei

last: Kahle


title: Complete genome sequence of Escherichia coli C - old model organism with a new application in biofilm research

city: Philadelphia

first: Joshua

last: Earl

state: PA

institute: Drexel University College of Medicine

summary: Escherichia coli strain C is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. We found that E. coli C forms more robust biofilms than the other four laboratory strains. Here we present the complete genomic sequence of this strain in which we utilized high resolution optical mapping to confirm a large inversion in comparison to other strains. DNA sequence comparison revealed the absence of several genes involved in biofilm formation, such as antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The main difference affecting biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream.  Analysis of gene expression profiles in planktonic and biofilm attached cells by the RNAseq method allows better understanding of this regulatory pathway in E. coli.

overall_design: Total RNA was extracted from a five days old slide biofilms which were transferred to a fresh LB Miller broth daily. As planktonic cells we used cells detached from the biofilm from the last, 5th day passage.  Planktonic (control) or biofilm (experiment)

first: Jaroslaw

last: Krol


title: Effect of sodium hydrosulfide on gene expression of intestinal epithelial cells

city: Nanjing

first: xiawei

last: Zhang

address: Weigang NO.1

institute: National Center for International Research on Animal Gut Nutrition

summary: The transcriptome sequencing was used to study effects of H2S on the intracellular processes in human colon carcinoma cell line Caco-2. The results establish that excessive H2S increased the expression of genes related to inflammatory response, provoked oxidative stress, weakened mitochondrial function and strengthened mitophagy and autophagy.

overall_design: Examinations of sodium hydrosulfide on gene expression of normal and inflammatory Caco-2 cells

first: Xiawei

first: Chunlong

last: Mu

first: Weiyun

last: Zhu


title: Transcriptome profiling of mutant INS gene-induced diabetes of youth (MIDY) and wild type pig livers.

first: Mattias

last: Backman

state: Bavaria

address: Feodor-Lynen-Straße 25

department: Genzentrum

institute: Ludwig Maximilian University of Munich

summary: Physiologically the liver is exposed to higher insulin concentrations than other organs. To evaluate functional consequences of insulin-deficient diabetes mellitus for the liver, we used a genetically engineered pig model of mutant INS gene induced diabetes of youth (MIDY). Liver samples of MIDY pigs and wild-type (WT) littermate controls were analyzed by RNA sequencing, label-free proteomics and targeted metabolomics/lipidomics to reveal pathways and key drivers significantly affected by chronic insulin deficiency and hyperglycemia. Gene set enrichment analysis of the ~500 transcripts that were differently abundant between MIDY and WT samples revealed pathways related to amino acid metabolism, beta-oxidation of fatty acids, gluconeogenesis and ketogenesis to be enriched in MIDY samples, whereas pathways related to extra cellular matrix and inflammation/pathogen defense response were enriched in the WT samples. Reduced insulin receptor activation and phosphorylation of protein kinase B (PKB, AKT) was associated with markedly increased levels of retinol dehydrogenase 16 (RDH16) and 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS2), the apparent key drivers of stimulated gluconeogenesis and ketogenesis in MIDY pigs. Profiling of acylcarnitines provided evidence for increased activity of carnitine palmitoyltransferase 1 (CPT1) shuttling fatty acids into the mitochondrial matrix for beta-oxidation and for increased omega-oxidation. In addition, several enzymes involved in amino acid degradation and enzymes of the urea cycle were increased in abundance, consistent with an increased use of amino acids for gluconeogenesis. Transcripts and proteins related to extracellular matrix, such as collagens, and inflammatory/immune mechanisms, such as C-reactive protein, proteins involved in or regulated by Toll-like receptor signaling and components of major histocompatibility complexes, were less abundant in MIDY vs. WT liver samples. Our study provides the first multi-omics analysis of liver in a clinically relevant large animal model for insulin-deficient diabetes mellitus.

overall_design: Hepatic mRNA profiles of 2-year old wild type (WT; N=5) and C94Y transgenic (MIDY; N=4) pigs.

first: Julia

last: Philippou-Massier

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Eckhard

last: Wolf


title: Identification of a novel TINCR-EGFR signaling pathway loop which initiates receptor tyrosine kinases cascade and confers tumorigenesis in human cancer

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing was performed to investigate the potential crosstalk between TINCR and microRNAs.

overall_design: microRNA profiles of T47D with TINCR knockdown and scramble were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript

first: Shouping

last: Xu

first: Da

last: Pang


title: Dissecting cell diversity and connectivity in skeletal muscle for myogenesis

city: Hangzhou

first: Yixiao

last: Liu

state: 浙江

address: Yuhangtang road

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

summary:
Purpose:The goal of this study is to determine the cellular identity and trascriptomic profile of mice skeletal muscle derived rapidly adhering cells.
Methods: By single-cell RNA seq to decode the cell types composition of adult male C57BL/6 mice.
Results: Single-cell transcriptome data of mice skeletal muscle is provided.
Conclusion: skeletal muscle derived rapidly adhering cells were classified into 7 cell types, in cluding one newly described cell subtype:teno-muscular cells(TMs)

overall_design: 563 mice skeletal muscle-derived single cells from  6~8 weeks old male C57BL/6 mice

first: Xiaohui

last: Zou

first: Hongwei

last: Ouyang

first: Bingbing

last: Wu


title: Gene expression profiling of wiltype and Ctr1 knockout MEFs with depleted cellular Cu levels

first: Donita

middle: Colette

last: Brady

address: 421 Curie Blvd. BRBII/III Room 612

department: Cancer Biology

institute: University of Pennsylvania

summary: The transition metal Cu is an essential micronutrient in biological systems. The majority of Cu is taken up into the cell through the Cu transporter CTR1 and thus, deletion of Ctr1 results in Cu deficiency. Here we performed transcriptional profiling of isogenic mouse embryonic fibroblast harboring conditional alleles for Ctr1 floxed out or intact through in vitro administration of doxycycline. The goal was to elucidate gene expression changes upon knockout of Ctr1.

overall_design: Gene expression by RNAseq of isogenic mouse embryonic fibroblasts (MEFs) either wildtype or null for Ctr1 in triplicate. In addition, MEFs null for Ctr1 were independently treated with 500mM of the Cu chelator BCS for 48 hours in triplicate. Total of 9 samples were analyzed.

middle: C

first: Tiffany

last: Tsang


title: Jak2 mediated phosphorylation and activation of TET2 in hematopoiesis

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: FDCP cells were stably transfected with JAK2V617F or WT JAK2 vectors and then examined for genome wide methylation with the HELP assay

overall_design: HELP assay was performed on DNA from Jak2 mutant and wildtype containing cells

first: Amittha

last: Wickrema


title: Identification of a novel TINCR-EGFR signaling pathway loop which initiates receptor tyrosine kinases cascade and confers tumorigenesis in human cancer [mRNA]

summary: RNA sequencing was performed to investigate the potential crosstalk between TINCR and its targets.

overall_design: mRNA profiles of UACC-812 with TINCR knockdown and scramble were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript


title: Expression data from liver of Cyclocarya paliurus triterpenic acids treated high-fat-diet-induced mice

first: YITING

last: WANG

address: No. 100, Shizi Street, Maogaoqiao Street

institute: Department of Natural Medicinal Chemistry & State Key Laboratory of Natural Medicines, China Pharmaceutical University

summary:
Diverse targets and metabolic pathways are involved in NAFLD, which accounts for the difficulties in achieving the predominant therapeutic effects in clinical practice. Lipid accumulation is the ‘first hit’ in the development of NAFLD in liver, the dysregulation of lipid disposal can lead to hepatic steatosis. Oxidative stress is the ‘second hit’ in the pathogenesis of NAFLD. CP triterpenic acid (CPT) had an ameliorative effect on metabolic diseases, such as non-alcoholic hepatic steatosis.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Mice were randomly distributed into three groups (n = 5 per group) and were fed with a standard chow diet (normal control group, NC group), an high fat diet [bile sodium 0.5%, cholesterol 2%, yolk 10%, lard 10%, standard diet 77.5% (w/w), about 4016 kcal/kg, 30% of calories from fat] (HFD group), or orally administrated with CPT (160 mg/kg) daily for 8 weeksafter 12 weeks of HFD feeding (CPT group). Mice were anesthetized by 10% chloral hydrate and sacrificed after starving for 12 h at the end of the experiments (0.3 ml/100g body weight). Liver samples were collected and frozen at -80 °C for later analysis.

first: Yiting

first: Zhiqi

last: Yin


title: Protective role of endothelial p53 in stress induced vascular malignancy.

city: New York City

first: Balvir

last: Kunar

state: New York

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

institute: Weill Cornell Medical College

summary: Accumulation of cellular stress induced mutations has a potential risk for oncogenic transformation. Once the damage is sensed by checkpoint pathway, such as p53, the aberrant cells are immediately eliminated from regular cell cycle system in order to protect life-threatening events. Here, we show endothelial cell (EC)-specific p53 deletion causes spontaneous endothelial tumors with severe hemolytic phenotypes in mice as is the case with hemangioma thrombocytopenia syndrome in human. As a result of the lack of genomic protection by p53, aggravated by oxidative and aging stress induces additional mutation in ECs especially in adipose tissue. This vascular-specific genomic unstability dysregulates the expression of critical genes such as cell cycle signaling leading to aggressive angiosarcomas.

overall_design: Expression profiling by high throughput sequencing data;  Illumina HiSeq 4000 (Mus musculus).

first: Masataka

last: Yokoyama

first: Shahin

last: Rafii


title: Single cell analysis reveals dynamics of transposable element expression following epigenetic de-repression

city: Rehovot

first: David

last: Brocks

address: Herzlstreet 234

country: Israel

institute: Weizmann Institute of Science

summary: De-repression of transposable elements (TEs) occurs concomitantly with the progressive loss of DNA methylation during carcinogenesis. The activation of promoters within high copy number TE families can thereby massively remodel the transcriptional and epigenetic state of cancer cells. This effect is accelerated following epigenetic therapy. However, whether TE de-repression is purely stochastic or co-regulated with genic transcriptional programs is poorly understood. Using single cell 5’ RNA-sequencing, we characterize over ten-fold variation in global TE expression per single cancer cell following epigenetic therapy . We uncover combinatorial TE expression patterns across thousands of transcribed TE loci from hundreds of conserved families. These signatures are associated with distinct cell cycle stages, stress responses and additional gene regulatory processes. We finally exemplify how sequence composition and epigenomic context cooperate to shape the dynamic transcriptional landscape of large TE families.. Single cell RNA-sequencing thereby implicates thousands of potent promoters within TEs as an underestimated source of regulatory heterogeneity in cancer.

overall_design: 5' single-cell RNA-seq of H1299 and HCT116 cells treated with a DNMT and HDAC inhibitor

first: Amos

last: Tanay


title: MLL RIP-seq

city: shanghai

first: rui

middle: heng

last: wang

state: shanghai

address: ruijin two street

department: insitute of hematology

institute: shanghaijiaotong university

summary: We uncovered an unexpected function of mixed-lineage leukemia (MLL) protein, which is a critical epigenetic factor and whose disruption leads to leukemogenesis, in the functional regulation of miRNAs. We reveal that the MLLC180 subunit alone can colocalize with miRNA-induced silencing complex (miRISC) components in cytoplasm processing bodies (P-bodies), where miRNA-mediated gene silencing takes place. In addition, we show that MLL was specifically required for miRNA-mediated translational repression, but not for miRNA or siRNA-mediated mRNA cleavage. Mechanistically, MLL was necessarily required for recruiting miRNA to the miRISC and P-body core, partly through its binding partner RAN. Furthermore, dysregulation of the miRNA repression function in MLL leukemic cells was essential for high-level expression of MYC, which ensured the survival of MLL leukemic cells. Thus, our investigation discovered that the MLL subunit alone can exert other functions in miRNA-mediated gene silencing apart from the epigenetic function of the whole MLL heterodimer. We also demonstrated as proof-of-principle that functional deregulation of miRNA may play an important role in cancer.

overall_design: Identify the binding RNAs and small RNAs of the MLL protein using RIP-seq method

first: Shouhai

last: Zhu

first: Han


title: A transcriptomic analysis reveals increased complexity of the alternative splicing landscape by Nsmce1 overexpression in mouse hippocampal neuronal cell

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

summary: Nsmce1 (NSE1 Homolog, SMC5-SMC6 Complex Component) is a Protein Coding gene, it was reported to function not only in positive regulation of response to DNA damage stimulus but also in the neurological diseases and disorders.

overall_design:
As a result, the expression of App, Mapt and Gsap could be inhibited by Nsmce1 overexpression and activated by the knockdown of Nsmce1. RNA sequencing (RNA-seq) was then used to evaluate and quantify the transcriptomes in response to the overexpression of Nsmce1 in mouse hippocampal neuronal HT-22 cells.
Inducible Nsmce1 in HT-22 cells were the treated samples and uninduced cells were used as controls. Experiments were performed in duplicate. Gene expression profiling analyses by high throughput sequencing were performed on mRNA samples isolated from the sense Nsmce1 in HT-22 cells (Nsmce1/+) and the wildtype cells.

first: Mengting

last: Gong


title: Telomere dysfunction activates YAP1 to drive tissue inflammation

city: Houston

first: Deepavali

last: Chakravarti

address: 1881East Rd

institute: MD Anderson Cancer Center

summary: Inflammatory bowel disease (IBD) is a challenging condition with limited therapeutic options. Inflammasome activation is integral to IBD pathogenesis, although the molecular instigators of its activation remain obscure. Here, we establish that telomere dysfunction activates the Yap1 transcriptional co-activator through pATM/c-Abl, which up-regulates expression of microbial receptors Nlrc4 and Nlrc5 and the cytokine pre-IL-18. Microbial engagement of these cytosolic receptors leads to production of mature IL-18, recruiting T cells and other immunocytes which secrete IFN-gamma to drive classical IBD pathology. Genotoxic stress per se (ionizing radiation) can also drive inflammasome activation. Alleviation of IBD pathology can be achieved via telomerase reactivation in intestinal epithelium, antibiotic treatment or pharmacological inhibition of Yap1 - reducing Nlrc4/5 expression as well as IL-18 and IFN-gamma production. Thus, telomere dysfunction-induced inflammasome activation identifies DNA damage signaling as a key instigator and promoter of IBD, illuminating potential novel therapeutic strategies for prevention and disease management.

overall_design: Total RNA profiles from large intestinal GFPsorted CBC cells and unsorted crypt epithelial cells  from mTert heterozygous mice and mTert null mice generation 3 and 4 and telomerase reactivated epithelial cells from generation 4 mice

first: Ronald


title: Transcriptional analysis of adult LRH-1 knockout livers reveals a novel role for LRH-1 in hepatic lipid homeostasis and phospholipid remodeling

city: San Francisco

first: Diego

last: Miranda

state: CA

address: 1550 4th Street

department: Cellular and Molecular Pharmacology

institute: Ucsf

summary: Purpose: To identify novel LRH-1 target genes in adult knockout livers.

overall_design: Methods & Results: Loss of LRH-1 in adult liver resulted in hepatic steatosis. To assess the role of LRH-1 in hepatic lipid metabolism, we performed transcriptional profiling on total RNA isolated from 14-week-old adult male knockout mice fed standard diet (SD) or high-fat diet (HFD) for 6 weeks. Mice infected with AAV8-eGFP served as controls. RNA-Seq analysis revealed novel LRH-1 gene targets involved in phosphatidylcholine metabolism and phospholipid diversity.

first: Holly

middle: A

last: Ingraham


title: Gene Expression data from CD133+CD15+ chordoma cells (Chordoma Cance Stem Cells) and CD133-CD15- chordoma cells

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

summary:
Chordoma is a rare, resistant bone tumor thought to be arised from remnants of embryonic notochord. Cancer stem cells (CSCs) are associated with tumorigenesis, recurrence and resistance in cancers.
Here, we used miRNA and mRNA transcriptome analysis to discover novel genes and networks in chordoma Cancer Stem Cells

overall_design: CD133+CD15+ and CD133-CD15- chordoma cells were sorted in Duplicate.

first: Emre

last: Tuysuz

first: Sukru

last: Gulluoglu


title: Expression DATA from E11.5 pancreatic buds treated with I-BET151 or JQ1 for 24h

city: Paris

first: lukas

last: huijbregts

address: 123 Boulevard Port Royal

institute: INSERM

summary: Bromodomain and Extra-terminal (BET) proteins are epigenetic readers that interact with acetylated lysines of histone tails. Recent studies have demonstrated their role in cancer progression, as they recruit key components of the transcriptional machinery to modulate gene expression. However, their role during embryonic development of the pancreas has never been studied. Using mouse embryonic pancreatic explants and human IPSC, we show that inhibition of BET proteins with either I-BET151 or JQ1 dramatically enhances the number of neurogenin3 (NEUROG3) endocrine progenitors, leading to an increased number of endocrine cells in the pancreatic explants. Despite inducing several β cell markers, BETi also strongly down-regulated Ins1 expression in developed explants and adult β cells. However, removal of BETi from explants prior to β cell development, as NEUROG3 expression peaks, further led to enhanced β cell development with higher expression of insulin and maturation markers UCN3 and MAFA. Altogether, these results show that BET proteins play a major role in the pancreas endocrine differentiation. Furthermore, they highlight the potential use of BETi to improve β cell replacement therapies.

overall_design: Mouse embryonic (E11.5) pancreatic buds were cultured for 24h in presence of 0.1% DMSO (CTRL) ro 500nM I-BET151 or 100nM JQ1

first: Lukas

last: Huijbregts

first: Christian

last: Honoré

first: Claire

last: Berthault

first: Mattias

last: Hansson

first: Virginie

last: Aiello

first: Latif

last: Rachdi

first: Raphaël

last: SCHARFMANN


title: Vascular organoids differentiation from human induced pluripotent stem cells (iPSC)

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: We have established a vascular organoid culture system with self-assembled endothelial networks that are covered by a basement membrane and pericytes. CD31+ endothelial cells, and CD140b positive pericytes were FACS sorted and RNA-seq was performed.

overall_design: CD31+ endothelial cells and CD140b+ pericytes from early formed vascular networks (d10) and vascular organoids (d14) were used for RNA -seq.

first: Josef

last: Penninger


title: Study of an allelic series using transcriptomic phenotypes

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

summary: Expression profiling holds great promise for genetics because of its ability to measure thousands of genes quantitatively. Although transcriptomes have recently been used to perform epistasis analyses for pathway reconstruction, there has not been a systematic effort to understand how expression profiles will vary among distinct mutants of the same gene. Here, we study an allelic series in C. elegans consisting of one wild type and two mutant alleles of mdt-12, a highly pleiotropic gene whose gene product is a subunit of Mediator complex, which is essential for transcriptional regulation in eukaryotes. We developed a false hit analysis to identify which populations of genes commonly differentially expressed with respect to the wild type are likely the result of statistical artifact. We concluded that expression perturbations caused by these alleles split into four distinct modules called phenotypic classes. To understand the dominance relationship between the two mutant alleles, we developed a dominance analysis for transcriptional data. Dominance analysis of these phenotypic classes support a model where mdt-12 has multiple functional units that function independently to target the Mediator complex to specific genetic loci.

overall_design: 7 genotypes; 3 samples per genotype except for the trans-heterozygote, which has 4 replicates

first: Paul

middle: W

last: Sternberg


title: Novel heart specific long non-coding RNAs contribute to pathogenesis of Arrhythmogenic Cardiomyopathy [ARVC patients' heart LV]

first: Jia

last: Li

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary:
Arrhythmogenic cardiomyopathy (AC) is an inherited cardiomyopathy characterized by fibrofatty replacement predominantly involved in right ventricle and clinically by ventricular arrhythmias.In this study, we set out to characterize the cardiac novel long-noncoding RNAs using deep RNA sequencing data from human heart tissues. Particularly, we identified AC specific novel lncRNAs that contribute to AC pathophysiology by comparing the lncRNAs transcripts of nine AC explanted hearts (RV), five non-diseased donor hearts (RV), four non-AC failing hearts (dilated cardiomyopathy, RV). To dissect the roles of novel lncRNAs in ARVC from LV, we also include six non-diseased donor hearts (LV; GSE107125) and six ARVC explanted hearts (LV) in the analysis. In the identified novel AC lncRNAs, a large part of them are derived from enhancer regions and acting as cis- elements to potentially regulate lipogenesis or lipid metabolism related genes. Finally, we validated several of these AC specific novel lncRNAs and their potential targets in independent patient samples. Collectively, we identified high-confidence AC specific novel lncRNAs from human samples and suggest their potential roles as cis- elements in AC pathology. Further study of these novel AC lncRNAs could provide new opportunities for diagnosis and therapeutic intervention.
Please note that the  GSE107157 records represent the 'five non-diseased donor hearts (RV) and six non-diseased donor hearts (LV)' data.

overall_design: RNAseq for ARVC patients' heart LV

first: Liang

last: Zhang

first: Deqiang

last: Sun

first: Jiangping

last: Song

first: Shengshou

last: Hu


title: Accessing Pluripotency from the Somatic Side

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: We report that Jdp2, Jhdm1b, Mkk6, Glis1, Nanog, Essrb and Sall4 (7F) convert MEFs to chimera competent iPSCs with fast kinetics. Time lapse microscopy reveal morphological changes distinct for 7F and Yamanaka factor (YF) reprogramming. Bulk transcriptomic analyses suggest that 7F and YF share 927 up and 548 down regulated genes, but differ in 1138 YF and 427 7F specifically activated genes. Single cell RNA sequencing reveals a fate path that can be further resolved into a cell fate continuum based on a MEF/ESC scoring system. A crossing point marks the transition in the continuum from somatic to pluripotent fates. By sampling the leading cells along this continuum, we identified transition stages marked by novel nu-clear factors and cell surface molecules.  Our results reveal an efficient path to pluripotency and suggest that cell fate is governed by intrinsic fac-tors accessible by diverse approaches

overall_design: To explore the dynamics process of the 7F reprogramming system, we isolated  singel cells at D0, D1, D3, D4, D5, D7 using Fluidigm C1 system, totally we got 461 high quality single cells data sets.

first: Duanqing

last: Pei


title: RNA-Seq analysis of T-ALL mouse samples and the effect of Miz1 POZ domain deletions on T-ALL expression profiles

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

summary: T cell acute lymphoblastic leukemia (T-ALL) is an aggressive disease mainly affecting children. Relapse rates are high and toxic chemotherapies that block DNA replication and induce DNA damage cause health problems later in life, underlining the need for improved therapies. We show that ablation of the BTB/POZ domain factor Miz-1 significantly delays Notch1-induced T-ALL in mice through induction of p53-dependent cell death. Leukemic cells that still emerge in this system activate DNA replication and strand elongation pathways, which are those targeted by current chemotherapeutic drugs such as cytarabine. Acute Miz-1 ablation enhances the effect of cytarabine treatment and eliminates leukemic cells completely in some cases, suggesting that targeting Miz-1 could render current T-ALL chemotherapies more effective.

overall_design: Mice expressing mutant Miz1 protein lacking the POZ domain as well as wild-type controls developped Notch induced T-ALL. The same experiments were carried out in a p53 null background. For each genotype, RNA-Seq was carried out in 2 mice.

first: Marissa

last: Rashkovan

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: Notch2 Expressed by Myofibers Influences Muscle Mass and Fiber Types

city: Nagasaki

first: Yusuke

last: Ono

address: 1-12-4 Sakamoto

country: Japan

institute: Nagasaki University

summary: Notch receptors play crucial roles in the cell-fate decisions of tissue stem cells during development and regeneration. Notch1-3 receptors are expressed by satellite cells and their progeny. Here we found that Notch2, but not Notch1 or Notch3, was expressed in fully differentiated myofibers. Using transgenic mice that expressed a muscle-specific active form of Notch2 (N2ICD-mTG), we found that Notch2 activation remarkably reduced muscle mass and strength with a shift toward slow fibers. Transcriptome analyses revealed that growth differentiation factor 11 (GDF11) was highly up-regulated in muscles of N2ICD-mTG mice, and crucially, N2ICD-induced muscle atrophy was rescued by siRNA-mediated reduction of GDF11 expression. These data suggest that Notch2 functions in muscle to regulate muscle mass, in part, through induction of GDF11 expression, and reveal a novel aspect of Notch signaling in a terminally differentiated adult tissue.

overall_design: Activated Notch2 (N2ICD)-induced gene expression in mouse muscle tissues was measured. A single experiment was performed.


title: Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (lung cancer)

city: La Jolla

first: Kang

address: 9500 Gilman Dr

institute: UCSD

type: Methylation profiling by high throughput sequencing

summary: To identify diagnostic and prognostic biomarkers, we compared methylation profiles of LUNC tissues and normal blood at 485,000 CpG markers and identified a marker panel differently methylated in LUNC. We developed diagnostic and prognostic prediction models with the selected panel and compared their efficacy in ctDNA to current available approaches. Our data indicate that cfDNA methylation patterns provide reliable biomarkers in the diagnosis, surveillance, and prognosis of LUNC.

overall_design: Base-pair resolution DNA methylation across 888 genomic ~100bp regions was analyzed in circulating tumor DNA (ctDNA) extracted from serum of 654 lung cancer patients

first: Michal

last: Krawczyk

first: Wenqiu

last: Wang

first: Ken

last: Flagg


title: CircRNA-Seq Analysis for Sciatic Nerve Injury of Rat

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

summary: Here, we established a rat sciatic nerve injury model and investigated the circRNA expression profiles by Next-generation sequencing. In all, 7222 distinct circRNA candidates were found in these tissues and 4942 of these circRNAs contained at least two unique back-spliced reads. On the basis of expression of circRNA analysis, we found 131 circRNAs to be significantly (p-value<=0.05, Fold-change>=2) differently expressed in injured sciatic nerve tissues compared with matched normal tissues. All these circRNAs are derived from 21 rat chromosomes.

overall_design: Establishment of the rat sciatic nerve injury:A 3-mm long sciatic nerve was crushed two times (15 seconds/each time, 3 seconds interval) with a hemostatic forceps. Then, muscle and skin layer were sutured with silk thread, followed by the application of topical antibiotic powder. Sham operation (exposure of the nerve) was performed in the other groups. Under aseptic conditions, all surgical operations were performed by the same surgeon. The rats were sacrificed and a 3 mm long crushed sciatic nerve, together with both nerve ends (1 mm long), was harvested 24 hours after surgery for RNA-seq analysis.

first: Z

last: Zhou

first: L

last: Zhu

first: A

last: Chen


title: Next Generation Sequencing Facilitates Comparative Transcriptomes Analysis for different Yarrowia lipolytica strains synthesizing different levels of lycopene as end products.

city: Tianjin

first: Duo

last: Liu

state: Tianjin

address: No. 92, Weijin Road, Nankai District

institute: Tianjin University

summary:
Purpose: According to comparative transcriptomes data, the differentially expressed genes within these selected Y. lipolytica strains can be digged out and further analyzed, seeking potential targets that were tuned drastically and might improve lycopene production when modified.
Methods: mRNA profiles of three Y. lipolytica strains yl_12, yl_11, yl_10 (each named as A4AX1-1, A4AX1-24, A4AX1-25 in related manuscript) were generated in triplicate using illumina. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample. The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data. The read counts for each gene in the genome were summarized as processed data.
Results: In all strain samples, the transcriptome data for all 4890 genes throughout genome were detected. The results showed that the expression levels of most genes basically kept unchanged. However, the levels of certain genes were tuned to a higher or a lower value.
Conclusions: There were 329 differentially expressed genes between strain yl_12 and yl_11 and this number was 490 for yl_12 vs. yl_10. The GO and KEGG enrichment of these differentially expressed genes would be further operated for exploring drastically regulated functions and pathways.

overall_design: The transcirptomes of different Yarrowia lipolytica strains were sequenced by Illumina, giving both unchanged genes and differentially expressed genes that would affect lycopene production.

first: Yingjin

last: Yuan


title: Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (COAD)

last: Zhang

summary: To identify diagnostic and prognostic biomarkers, we compared methylation profiles of COAD tissues and normal blood at 485,000 CpG markers and identified a marker panel differently methylated in COAD. We developed diagnostic and prognostic prediction models with the selected panel and compared their efficacy in ctDNA to current available approaches. Our data indicate that cfDNA methylation patterns provide reliable biomarkers in the diagnosis, surveillance, and prognosis of COAD.

overall_design: Base-pair resolution DNA methylation across 888 genomic ~100bp regions was analyzed in circulating tumor DNA (ctDNA) extracted from serum of 773 colon cancer patients


title: Expression data of renal cancer cell treated with Oncolytic virus and Vanadium compound

city: Ottawa

first: Mohammed

last: Selman

state: ON

address: 501 Smyth Road

department: Cancer Center

institute: Ottawa Hospital

summary:
We propose a strategy to boost the therapeutic efficacy of Oncolytic therapy by combining it with immuno-modulating agents targeting protein tyrosine phosphatases.
The mechanism of action was examined by microarray analysis using the Affymetrix Human PrimeView Array.

overall_design: 786-0 cells were plated in 6-well dishes and allowed to adhere overnight. The next day, cells were pretreated for 4hours with orthovanadate (150uM), metavanadadate  (150uM) or the vehicle. Following pre-treatment, the cells were infected with VSVΔ51 at an MOI of 0.01 or left uninfected. Twenty-four hours post infection, RNA was collected using an RNA-easy kit . Biological triplicates were subsequently pooled and RNA quality was measured using Agilent 2100 Bioanalyzer (Agilent Technologies) before hybridization. Hybridized to Affymetrix Human PrimeView Array . Microarray data was processed using Transcriptome Analysis Console (TAC) 3.0 under default parameters of Gene Level Differential Expression Analysis. Fold change in gene expression was calculated for each gene in relation to uninfected, untreated control.

first: Jean-Simon

last: Diallo


title: Small RNA profile from Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) infected Phalaenopsis amabilis

city: Taipei

first: Na-Sheng

last: Lin

address: No.128, Sec. 2, Academia Rd, NaKang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

summary: Viral siRNA generated from antiviral RNA silencing machinery was profiled using small RNA sequencing from Phalaenopsis orchid mixed infected with CymMV and ORSV

overall_design: Small RNA libraries from P. amabilis leaf tissues of different stages of CymMV and ORSV mixed infection were generated by using Illumina Miseq

first: Wen

last: Chang


title: Expression analysis of Listeria monocytogenes during adaptation in soil

city: Dijon

first: Pascal

last: Piveteau

address: 17 rue Sully

institute: Université de Bourgogne INRA

summary: Investigation of whole genome gene expression level changes in Listeria monocytogenes EGD-e during incubation (0, 15 min, 30 min)  in two types of soil extracts (TA, DA).

overall_design: A fifteen chip study using total RNA recovered from  a time course analysis (time 0, 15 min, 30 min) of incubation in two types af soil extracts (TA and DA). Three independent  cultures of Listeria monocytogenes EGD-e were done.  Each chip measures the expression level of 2857 genes from Listeria monocytogenes EGD-e.

first: Géraldine

last: Depret


title: Transcriptome sequencing analysis of sorghum callus with various regeneration capacities

status: Public on Dec 31 2019

city: yichang

first: chao

address: No.8,daxuelu Street

institute: CTGU

summary: The applications of plant callus regeneration has been widely spreaded in agricultural improvement. By using immature sorghum embryos as explants, progress in successful genetic transformation has been made in sorghum. However, the underlying mechanism of callus differentiation is still largely unknown in sorghum. Here, we described three types of callus with different abilities of redifferentiation (Callus I-III), undergoing distinct induction from immature embryo in the variety of Hiro-1. In comparison to the non-embryonic Callus III who lost the ability of regeneration, the Callus I produced only some characterized adventitious roots and the embryonic Callus II is sufficient to regenerate whole plants. Genome-wide transcriptome profiles were performed to reveal the underlying mechenisms. The numbers of differentially expressed genes for the three types of callus vary from 5906 to 8029. Principal component analysis analysis demonstrated that gene expression patterns of Callus I and II were totally different from that of Callus III and differential leaves from Callus II, indicating that the compassions of Callus I and II provide clues for revealing regulations of regeneration in sorghum callus. Notably, KEGG and GO analysis showed that plant ribosome, lignin metabolic process, and metabolism of starch and sucrose are main processes that are associated with callus differentiation. Taken together, the results contributed the elucidation of molecular regulation in three types of callus with several regeneration abilities in sorghum.

overall_design: mRNA profiles of three types of sorghum callus (namely Callus I, II and III) were generated by deep sequencing,using Illumina HiSeq.

first: Chao

first: Dechun


title: MST-312: a telomerase inhibitor effectively blocking MYC oncogenic functions

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

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

overall_design: Refer to individual Series


title: The role of Clk3 in the development of heart hypertrophy

city: Zürich

first: Christophe

last: Chabbert

state: Zurich

address: Otto-Stern-Weg 7, HPL H 17.2

department: Institute of Molecular Health Sciences

institute: ETH

summary: We used RNA-seq technology to characterise the extent of transcriptional response to transverse aortic compression (TAC) in mouse models, both in wild type and in Clk3-knocked down animals. We thereby provide an extensive characterization of the changes occurring at the genome-wide levels, including isoforms switches and splicing patterns.

overall_design: Examination of gene expression levels in the heart of wild type and Clk3 KO mice, after TAC.

first: Peter

last: Mirtschink


title: DNA methylation and hydroxymethylation mediated gene expression regulation network involved in 3-methylcholanthrene induced lung cell malignant transformation

city: chongqing

first: hongqiang

last: chen

address: Gaotanyan, Shapingba District, Chongqing

institute: Third Military Medical University

summary:
3-methylcholanthrene (3-MCA) is a typical representative PAH. It has strong toxicity and is a typical chemical carcinogen. However, the epigenetic mechanisms underlying 3-MCA-induced tumourigenesis are largely unknown.
In this study, a model of the 3-MCA-induced malignant transformation of human bronchial epithelial (HBE) cells was established successfully. The profiles of gene expression and DNA methylation and hydroxymethylation were obtained and analyzed with an Illumina HiSeq 4000. A large number of differentially expressed genes were screened out, and a number of genes that may be regulated by methylation were screened through Gene ontology (GO) analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis.

overall_design: 45 generations of HBE cells treated continuously with 1% DMSO and 10 μM 3-MCA

first: Hong-qiang

first: Wen-bin


title: DNMT3A Reads and Connects Histone H3K36me2 to DNA methylation [ChIP-seq]

city: shanghai

first: Yujiang

middle: Geno

last: Shi

address: 131 Dong An Road

department: Institute of Biomedical Science

institute: Fudan university

summary: DNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biological processes including gene silencing, gene imprinting, and X chromosome inactivation. It has long been questioned how de novo DNA 5mC patterns are established in different genomic regions and whether histone modifications crosstalk to the process. Here, we report a previously uncovered mechanism of histone mark H3K36me2 in recruiting and activating DNMT3A, primarily in the intergenic regions. Our biochemistry studies discovered that H3K36me2 could be specifically bound by DNMT3A PWWP domain and substantially stimulate DNMT3A activity, representing the first example of histone modification in activating DNMT3A activity. Using multiple myeloma model, KMS11, we further found that the genome-wide gain-of-H3K36me2 resulted in global increase of 5mC, primarily in the intergenic regions. Importantly, DNA inhibitor treatment specifically blocked KMS11 growth demonstrating the functional importance of this regulatory pathway.

overall_design: Examination of H3K36me2 in 2 cell types.

first: Feizhen

last: Wu


title: DNMT3A Reads and Connects Histone H3K36me2 to DNA methylation


title: DNMT3A Reads and Connects Histone H3K36me2 to DNA methylation [MeDIP-Seq]

overall_design: Examination of 5mC in 2 cell types.


title: Gliopathic Bang Sensitive Siezure Common Expression

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: In order to identify common gene expression across other gliopathic bang senstiive genes (i.e. genes that when knocked down or over expressed by repo-GAL4 cause seizures) we crossed six UAS-RNAi or UAS-over-expression lines for  known bang senstive genes to repo-GAL4.  We pooled total RNA from brains of these animals in equal amounts and ran microarray analysis to search for transcripts that are common among these six seizure associated genes.

overall_design: Controls are empty TRiP RNAi vector crossed to repo-GAL4.  Experimental pool is SesB-RNAi; COX7A-RNAi; UAS-Dube3a; UAS-htt.12Q.FL; comt-RNAi; nrv2-RNAi and ATPalpha-RNAi crossed to repo-GAL4.

first: Lawrence

middle: T

last: Reiter

first: Kevin

last: Hope


title: Development of lncRNA expression of long-term cigarette smoking extract esophageal cell

city: Shantou

first: Caixia

last: Liu

address: Xinling Road, No.22, Shantou

department: Department of Preventive Medicine

institute: Shantou University Medical College

summary: To invstigate lncRNA expression in long-term cigarette smoking in immortal esophageal cell SHEE, we have employed the  microarray lncRNA expression profile as a platform to identify cigaretted-related oncogenes and  cancer surpressors.

overall_design: SHEE cells were exposed to cigarette smoking extract (15µg/ml) or DMSO for 48 hours. The exposure lasted 30 passages.Two independent experiments were performed.

first: Shukai

last: Zheng

first: Meijie

last: Ye


title: LIN28B is a barrier to the maturation of human embryonic stem cell derived pancreatic β cells

city: San Francisco

first: Cassandra

last: Belair

address: 35 Medical Center Way

department: Urology

institute: UCSF

summary: Comparative RNA and small RNA sequencing analysis of in vitro differentiated β like cells, in vivo matured β cells, adult islet cells, and  Lin28 deficient in vitro differentiated β like cells

overall_design: We performed RNA-seq and small-RNA seq on human ESCs differentiated into β like cells in vitro, same  cells transplanted into kidney capsule of mouse recipients, and fresh human islets.  We also performed RNA-seq on hESCs genomically modified with dox inducible CRISPR knockout of LIN28 and then differentiated into β like cells plus/mius doxycycline

first: Xin

last: Zhou


title: Dermal sheath contraction powers stem cell niche relocation during hair cycle regression

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: Tissue homeostasis requires the balance of growth by cell production and regression through cellular loss. In the hair cycle during follicle regression, the niche traverses the skin through an unknown mechanism to reach the stem cells and prime regeneration. Here, by cell specific ablation and intravital imaging in live mice, we identify the follicle-lining dermal sheath as the key driver of tissue regression and niche relocation via smooth muscle contractile machinery that generates centripetal constriction force. We reveal the calcium/calmodulin/myosin light chain kinase pathway as the mechanism of sheath contraction that when blocked inhibits follicle contraction and impedes regression and niche relocation. Thus, our study identifies the dermal sheath as a smooth muscle that drives regression for reuniting niche and stem cells to regenerate tissue structure during homeostasis.

overall_design: Dorsal skins were dissected from P5 mice dissociated into single cells, and FACS sorted for dermal sheath, dermal papilla, and dermal fibroblasts.

first: Nicholas

last: Heitman

first: Rachel

last: Sennett

first: Ka-Wai

last: Mok

first: Nivedita

last: Saxena

first: Devika

last: Srivastava

first: Laura

last: Grisanti

first: Zichen

last: Wang

first: Avi

last: Ma'ayan

first: Panteleimon

last: Rompolas


title: Expression data of LN229 cells treated with 23 Pa compressive solid stress (CSS) or no CSS

city: COLUMBUS

first: Yixiao

last: Cui

state: OH

address: 1502 King Ave Unit D

institute: The Ohio State University

summary:
Glioblastoma ( GBM) is an astrocytic brain tumor with median survival times of < 15 months, primarily as a result of high infiltrative potential and development of resistance to therapy (i.e., surgical resection, chemoradiotherapy). A prominent feature of the GBM microenvironment is compressive solid stress (CSS) caused by uninhibited tumor growth within the confined skull.
We used microarrays to explore the gene expression of LN229 cells treated with 23 Pa CSS as compared to no CSS. The purpose is to detect the up-regulated genes induced by CSS.

overall_design: LN229 cells were treated either under 23 Pa CSS or no CSS for 18 hrs and then extracted for RNA. RNA samples were then purified and processed on Affymetrix Human Transcriptome Array 2.0 chip.

first: Jessica

last: Winter


title: Progenitor cell combination normalizes retinal vascular development by enhancing pericyte ensheathment in the oxygen-induced retinopathy (OIR) model

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

summary: Retinopathy of prematurity (ROP) is a disorder of the developing retina of preterm infants. ROP can lead to blindness due to abnormal angiogenesis that is the result of suspended vascular development and vaso-obliteration leading to severe retinal stress and hypoxia. We tested the hypothesis that a combined treatment with two human progenitor populations, the CD34+ cells, bone marrow-derived, and the endothelial colony-forming cells (ECFCs) synergistically protected the developing retinal vasculature in a murine model of ROP, the oxygen-induced retinopathy (OIR)., CD34+ cells alone, ECFCs alone, or a combination thereof were injected intravitreally at either P5 or P12 and pups were euthanized at P17. Retinas from OIR mice injected with ECFCs or the combined treatment revealed formation of the deep vascular plexus (DVP) while still in hyperoxia, with normal appearing connections between the superficial vascular plexus (SVP) and the DVP. The combination therapy prevented aberrant retinal neovascularization and was more effective anatomically and functionally at rescuing the ischemia phenotype than either cell type alone. The beneficial effect of the cell combination was the result of their ability to orchestrate an acceleration of vascular development and more rapid ensheathment of pericytes on the developing vessels.

overall_design: We used a neonatal mouse model of OIR to test the effect of cell treatment (ECFC, CD34+, or the combination thereof) on retinopathy of prematurity. The injections were done at two different developmental stages (P5 or P12), and retinas were collected for various analyses at P12 or P17, respectively.  For microarray analysis, three retinas per experimental conditin were used.

first: Sergio

last: Li Calzi

first: Lynn

last: Shaw

first: William

last: Shelley

first: Xiaoping

last: Qi

first: Judith

last: Quigley

first: Seth

last: Fortmann

middle: E

last: Boulton

first: Mervin

last: Yoder

first: Maria

middle: B

last: Grant


title: Transcriptional profiling of colonic Regulatory T (Treg) cells, CD4+ conventional T (Tconv) cells, dendritic cells (DCs), and epithelial cells (ECs) from Vdr WT- or Vdr KO-Foxp3 reporter mice

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We reported transcriptional characterization of Treg cells, Tconv cells, and DCs isolated from coloinc lamina propria of Vdr WT- or Vdr KO-Foxp3 reporter mice. We also reported transcriptional characterization of colonic ECs isolated from Vdr WT- or Vdr KO-Foxp3 reporter mice.

overall_design: Gene expression profiles of colonic Treg cells, Tconv cells, DCs, and ECs from Vdr WT- or Vdr KO-Foxp3 reporter mice.

first: Xinyang

last: Song

first: Yanbo

last: Zhang

first: Dennis

last: Kasper

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: RNA-Seq of human adipose tissue (siNT vs siRND3 KD)

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

summary: Total RNA-Seq of Human adipose tissue were sequenced on the Illumina HiSeq4000 platform

overall_design: Individual samples were treated with either a control/vehicle RNA treament (siNT) or a targetted siRND3 KD treatment

first: Simon

last: Dankel