title: Role of Selenium Intake for Risk and Development of Graves’ Disease

status: Public on May 30 2021

city: Xi'an

first: YuFeng

last: Liu

state: ShanXi

address: The First Affiliated Hospital of Xi'an Jiao Tong University

country: China

institute: mouse

summary: The trace element selenium (Se) plays an important role in thyroid hormone metabolism. Low Se intake is associated with atuoimmune hypothyroidism. The interaction of Se and Graves’ disease (GD) is only poorly characterized. We have investigated the importance of dietary Se supply for GD by performing a more in-depth analysis of a large cross-sectional study of 6152 participants from two counties within the Shaanxi Province, China, which are characterized by different habitual Se intakes, and studied the effects of different dietary Se supply (0.02, 0.18, 0.6 or 2.0 ppm Se) on disease development in a mouse model of GD. In the cross-sectional study, prevalence of GD in the two areas of different Se intake was similar, and the Se status of GD patients was not different from healthy control subjects. The dietary Se supply in the animal model was not affecting thyroid hormone levels, malondialdehyde concentrations, total antioxidant capacity or the titer of GD-causing TSH receptor autoantibodies (TRAb). Expression analysis of transcripts in spleen indicated regulatory effects of Se intake on genes implicated in the immune response, erythropoiesis and oxygen status. However, the humoral immune response including the ratio of CD4/CD8 or Th1/Th2 cells, and the concentration of Treg cells were similar between the experimental groups despite their varying Se intakes. Our data from both the epidemiological analysis and animal experiment do not indicate a major role of Se in the development of GD, and highlight that autoimmune hypothyroidism and GD differ in their relation to Se status.

overall_design: Nine samples were analyzed in three groups, and there were three replicated samples in each group

first: Wang

last: Yue

first: Zhao

last: Fengyi

first: Eddy

last: Rijntjes

first: Wu

last: Liping

last: Qian

first: Liu

last: Yufeng

first: Chen

last: Pu

first: Hu

last: Shiqian

first: Zhang

last: Meng

first: Hou

last: Peng

first: Lutz

last: Schomburg

first: Shi

last: Bingyin


title: LncRNA data in mice hearts after swimming exercise training or sedentary

status: Public on May 31 2021

city: Shanghai

first: Lijun

last: Wang

address: 333 Nan Chen Road

institute: Shanghai University

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

summary: This study was to identify lncRNAs responsible for exercise-induced cardiac physiological growth

overall_design: Total RNAs were extracted from mice hearts from  swimming exercise training or sedentary group (n=5 per group), and then subjected to Agilent mouse LncRNA array analysis (4*180K，Design ID：049801).

first: Junjie

last: Xiao

first: Xinli

last: Li


title: Time course of transcriptional reprogramming in bovine nuclear transfer embryos

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

type: Expression profiling by high throughput sequencing

summary: Somatic cell nuclear transfer (SCNT) into an enucleated oocyte can reprogram a differentiated nucleus to a totipotent state. However, the time course of transcriptional reprogramming has not been determined. To monitor the inactivation of somatic genes after SCNT in the bovine model system, we determined transcript levels of 159 genes highly expressed in fetal fibroblast nuclear donor cells, but not in metaphase II recipient oocytes. For 18 of these genes significantly higher transcript levels were found in four-cell SCNT embryos compared with four-cell embryos derived by in vitro fertilization (IVF), indicating incomplete silencing of somatic genes at this stage. RNA sequencing revealed that nearly 600 genes with no transcripts in oocytes were activated in eight-cell IVF embryos, in agreement with major embryonic genome activation (EGA). De novo transcription in SCNT embryos was delayed (16 genes before the 16-cell stage, 300 and >800 genes at the 16-cell and blastocyst stages). Intron-containing primary transcripts as another option to detect embryonic gene transcription revealed activation of >2,200 genes in IVF embryos at the eight-cell stage, while only 828 genes were activated in SCNT embryos. At the 16-cell stage, a higher number of activated genes was found in SCNT (1,917) than in IVF embryos (738). Self-organizing tree algorithm clustering confirmed that in SCNT embryos transcription of genes that are normally activated during major EGA is delayed. Our study provides detailed insight into the timing of genome activation in cloned embryos that is substantially different from IVF embryos in spite of similar developmental kinetics.

overall_design: The following cell stages were collected for NT embryos: embryos at the four-cell, eight-cell, 16-cell, and blastocyst stage. Three biological replicates of each stage were sequenced on an Illumina GAIIx. Differentially abundant mRNA-species, de novo transcription and global gene expression trends were compared to investigate the time course of embryonic reprogramming in NT embryos.

first: Mari

last: Heininen-Brown

first: Kilian

last: Simmet

first: Julia

last: Philippou-Massier

first: Stefan

last: Krebs

first: Valeri

last: Zakhartchenko

first: Eckhard

last: Wolf

first: Helmut

last: Blum


title: RNA-Seq analysis of in vitro cultivated bovine fetal fibroblasts (BFF116)

overall_design: Sequencing libraries were constructed from three biological replicates of 7 × 104 bovine fetal fibroblast cells (BFF116) that served as nuclear donor cells.


title: Effect of Cell Division on Cell Differentiation (ChIP-Seq HUvsNoc)

city: Cambridge

first: Rodrigo

middle: Andres

last: Grandy

address: Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way

department: Surgery

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We addressed the role of cell division during differentiation by blocking the progression of the cell cycle during mesendoderm differentiation. Human pluripotent stem cells (H9 cells) were synchronized in their cell cycle and then induced to differentiate into mesendoderm for 24h. To block the cells in their S phase, we added Hydroxyurea (200 uM) at the beginning of the differentiation process. To block the cells in their G2/M phases, we added nocodazole (100 ng/ml) 8h after the induction of differentiation. At the end of the experiment, the cells were harvested and processed for RNA extraction.

overall_design: Four different conditions were analyzed: Undifferentiated (UD), Mesendoderm (E24), Mesendoderm + Hydroxyurea (E24HU), and Mesendoderm + nocodazole (E24Noc). Two biological replicates were generated for each condition.


title: Transcriptomics analysis of P.lundensis in in vivo and in vitro growth conditions

status: Public on May 28 2021

city: Ann Arbor

first: Keerthikka

last: Ravi

state: Michigan

address: 1105 N University st

department: Molecular, Cellular and Developmental Biology

country: USA

institute: University of Michigan

summary: Pseudomonas lundensis is an environmental psychrotrophic bacterium and a leading causative of frozen food spoilage.  Here we present the transcriptomics study of P. lundensis strain AU1044, in aerobic in vitro growth conditions both 4°C and 37°C, and in vivo germ-free mice. The difference in the expression profile of several regulatory and metabolic genes over these three conditions highlights the ubiquitous nature of this bacterium.

overall_design: 3 sample conditions were analysed. The experiemnt for in vrito culture samples is as follows. P. lundensis AU1044 was cultured in LB broth under aerobic conditons at 4°C and 37°C. The in vitro experminet was done in quadrepilicates. The experiment for the invivo samples were set up as follows. Gnotobiotic balb/c mice (n=6) were oraly inncoculated with AU1044. After 14 days of innoculation, the cecal content was harvested and used as the source for bacterial RNA isolation.

first: Nicole

middle: R

last: Falkowski

first: Garry

middle: B

last: Huffnagle


title: Efficiency of Influenza virus infection in mouse is reliant on NS1-dependent antagonism of a hosts immune system

city: Hong Kong

first: Honglin

last: Chen

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

summary: The chracterization of interactions between a virus and its live host provide clues as to how these pathogens spread within a population. The identification of changes in the expression of select gene networks at a cellular level will enable the the determination of how a host response to infection. Such changes may indicate stratagies of viral-induced antagonism on host immune processes in select cell types.

overall_design: Data was derived from Influenza infected mouse experiments. Mice were infected for 24 hours with wildtype WSN (H1N1) or a mutant with deficient NS1 functionality and were subsequently euthanized. Lung tissue was harvested and homogenized. Experiments were done in duplicate. Cells were isolated and used in scRNA-seq library preparation (10x Genomics).

first: Bobo

middle: Y

last: Mok

first: Conor

last: Cremin

first: Rachel

last: Tan


title: Transcription factor AmyR and Molecular brake Hat1 modulate amylase gene expression in Penicillium oxalicum

city: Qingdao

first: yueyan

last: hu

address: Binhai road 72

institute: Shandong university

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), Hat1 deletion strain (ΔHat1) and AmyR deletion strain (ΔAmyR) in 2% starch as carbon sources. The correlation analysis results between the various samples showed that the gene expression levels of the wild strain and the ΔHat1 strain  were significantly different, and the gene expression levels between ΔAmyR and the wild strain were also significantly different. The deletion of Hat1 significantly up-regulates the expression levels of amylase genes of Penicillium oxalicum,  and the absence of AmyR can significantly down-regulate the expression level of amylase genes genes, indicating that Hat1 and AmyR can cause a difference in amylase synthesis by affecting the expression of amylase genes. The information provided by this study indicates that Hat1 and AmyR functions are necessary for the amylase activity of Penicillium oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Hat1 deletion mutant strains and AmyR deletion strain in 18h in modifeid Mendal’s medium with 2% starch as carbon sources. Three replicates were included for each samples.

first: Yueyan

last: Hu

first: Yuqi

last: Qin


title: The contribution of lipid droplets formation-related genes during adipogenesis to osteoblastogenesis

city: Jiujiang

first: Xiaoyuan

last: Xu

address: 17 Lufeng Road

institute: Jiujiang University

summary: We tried to find out the contribution of lipid droplets formation-related genes during adipogenesis to osteoblastogenesis through RNA-Seq technique. Among the seventy-nine documented genes, APOB (apolipoprotein B), CES1 (carboxylesterase 1), and CIDEC (cell death inducing DFFA like effector c) were differentially expressed during osteoblastogenesis. We further confirmed gene function of APOB during osteoblastogenesis using lentivirus vector system. This study would provide the vital clues and molecular targets for balance regulation of hMSCs differentiation and new treatment strategy in metabolic bone diseases.

overall_design: Examination of 4 different sampling time during adipogenesis and osteoblastogenesis from human mesenchymal stem cells.

first: Weidong

last: Li

first: Ping

last: Wu

first: Jianyun

last: Liu

first: Ying

last: Gong


title: Profiling expression of coding genes, long noncoding RNAs, and circular RNAs in the rice photo-thermosensitive genic male sterile line Wuxiang S

city: Wuhan

last: Wang

state: Hubei

address: No. 299 bayi road

department: College of Life Sciences

institute: Wuhan University

summary: In order to systematically identify the possible regulatory roles of (long nocoding RNAs) lncRNAs and (circular RNAs) cirRNAs in the rice photo-thermosensitive genic male sterile (PTGMS) line that were involved in fertility transition, 18 RNA libraries from rice young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F))  at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3), and the microspore formation stage (P4) were constructed, with three biological replicates for each condition. These libraries were sequenced using an Illumina Hiseq 2500 platform, and approximately 214.54 Gb clean reads were generated. we performed genome-wide identification and characterization of lncRNAs circRNAs using high-throughput strand-specific RNA sequencing (ssRNA-seq) technology and bioinformatics tools to investigate the expression profiles of circRNAs in the PTGMS rice line WXS and their potential roles in the fertility transition.A total of 3948 lncRNAs and 9994 circRNAs were indentifiled  in WXS rice, and our findings clearly revealed that lnRNAs and circRNAs might be endogenous noncoding regulators of flower and pollen development in the PTGMS rice line.

overall_design: Rice coding genes, long noncoding RNAs, and circular RNAs profile of young panicles of WXS (S) and WXS (F) at the P2, P3 and P4 stages by deep sequencing, in triplicate, using Illumina HiSeq Xten.

first: Yi

last: Ding


title: Ectopic expression of Sox9 led to differential gene expression in HepG2 cells

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

summary: We generated the HepG2 subline stably expressing Sox9 (HepG2-Sox9) and performed transcriptome RNA sequence.

overall_design: Total RNA was extracted from HepG2 subline cells with TRIzol reagent. The RNA purity and integrity were analyzed with the Agilent Bioanalyzer 2100 (Agilent). The mRNA was purified from total RNA after removal of rRNA and sequenced on an Illumina Hiseq2000 system.

first: Zengrong

last: Ren

first: Yu

first: Junfeng

last: Zhang


title: Single-cell transcriptomics of microglia isolated from the hypothalamic/thalamic region of E15.5 brains

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Microglia are the resident immune cells of the central nervous system (CNS) and are derived from yolk sac progenitors. In the embryo, microglia invade the CNS starting at embryonic day 9.5 (E9.5) and continue to colonize alongside neural development. Microglia also mature across development, altering their morphology and expression signatures from embryonic to adult stages, suggesting differing roles for microglia in the developing brain than in the adult. While microglia were originally thought to be resting immune cells responsible for cleaning up cellular debris, studies are now showing that microglia are highly dynamic cells involved in proper postnatal development of the brain and adult neuronal plasticity. Although recent reports have demonstrated that microglia in the embryonic brain are responsive to maternal stress, causing changes in neural development that lead to autistic- and schizophrenic-like behaviours later in life, the actual effects of microglia on embryonic developmental programs are just emerging. Our lab studies the hypothalamus, a brain region that controls a variety of physiologies including energy balance, reproduction, and even parenting behaviors, and it is also responsive to maternal stress. Interestingly, my previous work has shown that that the hypothalamus uniquely is comprised of at least two distinct populations of microglia. The first group of microglia are ramified, and appear to be passively surveying the hypothalamic mantle as we would expect. The second cluster of microglia is amoeboid and activated, and are located adjacent to the ventricular zone (VZ) where hypothalamic neural progenitor cells (NPCs) reside. Given that this second group of microglia is in direct contact with NPCs, we hypothesize that microglia located in the VZ of the hypothalamus play an important role during embryonic development to organize the neurons and neuronal connections required for proper hypothalamic function. In order to identify the expression profiles of microglia in the VZ as compared to microglia present in the mantle of the hypothalamus, we used Cx3cr1-Cre; Rosa26tdTomato mice to mark microglia. We then micro-dissected the hypothalamic/thalamic region of the E15.5 brains and used flow cytometry to extract tdTomato+ microglia. We then performed single-cell RNAseq on the microglia to determine the transcriptomic phenotype of these two populations.

overall_design: To isolate microglia from the hypothalamic/thalamic region of the E15.5, we generated Cx3cr1Cre:tdTomato+ve dams that were treated with tamoxifen while pregnant (E10.5-E11.5). We FACS collected viable Cx3cr1Cre:tdTomato+ve cells at E15.5 from the hypothalamic/thalamic region of the brain. The sample was processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 375 cells, with an estimated doublet rate of ~0.4%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

first: Jessica

last: Rosin

first: Deborah

last: Kurrasch


title: Transcriptome analysis of embryonic cholangiocytes

city: Brussels

first: Lila

last: Gannoun

address: Avenue Hippocrate 75

department: Institut de Duve

country: Belgium

institute: Université Catholique de Louvain

summary: Purpose: The aim of this study is to propose a computational model which can help in unravelling the mechanisms of initial bile duct lumen formation. Guided by the quantification of morphological features and expression of genes in developing bile ducts (cholangiocytes) from embryonic mouse liver, hypotheses for the mechanisms of biliary lumen formation were generated and tested with the model. Here, the RNA-sequencing data were collected from purified embryonic cholangiocytes at two developmental stages (E16 and E18).

overall_design: Three samples of E16 cholangiocytes and three samples of E18 cholangiocytes were analyzed in this study.

first: Frédéric

middle: P

last: Lemaigre

first: Axelle

last: Loriot


title: Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: A high repeat to gene expression ratio identifies AML patient subgroups with a favorable prognosis, whereas a low repeat to gene expression is prevalent in AML patient subgroups with a poor prognosis.

overall_design: Blood samples of pre-therapeutic and newly diagnosed AML patients.

first: Megumi

last: Onishi-Seebacher

first: Thomas

last: Jenuwein


title: Transcription factor CrzA modulate fungal development and cellulolytic gene expression in Penicillium oxalicum

status: Public on May 29 2021

city: QingDao

first: Kaili

last: Zhao

address: National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road

institute: ShanDong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), CrzA deletion strain (ΔCrzA) and CrzA recover strain (ReCrzA) in 2% starch as carbon sources. The correlation analysis results between the various samples showed that the gene expression levels of the wild strain and the RecrzA strain were similar, and the gene expression levels between ΔcrzA and the wild strain were significantly different. The deletion of CrzA significantly down-regulates the expression levels of conidia pigment synthesis genes, and spore wall synthesis-related genes of Penicillium oxalicum, and also has a regulatory effect on the expression levels of genes related to the sporulation process. And the absence of CrzA can broadly down-regulate the expression level of cellulase-encoding genes, indicating that CrzA can cause a decrease in cellulase synthesis by affecting the expression of cellulase-encoding genes. The information provided by this study indicates that CrzA function is necessary for the mycelial development and cellulase activity of Penicillium oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, CrzA deletion mutant strains and CrzA recover strain in 18h in modifeid Mendal’s medium with 2% starch as carbon sources. Three replicates were included for each samples.

first: Yueyan

last: Hu

first: Yuqi

last: Qin


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

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

institute: Zhejiang University

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

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

first: Hongyan

last: Diao


title: miRNA profile in tissue and circulating exosomes obtained from patients with colorectal cancer at different stages

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of this study was to use a Next Generation Sequencing (NGS) approach to discover novel miRNAs to track the progression of colorectal cancer. A total of 28 patients were recruited for this study and 3 samples were taken from each patient (exosomes, cancer tissue and adjacent normal tissue). Susbequently, patients were randomly pooled into two groups based on the cancer stage e.g. 6 patients with stage 1 colorectal cancer were pooled into two groups randomly, with each group consisting of 3 patients. This was performed for exosomes and cancer tissue, but for adjacent normal tissue patients were pooled into a single group based on the cancer stage.

overall_design: miRNAs were profiled from tissues and exosomes using next generation seqeuencing (Illumina NextSeq 500 platform).

first: Jian

last: Sheng

first: Carlos

last: Salomon


title: Mitochondria-targeted partial inhibiton of complex I increase health and lifespan in mice.

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: We performed next-generation RNA sequencing (RNA-seq) using brain tissue from 23 months old vehicle and CP2-treated non-transgenic (NTG) and Young (3 months old) WT mice. By comparing transcriptomic data of vehicle and CP2-treated NTG_Old mice, we found processes affected by CP2 such as genes involved in regulation of circadian rhythm, immune system, oxidant detoxifications. In comparison to Young mice, CP2 treatment in NTG_Old mice downregulated the expression of gene sets involved in regulation of oxidative stress and lipid metabolism, which were both upregulated with old age in vehicle-treated NTG_Old mice.

overall_design: mRNA profiles of 23 months old non-transgenic (NTG) and non-treated and CP2 (mitochondrial complex I  inhibitor)-treated APP/PS1 mice were generated by deep sequencing, using Illumina HiSeq 4000 with paired end 101-bp read length.

first: Eugenia

last: Trushina


title: The Molecular and Epigenetic Mechanisms of Innate Lymphoid Cell (ILC) Memory and its Relevance for Asthma

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

summary: Repetitive exposure of Rag1-/- mice to the Alternaria allergen extract generated a form of memory that elicited an asthma-like response upon a subthreshold recall challenge 3-15 weeks later.  This memory was associated with lung ICOS+ST2+ILC2s.  Genetic, pharmacologic and antibody-mediated inhibition, and adoptive transfer established an essential role for ILC2s in memory-driven asthma.  ATAC-seq demonstrated a distinct epigenetic landscape of memory ILC2s, and identified Bach2 and AP1 (JunD and Fosl2) motifs as major drivers of altered gene accessibility.  scRNA-seq, gene knockout and signaling studies suggest that repetitive allergenic stress induces a gene repression program involving Nr4a2, Zeb1, Bach2, and JunD, and a preparedness program involving Fhl2, FosB, Stat6, Srebf2 and MPP7 in memory ILC2s. A mutually regulated balance between these two programs establishes and maintains memory.  The preparedness program (e.g. Fhl2) can be activated with a subthreshold cognate stimulation, which downregulates repressors and activates effector pathways to elicit the memory-driven phenotype.

overall_design: Total 17 samples. 11 samples from Rag1 KO mice and 6 samples from wild-type C57B/6 mice.  Study groups:  1) Alt/Alt: mice senstized with the Alternaria allergen (Alt) and underwent recall challenge with Alt; 2) Alt/-:mice  sensitized with Alt and underwent no (-) recall challenge;  3) Sal/Alt: mice senitized with saline (Sal) and underwent recall challenge with Alt. 4) Sal/-: mice sensitized with Sal  and underwent no (-) recall challenge. Each groups had three replicates except Alt-; which had two biological replicates. 6 samples were from wild type C57BL/6 mice.  This study had two groups Alt/Alt and Sal/Alt,each groups had three bilogical replicates.

first: Mukesh

last: Verma


title: Genome wide microRNA methylome in oral cancer: searching for biomarkers in tobacco users along with possible association with patient’s survival

city: Kolkata

first: BIDYUT

last: ROY

state: West bengal

address: 203 bt road

department: human genetics unit

country: India

institute: indian statistical institute

type: Methylation profiling by high throughput sequencing

summary: We performed reduced representative bisulfite sequencing (RRBS) data on 16 pairs of tumor and adjacent normal tissues from oral squamous cell carcinoma patients to identify methylated biomarkers for disease identification

overall_design: DMAP pipeline was used to compare methylation frequencies between cancer and paired normal tissues to get list of differentially methylated regions or DMR

first: Bidyut

last: Roy


title: Analysis of sexually dimorphic accumulation of taxoids identifies a female-specific MYB-bHLH complex involved in the paclitaxel biosynthesis of Taxus media

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

summary: Taxol is an efficient anticancer drug accumulated in Taxus trees. Taxus media, a large-scale cultured species, is a dioecious woody tree with high taxol yielding. However, the sexually dimorphic accumulation of taxoids in T. media is largely unknown. Our study identified a large number of differentially accumulated metabolites and differentially expressed genes, revealing the comprehensive differences between the female and male T. media trees. LC-MS analysis confirmed the high accumulation of taxoids in the female trees. Expression analysis showed that most Taxol biosynthesis-related genes were predominantly expressed in the female trees. To investigate the regulation mechanism underlying the sexually dimorphic accumulation of taxoids, a female-specific expressed gene, TmMYB39, was identified and its full-length sequence was cloned. Multiple sequence alignment and phylogenetic analyses showed that TmMYB39 is a typical R2R3-MYB factor and the subcellular localization of TmMYB39 is shown to be the nucleus. Furthermore, Y2H and BiFC assays showed that TmMYB39 interacts with TmbHLH13. Partial promoter sequences of 10 taxol biosynthesis-related genes were isolated, which were used for screening of the MYB recognition elements. TmMYB39 binds to the promoters of several taxol-related genes, such as GGPPS, T7OH, T10OH, T13OH, and TBT genes. Interaction between TmMYB39 and TmbHLH13 affected the expression of GGPS and T10OH genes, suggesting that TmMYB39 might function in the regulation of taxol biosynthesis through a ‘MYB-bHLH’ module. Our data provided a potential explanation for the sexually dimorphic accumulation of taxoids.

overall_design: we were compared female and male Taxus media trees

first: C

last: Shen


title: RNA-seq analysis of cRel+/+ and cRel-/- Tregs

city: Melbourne

first: Thomas

last: Fulford

state: Vic

address: 792 Elizabeth St

department: DMI

institute: University of Melbourne

summary: cRel is a transcription factor critical for the development of Tregs in the thymus. We examined the impact the lack of cRel has on Tregs at different stages of ontogeny (thymic pre-Tregs, thymic 'de novo' Tregs and mature spenic Tregs).

overall_design: mRNA expression was examined in Tregs at various life stages from cRel+/+ or cRel-/- mice.

middle: S

first: Haroon

last: Naim

first: Adele

last: Barugahare

first: David

last: Powell

first: Steve

last: Gerondakis


title: Effect of Cell cycle regulator CDK1 on Cell Differentiation (RNA-IP CDK1 inh KD)

city: Cambridge

first: Rodrigo

last: Grandy

address: Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way

institute: University of Cambridge

summary: We addressed the role of cell cycle regulator CDK1 during differentiation by either inhibiting its activity with the specific inhibitor RO3306 (10µM) or by knocking its expression down using specific shRNAs, during mesendoderm differentiation. Human pluripotent stem cells (H9 cells) were synchronized in their cell cycle and then induced to differentiate into mesendoderm for 24h. shRNAs against CDK1 were induced 4 days before starting the differentiation. The CDK1 inhibitor was added to the medium 8h after the induction of differentiation. At the end of the experiment, the cells were harvested and processed for total RNA extraction. RNA-IP was carried out using RiboCluster Profiler RIP-Assay Kit (MBL) following the manufacture’s recommendations.

overall_design: Four different conditions were analyzed: Undifferentiated (UD), Mesendoderm (E24), Mesendoderm + CDK1 inhibityor (E24RO), Mesendoderm  without induction of shRNA_CDK1 with tetracycline (E24woTET), and Mesendoderm plus induction of shRNA_CDK1 with tetracycline (E2TET). Two biological replicates were generated for each condition.


title: Excessive mechanical strain accelerates intervertebral disc degeneration by disrupting the intrinsic circadian rhythm

city: Beijing

first: Shenglong

last: Ding

state: Beijing

address: No. 1, Dongjiaomin Lane, Dongcheng District

institute: Beijing TongRen Hospital, Capital Medical University

summary: Nucleus pulposus cells  were stretched using a FX-5000T Flexcell tension plus system (Flexcell International Corp., USA)  with 18% elongation (0.2 Hz) for 24 h

overall_design: To compare the effects of  cyclic tensile strain on the circadian clock-related genes in nucleus pulposus cells

first: Libo

last: Jiang

first: Taiwei

last: Zhang

first: Qichen


title: Expression data from Club cells of wt/cTg and Atgl KO/cTg

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary:
ATGL= the rate-limiting enzyme for intracellular lipolysis. Atgl KO/cTg = Mice lacking Atgl except for cardiac transgenic overexpression of Atgl (Atgl -/- ,Myh6Atgl+/+) to rescue early age death deu to cardiomyopathy. wt/cTg = respective control.
The airways of the lung are constantly exposed to inhaled toxic substances, resulting in cellular damage. Within bronchii, club cells make up majority of the cell population in the terminal bronchiolar epithelia. Club cells are known for their ability to metabolize environmental toxins and constantly repairing small impacts in the epithelial layer. Considering the importance of club cells in maintaining bronchiolar epithelial integrity, we porformed gene expression data analysis to decipher the possible dysregulated gene expression thereby corresponding molecular pathways in our mice lacking ATGL.

overall_design: Club cells were isolated from 3 or 4 mice and pooled together per sample. Overall, 4 sets of Atgl KO/cTg versus wt/cTg samples were used. i.e. in total, 16 Atgl KO/cTg and 14 wt/cTg mice were used for the study.

first: M

middle: K

last: Manu

first: W

middle: V

last: Paul


title: The transcriptome and genome-wide mapping of Hif1α binding sites in kidney tubule cells

city: nanjing

first: Aiping

last: Duan

address: zhongshan east road 305

institute: Jinling hospital

summary: To understand the transcription regulation of HIF1α in kidney tubule cells, we stabilized HIF1α with 50μM FG-4592 in HK2 cells. We captured ChIPseq of HIF1α and constructed transcription profile under FG-4592.

overall_design: Kidney tubule cell culture HK2 were subjected to ChIP-seq, RNA-seq.

first: Li

last: Wenju

first: Duan

last: Aiping

first: Yang

last: Jingping


title: Molecular mechanisms by which splice modulator GEX1A inhibits leukemia development and progression

city: Maywood

first: Jiwang

state: Illinois

address: 2160 S. 1st Ave

institute: Loyola University Medical Center

summary: We examined the anti-leukemic effects of a natural splice modulator, GEX1A, through comparing RNA expression and splicing changes observed between pre-determined GEX1A-sensitive cells and GEX1A-resistant human leukemic cell lines. We found that GEX1A downregulates many pro-survival genes in the GEX1A-sensitive cell types through intron retention and other althernative splicing changes, notably in the FASTK, MCL1, and FLT3 transcripts. Additionally, GEX1A lead to an upregulation of many pro-apoptotic factors within the sensitive cell types, such as FAS, TNFRSF10B, CDKN1A, and TP53INP1. Overall, 573 genes were differentially expressed in the sensitive cell types only, whereas 604 genes were differentially expressed in the resistant cell types only. This study demonstrates that GEX1A selectively kills certain leukemic cells via apoptotic induction, notably through pro-survival factor downregulation and pro-apoptotic factor upregulation.

overall_design: Comparison of 2 GEX1A-sensitive human leukemic cell types (Molm-13, MV4:11) to 2 GEX1A-resistant cell types (HL-60, K562), both vehicle-treated and GEX1A-treated at 100 nM for 6 hrs.

first: Mark

last: Sellin

first: Wei

last: Wei


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type Transcriptomes Treated with DSS, Water, DSS plus Montmorillonite Respectively

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Conclusion: Montmorillonite can rescue colon Elf4 expression of mice treated with Dextran sulfate (DSS).

overall_design: Seven-week-old WT male mice were divided into three groups, and treated with 2% DSS (group D), water (group W), 2% DSS plus Montmorillonite powder (DS) respectively for 7 days. At Day 7, the distal colon was taken out and the RNA was extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis.

first: Fuping

last: You


title: Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

overall_design: RNA-expression in SARS2-infected wildtype and DDX1 knock-down A549-Ace2 cells

first: Marko

last: Noerenberg

first: Natasha

last: Johnson

first: Wael

last: Kamel

middle: I

first: Alfredo

last: Castello


title: Analysis of PHF12/SUDS3 functions within HEK293T cells.

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

summary: Transcription products influenced by decreased PHF12 or SUDS3 are analyzed and compared.

overall_design: HEK293T cells were transfected with control siRNA, siRNA targeting PHF12, or siRNA targeting SUDS3. Total RNA was isolated from cells for RNA-seq analysis.

last: Adams

first: Mike

last: Washburn


title: RNA sequencing of Harpegnathos saltator workers's non-visual brains, ovaries, and fat bodies injected with  juvenile hormone (JH) or ecdysone (Ec).

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

summary: In ant Harpegnathos saltator, workers can become the reproductive gamergates in a queenless condition. During the worker-to-gamergate transition, juvenile hormone signaling decreases but ovarian ecdysone production increases in the gamergate.  Injecting juvenile hormone analog (JHA or methoprene) induces expression of worker-biased genes in the brain , while ecydsone promotes expression of ecdysone-responsive genes in ovaries.

overall_design: Harpegnathos workers were injected with either solvent (EtOH), methoprene or 20-hydroxyecdysone (20E). Three tissues  (the non-visual brain, abdominal fat body and ovary) from three individuls were harvested 12 hours post the injection and subjected for RNA-seq.

first: Nikos

last: Konstantinides

first: Comzit

last: Opachaloemphan

first: Danny

last: Reinberg

first: Claude

last: Desplan


title: Histone methyltransferase Ezh2 negatively regulates NK cell terminal maturation and function

first: Minghang

last: Yu

address: No.10 Xitoutiao, You An Men

institute: Capital Medical University

summary: Deletion of Ezh2 promotes NK cell terminal differentiation and cytotoxicity with increased IFN-γ production by a potential target Pbx1.

overall_design: mRNA profiles of natural killer cells from 8-week old wild type (WT) and Ezh2ΔNK mice

first: Xi

last: Wang

first: Miaoran

last: Xia

first: Nianzeng

last: Xing


title: Transcriptomic analysis of adipocyte Tsc1 knockout mammary glands.

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

institute: University of Michigan

summary: We report here the adipocyte-specific ablation of Tsc1 and its affects on lactation and mammary gland function.  In this dataset, mammary glands from wild-type and adipocyte Tsc1 knockout mice were isolated during lactation and analysed by RNAseq.  Deletion of Tsc1 is predicted to activate mTORC1 in both peripheral and mammary adipocytes.  This study demonstrates that deletion of Tsc1 in adipocytes changes mammary gland histology, and function resulting in changes to breastmilk composition.

overall_design: Examination of mammary glands from wild-type and knockout mice

first: Noura

last: El Habbal

first: Brigid

last: Gregg

first: JeAnna

last: Redd


title: Regulation of retinal neurogenesis by somatostatin signaling

city: Baltimore

first: Kurt

last: Weir

address: 733 North Broadway

institute: Johns Hopkins School of Medicine

summary:
Purpose: Neuropeptide signaling has been reported to impact neurogenesis in the central nervous system. However, these studies have typically been conducted using pharmacological agents in ex vivo preparations, and in vivo evidence for their developmental function is generally lacking. The goal of this study is to identify the impact of somatostatin signaling on retinal neurogenesis and development both ex vivo and in vivo.
Methods: Mouse retinal explants grown ex vivo from E14-P0 and treated with a range of doses of agonist for the somatostatin receptor Sstr2 were multiplexed according to the MULTI-seq protocol and used to generate a single scRNA-seq expression library. Retinas from P0 littermates representing an allelic series (+/+, +/-, -/-) of Sstr2 KO mice were mutliplexed according to the MULTI-seq protocol and used to generate a single scRNA-seq expression library. Retinas from P14 littermates representing an allelic series (+/+, +/-, -/-) of Sstr2 KO mice were mutliplexed according to the MULTI-seq protocol and used to generate a single scRNA-seq expression library. Sequencing was performed on an illumina sequencer. Bcl files were analyzed by Cellranger. Samples were deconvoluted with the deMULTIplex r package and clustering and gene expression analysis were performed with the Seurat and Monocle2 r packages.
Results: Cell type proportions were found to be impacted by Sstr2 signaling ex vivo with increasing levels of Sstr2 agonist found to decrease photoreceptor proportion and increase primary progenitor proportion. Sstr2 KO was not found to have an impact on cell type proportion in vivo at either P0 or P14. Sstr2 pharmacologic manipulation and Sstr2 KO did produce complementary gene expression changes in neurogenic progenitors indicating that somatostatin signaling downregulates neurogenesis.
Conclusions: Our study demonstrates a role for somatostatin in retinal development by downregulating neurogenesis in neurogenic progenitors. However, it also demonstrates that somatostatin signaling is dispensable for in vivo retinal development and likely redundant with other cell extrinsic signals released during the same period.

overall_design: There are three scRNA-seq expression libraries of multiplexed samples. One library consists of mouse retinal explants grown from E14 to P0 treated with a range of concentrations of Sstr2 agonist (2 samples: 0 Sstr2 agonist, 2 samples: 5 nM Sstr2 agonist, 2 samples: 50 nM Sstr2 agonist, 2 samples: 500 nM agonist). One expression library consists of P0 mouse littermates representing an allelic series of Sstr2 KO (1 sample: +/+, 2 samples: +/-, 2 samples: -/-). One expression library consists of P14 mouse littermates representing an allelic series of Sstr2 KO (1 sample: +/+, 2 samples: +/-, 2 samples: -/-).

first: Dong

middle: W

last: Kim

first: Seth

last: Blackshaw


title: Single-cell Sequencing Analysis Identifies Intratumoral Cell Population in Head and Neck Squamous Cell Carcinoma from 4NQO-induced Mice upon anti-CD276 Therapy

city: Guangzhou

first: Cheng

address: 56 Lingyuan Road West

institute: Sun Yat-sen University

summary: In this study, we aimed to identifies the landscape alterations of intratumoral cell population in HNSCC from 4NQO-induced mice upon anti-CD276 treatment by using single cell sequencing analysis.we characterized the alterations of intratumoral cell population by separating cancer cells and yielded 6 distinct cancer cell subpopulations defined by the transcriptional state of cells and known marker genes, including the sunpopulation with pEMT, stress, typical epithelial differentiation, high cell-cycling, metabolism and immune fetures. In response of CD276 treatment, the frequecey of cells with pEMT, cell cycling and immune features are dcreased as compared to the vehicle control mice.

overall_design: Single-cell transcriptomic analysis of murine HNSCC from 4NQO-induced mice treated with anti-CD276 and control antibodies.

first: Cun-yu


title: Understanding oxidative stress responses in pancreatic islet cells by single cell RNA-sequencing analysis

city: College Station

first: Qian

last: Xu

state: texas

address: 660 Raymond Stotzer Pkwy College Station 77843

department: College of Veterinary Medicine & Biomedical Sciences

institute: Texas A&M

summary: We found these ROS generation is regulated by lncRNA MALAT1 and genetic ablation of MALAT1 drastically reduced ROS level and oxidative stress in mouse islet cells with the benefits of improved insulin responses in MALAT1-/- mouse. The pancreatic islet consists of five cell types (α, β and γ/PP, δ and ε cells) and very little is known about the xenobiotic detoxification pathways in these cells and their sensitivity to toxicants. We utilized single-cell RNA sequencing to analyze the role of MALAT1 in regulating oxidative stress response and insulin secretion function in distinct pancreatic cell population. We also treat the isolated pancreatic islets with 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) (10 nM, 12h) to investigate the xenobiotic detoxification pathways regulation in both MALAT1 KO and WT pancreatic islets. Our result showed that a subset of genes in T2DM related pathways were significantly regulated in MALAT1 -/- β cells, with significantly unregulated INS1, INS2, and PDX1. Nrf2/detoxification pathway was also significantly activated in MALAT1 -/-  β cells.  In addition, MALAT1 expression level was elevated in the T2DM patients pancreatic islets cells.   This study provides insights for mechanisms of regulation of oxidative stress by MALAT1-Nrf2 interaction which has the potential as a therapeutic target for the treatment of T2DM.

overall_design: Single-cell transcriptome analysis in pancreatic islets from C57BL/6 mice and MALAT1 null mice.

first: Yanan

last: Tian

first: Jingshu

last: Chen

first: Sui

last: Ke

first: Shu

last: Tang


title: Expression data of circRNAs from the Ricin Toxin-induced RAW264.7 macrophage cells

city: Changchun

first: Yingshuang

state: Jilin

address: NO.1163 Xinmin Street

institute: Jilin University School of Public Health

summary: Increasing studies have concentrated on investigating circular RNAs (circRNAs) as pivotal regulators in the progression of numerous diseases and biological processes and abundant evidence shows that circRNAs are participated in the regulation of innate immune responses. Several studies showed that Ricin Toxin (RT) could induce inflammatory injury. There was no research on the particular functions and underlying mechanisms of circRNAs in RT-induced inflammation. Herein, RNA sequencing performed on RT-treated and normal RAW264.7 macrophage cells was used to investigated the differentially expressed circRNAs. Based on the dataset, the expression of circEpc1 (mmu_circ_0000842) was identified higher in RT-treated cells. Moreover, gain-and-loss function assays showed that circEpc1 function as a promoter in RT-induced inflammation in vivo and in vitro. Mechanistically, circEpc1 acted as a miR-5114 sponge to relieve the suppressive effect of miR-5114 on its target NOD2 and thereby activating NF-κB and MAPK signaling pathways. This study illuminated a link between RT-induced inflammation and the circEpc1 regulatory loop and provided novel insight into the functions of circRNA in innate immune, which may emerge as a potential target in immunotherapy to control the RT-induced inflammatory injury.

overall_design: RNA sequencing performed on 3 groups of RT-treated (20 ng/mL for 8h) and 3 groups of normal RAW264.7 macrophage cells was used to investigated the differentially expressed circRNAs

first: M

middle: X

last: Dong

first: X

middle: H

last: Zhang

first: H

middle: T

first: Y

last: Chang

first: C

last: Sun

first: J

first: N

last: Zhao

first: K

first: G

middle: C

first: W

last: Liu


title: RNA-seq analysis of CD276-high/EpCAM+ cells from HNSCC patient-derived-xenograft

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: We performed RNA sequencing (RNA-seq) to compare the gene expression pattern between CD276-high/EpCAM+ and CD276-low/EpCAM+ cells isolated from human HNSCC PDX. We identified a cohort of key oncogenes associate with cancer stemness enriched in CD276-high cells. Suggesting CD276 may play a positive role in maintaining cancer stem cells in human head and neck squamous cell carcinoma.

overall_design: Examination of RNA-seq of CD276-high/EpCAM+ and CD276-low/EpCAM+ cells


title: Axial Elongation of Caudalized Human Pluripotent Stem Cell Organoids Mimics Neural Tube Development

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

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

overall_design: Refer to individual Series


title: Axial Elongation of Caudalized Human Pluripotent Stem Cell Organoids Mimics Neural Tube Development [scRNA-Seq]

summary: During mammalian embryogenesis, axial elongation of the neural tube is critical for establishing the anterior-posterior body axis, but is difficult to interrogate directly because it occurs post-implantation. Here we report an organoid model of neural tube extension using human pluripotent stem cell (hPSC) aggregates that recapitulates the morphologic and temporal gene expression patterns of neural tube development. Axially extending organoids consisted of longitudinally elongated epithelial compartments and contained TBXT(+)SOX2(+) neuromesodermal progenitors, PAX6(+) Nestin(+) neural progenitor populations, and MEOX1(+) paraxial mesoderm populations. Wnt agonism stimulated axial extensions in a dose-dependent manner and elongated organoids displayed regionalized rostral-caudal HOX gene expression, with hindbrain (HOXB1) expression distinct from brachial (HOXC6) and thoracic (HOXB9) expression. CRISPR interference-mediated silencing of BMP inhibitors induced elongation phenotypes that mimicked murine knockout models, and knock-down of the downstream Wnt target, TBXT, increased neuroepithelial compartmentalization and resulted in multiple extensions. These results indicate the potent morphogenic capacity of hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early human nervous system development.

overall_design: Axially elongating organoids were dissociated at day 10 of differentiation to examine the relative proportions of neural, mesodermal, and progenitor populations and assess their similarity to human spinal cord development

first: Ashley

last: Libby

first: David

middle: A

last: Joy

first: Nicholas

last: Elder

first: Emily

last: Bulger

first: Martina

middle: Z

last: Krakora

first: Eliza

last: Gaylord

first: Federico

last: Mendoza-Camacho

first: Jessica

last: Butts


title: Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae

status: Public on May 27 2021

city: Tianjin

first: Yuping

last: Lin

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize xylodextrins in aerobic condtions but not anaerobic conditions. We sequenced mRNA from anaerobically fed-batch cultures of the engineered S. cerevisiae grown on xylodextrins with or without the continuous feeding of xylose in biological duplicate. Dynamic changes of gene expression during xylose feeding experiment revealed by RNA deep sequencing indicated that xylose helps anaerobically xylodextrin-grown cells to recover mithondrial function thereby resuming xylodextrin consumption. Furthermore, different portions of genes involved in ribosome biogenesis showed either decreased or increased transcriptions. The underlying mechanism remains to be elucidated.

overall_design: The mRNA levels of fed-batch cultures anaerobically grown on xylodextrins with or without the continuous feeding of xylose were examined by deep sequencing, in duplicate, using Illumina Genome Analyzer-II. After inoculation, cells were cultured as follows: without xylose feeding for 20 h, with xylose feeding for 24 h, and without xylose feeding until total 72 h of fermentation. Samples were taken as follows: right before xylose feeding (0 h); 0.5 h, 1 h, 2 h, 4 h and 24 h with xylose feeding; 8 h and 24 h after stopping xylose feeding.

first: Xin

first: Jamie

last: Cate


title: Transcriptome analysis of Bcl11b-deficient murine NK cells

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

summary: Epigenetic landscapes can provide insight into regulation of gene expression and  cellular diversity. Here, we examined the transcriptional and epigenetic profiles of  seven human blood NK cell populations, including adaptive NK cells. The BCL11B  gene, encoding a transcription factor (TF) essential for T cell development and  function, was the most extensively regulated, with expression increasing throughout  NK cell differentiation. Several Bcl11b-regulated genes associated with T cell-signaling  were specifically expressed in adaptive NK cell subsets. Regulatory networks revealed  reciprocal regulation at distinct stages of NK cell differentiation, with Bcl11b repressing  RUNX2 and ZBTB16 in canonical and adaptive NK cells, respectively. A critical role  for Bcl11b in driving NK cell differentiation was corroborated in BCL11B mutated  patients and by ectopic Bcl11b expression. Moreover, Bcl11b was required for  adaptive NK cell responses in a murine CMV model, supporting expansion of these  cells. Together, we define the TF regulatory circuitry of human NK cells and uncover a  critical role for Bcl11b in promoting NK cell differentiation and function.

overall_design: Examination of changes in transcriptome of murine WT and Bcl11b KO NK cells during MCMV infection

first: Helm

last: Eric

first: Drashansky

last: Theodore

first: Avram

last: Dorina


title: Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells [scRNA-seq]

city: Portland OR

first: Anthony

middle: Paul

last: Barnes

state: OR

address: HRC 545B, 3181 SW Sam Jackson Park Rd

institute: OHSU

summary:
Purpose: The goal of this study is to determine alterations in heart endothelial cell transcripts and cell populations associated with aging.
Methods: Endothelial single cell mRNA profiles of 3 month and 24 month old wild-type mice were generated by 10X Genomics
Results: Using an optimized data analysis workflow, we mapped about 50 thousand  reads per cell
Conclusions: Our study represents the first  analysis of aged cardiac endothelial cell transcriptomes using single cell RNA-seq technology, identifiying specific transcripts and cell populations affected by age.

overall_design: Endothelial cell mRNA profiles of 3 month old and 24 month old mice

first: Uchenna

last: Emechebe

first: Jonathan

last: Nelson

first: Nabil

middle: J

last: Alkayed

first: Sanjiv

last: Kaul

first: Andrew

last: Adey


title: Long noncoding RNA FENDRR inhibits lung fibroblast proliferation via a reduction of beta-catenin

status: Public on May 26 2021

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: Adenovirus-mediated FENDRR transfer to the lungs of mice reduced asbestos-induced fibrotic lesions and collagen deposition.RNA sequencing analysis  was used to profile the gene expression in the lungs of asbestos-treated (VC-Cro) mice compared to control (VC-TiO2).

overall_design: RNA sequencing analysis of FENDRR- and asbestos-treated mice

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Lakmini

last: Kumari Senavirathna


title: Lysosome-dependent LXR and PPARdelta Activation upon Efferocytosis in Human Macrophages

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: Efferocytosis is critical for tissue homeostasis, as its deregulation is associated with several autoimmune pathologies. While engulfing apoptotic cells, phagocytes activate transcription factors, such as peroxisome proliferator-activated receptors (PPAR) or liver X receptors (LXR) that orchestrate metabolic, phagocytic, and inflammatory responses towards the ingested material. Coordination of these transcription factors in efferocytotic human macrophages (MF) is not fully understood. In this study, we evaluated the transcriptional profile of MF following the uptake of apoptotic Jurkat T cells using RNA-seq analysis. Results indicated upregulation of PPAR and LXR pathways but downregulation of sterol regulatory element-binding proteins (SREBP) target genes. Pharmacological inhibition and RNA interference pointed to LXR and PPARdelta as relevant transcriptional regulators, while PPARdelta did not substantially contribute to gene regulation. Mechanistically, lysosomal digestion and lysosomal acid lipase (LIPA) were required for PPAR and LXR activation, while PPARdelta activation also demanded an active lysosomal phospholipase A2 (PLA2G15). Pharmacological interference with LXR signaling attenuated ABCA1-dependent cholesterol efflux from efferocytotic MF, but suppression of inflammatory responses following efferocytosis occurred independently of LXR and PPARdelta. These data provide mechanistic details on LXR and PPARdelta activation in efferocytotic human MF.

overall_design: mRNA-seq of human primary macrophages co-cultured with apoptotic Jurkat T cells at a 1:3 ratio for 3 hours, followed by AC removal and subsequent incubation for 3 hours. (n=6)

first: Ana

last: Mota

first: Dmitry

last: Namgaladze


title: ATAC-seq in cultured renin lineage cells with the Lmna gene knockout.

city: Charlottesville

first: Hirofumi

last: Watanabe

address: 409 Lane Rd, Bldg MR4

department: Department of Pediatrics, Child Health Research Center

institute: University of Virginia School of Medicine

summary: ATAC-seq was performed to identify the effects in the knockout of the Lmna gene in renin lineage cells.

overall_design: Evaluation of accessible chromatin in renin lineage cells. Two replicates of control cells and Two replicates of Lmna knockout cells.


title: Single cell transcriptome analysis of human oocyte aging

city: Shanghai

first: lihua

last: Yuan

address: cailun road num 1200

institute: Shanghai university of traditional Chinese medicine

summary: To investigate the effects of women age on oocyte developmental competency, we used single-cell RNA sequencing to detect global gene transcriptome and identify key genes affected by advanced age in human mature oocytes.

overall_design: We isolated mRNA from MII oocytes obtained from ICSI patients (six oocytes from younger (＜30 years) and six oocytes from older (≥40 years) patients for scRNA-seq.

first: Lihua

first: Ping

last: Yin

first: Guoqing

last: Tong

first: Wuwen

last: Zhang


title: Messenger RNA expression profiling in L3mbtl3 WT versus L3mbtl3 KO/+ mouse cerebella.

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

summary: The NOTCH/RBPJ pathway governs cell proliferation in many biological contexts, including SHH and Group#3 medulloblastoma (MB) tumorigenesis. Using our proteomic platform, we discovered an interaction between RBPJ, a key co-factor of NOTCH for the modulation of the NOTCH/RBPJ signaling pathway, and L3MBTL3, a methyllysine reader. L3MBTL3 is recruited by RBPJ on chromatin at the enhancers of NOTCH/RBPJ target genes to repress their expression. Deletions of the L3MBTL3 locus are observed in patients with WNT and Group#3 MB and expression of L3MBTL3 in the SHH MB-derived cell DAOY inhibits cell growth, suggesting a putative tumor suppressor role for L3MBTL3 in MB. To further investigate the putative role of L3MBTL3 as a suppressor of MB tumorigenesis, we explored the transcriptome of L3mbtl3 KO mouse cerebella using RNA-seq.

overall_design: RNA was obtained from P15 mouse cerebella, three (3) from wild-type and four (4) from 4 L3mbtl3 KO/+ mice.

first: Honglai

first: Jean-François

last: Rual


title: New insights into the regulatory mechanism of m6A mRNA methylation on muscle stem cells

first: Yu

last: Liang

address: Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital

summary: In the conditional knockout mouse model, explore the role of m6A modification in the process of muscle damage repair.The molecular regulation mechanism of m6A modification on muscle regeneration was found through the study of related signaling pathways.

overall_design: m6A MeRIP-Seq was used to identify the differential methylated mRNAs during muscle injury.

first: Shuibin

last: Lin


title: Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells

first: Anthony

last: Barnes


title: Axial Elongation of Caudalized Human Pluripotent Stem Cell Organoids Mimics Neural Tube Development [RNA-Seq]

first: Todd

last: McDevitt

overall_design: Neural axially elongating and non-elongating organoids had total RNA extracted at days 1, 3, 5,7, and 10 of the differentiation to compare the evolution of organoid expression signatures over the development of axial extensions

first: Ashley

middle: R

last: Libby

first: David

last: Joy

first: Nicholas

last: Elder

first: Emily

last: Bulger

first: Martina

last: Krakora

first: Eliza

last: Gaylord

first: Federico

last: Mendoza-Camacho

first: Jessica

last: Butts


title: Changes in chromatin accessibility when expressing two sets of t(6;11) fusion proteins

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

summary: We have cloned two sets of t(6;11) fusion genes with breakpoints in the majorand minor BCR of the MLL/KMT2A gene. Both setsof fusion genes were stably transfected alone or in combiantion to analyze their molecular power

overall_design: All fusion genes (n=4) were constructed by fusing distinct cDNA portions of MLL/KMT2A with AF6/AFDN via a short intronic sequence

first: Rolf

last: Marschalek


title: Meta-analysis of smooth muscle lineage transcriptomes in atherosclerosis and their relationships to in vitro models

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

summary: We identified 24 cell clusters in the meta-analysis of single cells from atheroscleroticlesions with notable heterogeneity across studies, especially for macrophage populations. Trajectory analysis of VSMC lineage positive cells revealed several possible paths of state transitions with one traversing from contractile VSMC to macrophages by way of a proliferative cell cluster. Transcriptome comparisons between in vivo and in vitro states underscored that data from three (in vitro) cholesterol treated VSMC experiments did not mirror cell state transitions observed in vivo. However, all in vitro macrophage profiles analyzed (M1, M2, and oxLDL) were more similar to in vivo profiles of macrophages than VSMC were to in vivo profiles of VSMCs, with oxLDL loaded macrophages showing the most similarity to in vivo states.

overall_design: Meta-analysis of scRNA-seq data from VSMC lineage traced cells across five experiments of murine atherosclerosis was performed. In vivo expression profiles were compared to three in vitro datasets of VSMCs loaded with cholesterol and three datasets of polarized macrophages.

first: A

last: Conklin

first: C

middle: E


title: Impact of plant cell wall derived sugars on transcriptional and post-transcriptional control in Saccharomyces cerevisiae

first: Yuping

summary: Saccharomyces cerevisiae cannot metabolize non-glucose sugars including cellobiose, xylose, xylodextrins in nature, which are prevalent in plant cell wall. Here, one engineered S. cerevisiae strain, which expresses a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa; XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize the above non-glucose sugars. We sequenced mRNA from exponential cultures of the engineered S. cerevisiae grown on glucose, cellobiose, xylose or xylodextrins as a single carbon source in both aerobic and anaerobic conditions in biological triplicate. Differences in gene expression between non-glucose sugar and glucose metabolism revealed by RNA deep sequencing indicated that non-glucose sugar metabolism induced mitochondrial activation and reduced amino acid and protein biosynthesis under fermentation conditions.

overall_design: The mRNA levels in glucose-grown, cellobiose-grown, xylose-grown and xylodextrins-grown cells of engineered Saccharomyces cerevisiae in both aerobic and anaerobic conditions were examined by deep sequencing, in triplicate, using Illumina Genome Analyzer-II.

first: Xin

last: Li

first: Jamie

last: Cate


title: Transcriptomic profiling of brassinosteroids response genes in soybean (Glycine max L.)

city: Fuzhou

first: wenfei

last: Wang

state: Fujian

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

department: Haixia Institute of Science and Technology

institute: Fujian Agriculture and Forestry University

summary: Brassinosteroids (BRs) are a series of sterol hormones in plants, which play important physiological roles in many aspects of plant growth and development processes. Exogenous application of BR and its inhibitors PPZ to investigated the roles of BR in soybean root growth and development. Transcriptome sequencing analysis was performed to identified lots number of differential expression genes(DEGs) by eBL (2,4-epicastasterone, 24-epiCS) and PPZ (propiconazole) treatment of soybean root tips(1 cm).

overall_design: Soybean seeds were germinated in vermiculite for 3 days. 3-day-old soybean seedlings were transferred to hydroponics medium for 5 days, then with 0.1 μM PPZ  and mock treatment separately for another 2.5 days. 3-day-old soybean seedlings were transferred to hydroponics medium for 7 days, then treated with 0.01 nM eBL and mock for another half a day. PPZ_BR treatment is that 5-day-old hydroponic cultured soybean seedlings treat with 0.1 μM PPZ for 2 days and then with 0.01 nM BL for half a day.

first: Wang

last: Wenfei

first: Min

last: Wanling

first: Cheng

last: Ling

first: Li

last: Man


title: Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells [bulk RNA-seq]

first: Anthony

last: Barnes

summary:
Purpose: The goal of this study is to determine alterations in heart endothelial cell transcripts associated with aging. This is accomplished by comparing endothelial transcriptomes from young and aged organs (heart, brain and kidney).
Methods: Endothelial mRNA profiles of 3 month and 24 month old wild-type mice were generated by next generation sequencing using libraries generated via SmartSeq V4 chemistry (Takara) and sequenced on an HiSeq 2500 (Illuina). Tophat2 with default parameters was used to align the sequenced reads against the mouse genome using the GRCm38. HTSeq python software with default parameters was used to quantify the transcripts of the aligned reads using the corresponding GRCm38 gene annotation model from Ensembl.
Results: Highly enriched populations of endothelial cells (ECs) isolated from the heart, brain and kidney of young (3 months) and old (24 months) C57/BL6 mice were profiled for RNA expression via bulk RNA sequencing. Approximately 700 cardiac endothelial transcripts significantly differ by age. Gene set enrichment analysis indicated similar patterns for cellular pathway perturbations. Receptor-ligand comparisons indicated parallel alterations in age-affected circulating factors and cardiac endothelial-expressed receptors. Single-cell RNA-seq analysis identified 9 distinct endothelial cell subtypes in the heart with an age-associated population shift observed for an Aplnr-enriched endothelial cell clusters.
Conclusions: Gene and pathway enrichment analyses show that age-related transcriptional response of cardiac endothelial cells is distinct from that of endothelial cells derived from the brain or kidney vascular bed. Furthermore, single-cell analysis identified 9 distinct EC subtypes, and shows that Aplnr-enriched subtype is reduced with age in mouse heart. Finally, we identify age-dysregulated genes in specific aged cardiac endothelial subtypes.

first: Uchenna

last: Emechebe

first: Jonathan

last: Nelson

first: Nabil

last: Alkayed

first: Sanjiv

last: Kaul

first: Andrew

last: Adey

middle: P


title: Early infiltrating macrophage subtype correlates with late stage phenotypic outcome in a mouse model of hepatorenal fibrocystic disease

city: Birmingham

first: David

last: Crossman

state: AL

address: 720 20th Street South

department: Genetics

institute: University of Alabama at Birmingham

summary: Abstract: Hepatorenal fibrocystic disease (HRFCD) is a genetically inherited disorder related to primary cilia dysfunction in which patients display varying levels of fibrosis, bile duct expansion, and inflammation. In mouse models of HRFCD, the phenotype is greatly impacted by the genetic background in which the mutation is placed. Macrophages are a common factor associated with the progression of HRFCD and are also strongly influenced by the genetic background. These data led us to hypothesize that macrophage subtypes that change in relation to genetic background are responsible for the variable phenotypic outcomes in HRFCD.  To test this hypothesis, we utilized a mouse model of HRFCD (Ift88Orpk mice) on the C57BL/6 and BALB/c inbred backgrounds that have well-documented differences in macrophage subtypes. Our analyses of infiltrating macrophage subtypes confirm that genetic strain influences the subtype of infiltrating macrophage present during normal postnatal liver development and in Ift88Orpk livers (Ly6clo in C57BL/6 vs Ly6chi in BALB/c).  Each infiltrating macrophage subtype was similarly associated with a unique phenotypic outcome as analysis of liver tissue shows that C57BL/6 Ift88Orpk mice have increased bile duct expansion, but reduced levels of fibrosis compared to BALB/c Ift88Orpk livers. RNA sequencing data suggest that the ability of infiltrating macrophage subtypes to influence phenotypic outcome may be due to unique ligand-receptor signaling between infiltrating macrophages and cilia dysfunctional biliary epithelium. To evaluate whether specific macrophages subtypes cause the observed phenotypic divergence, we analyzed the liver phenotype in BALB/c Ift88Orpk mice on a CCR2-/- background. Unexpectedly, loss of Ly6chi macrophages, which were strongly enriched in BALB/c Ift88Orpk mice, did not significantly alter liver fibrosis. These data indicate that macrophage subtypes may correlate with HRFCD phenotypic outcome, but do not directly cause the pathology.

overall_design: 16 samples were sequenced. Each sample was generated by combining an approximately equal amount RNA from 6-8 mice into a single tube followed by RNA sequencing.

first: Kurt

last: Zimmerman

last: Song

first: Ernald

last: Aloria

first: Zhang

first: Juling

last: Zhou

first: Sarah

last: Bland

first: Alex

last: Yashchenko

middle: K

first: Michal

last: Mrug

first: Bradley

last: Yoder


title: Implication of Repeat Insertion Domains in the Trans-Activity of the Long non-coding RNA ANRIL [ANRIL_DEx8_Affy]

city: Vandoeuvre-lès-Nancy

first: Sylvain

last: Maenner

address: 9 Avenue de la Forêt de Haye

department: CNRS-UL

institute: IMoPA

summary: To identify the genes differentially expressed upon removal of the Exon8 of the lncRNA ANRIL in HEK293 cells

overall_design: We analyzed WT and CRISPRed engineered HEK293 cells lacking Exon8 of the lncRNA ANRIL using the Affymetrix Human Clariom D chips. Array data were processed using the  Transcriptome Analysis Console (TAC) Software. Five biological replicates were included in the analysis.

first: Charbel

last: Alfeghaly

first: Aymeric

last: Sanchez

first: Raphael

last: Rouget

first: Quentin

last: Thuillier

first: Valérie

last: Igel-Bourguignon

first: Virginie

last: Marchand

first: Christiane

last: Branlant

first: Yuri

last: Motorin

first: Isabelle

last: Behm-Ansmant


title: Implication of Repeat Insertion Domains in the Trans-Activity of the Long non-coding RNA ANRIL

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: Targeted inhibition of GFI1/KDM1A combined with BET inhibitor augments lethal activity against AML including post-MPN sAML cells [ATAC-seq]

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: To determine the impact of inhibition of KDM1A/LSD1 through genetic manipulation or with irreversible LSD1 inhibitors on global chromatin accessibility and occupancy of H3K27Ac and BRD4 in AML and post-MPN sAML cells.

overall_design: Examination of Acetylated K27  histone H3 modification and BRD4  occupancy by ChIP-Seq analysis and chromatin accessibility by ATAC-Seq analysis in AML OCI-AML5 cells with CRISPR/Cas9 mediated knockout of KDM1A or following treatment with an irreversible inhibitor of LSD1 (INCB059872). Examination of BRD4 occupancy in untreated and OTX015-treated cells. Examination of chromatin accessibility  in secondary AML SET2 and its OTX persister resistant derivative (SET-2-OTX P/R) following treatment with INCB059872.

middle: N

first: Warren

last: Fiskus


title: PDGF-D activation by macrophage-derived uPA promotes AngII-induced cardiac remodeling in obese mice

city: shanghai

first: zebei

last: zhang

address: 197 ruijin No.2 road

institute: shanghai institute of hypertension

summary: Obesity-induced secretory disorder of adipose tissue-derived factors is important for cardiac damage. However, whether platelet-derived growth factor-D (PDGF-D), a newly identified adipokine, regulates cardiac remodeling in Angiotensin II (AngII)-infused obese mice is unclear. Here, we found obesity induced PDGF-D expression in adipose tissue, as well as more severe cardiac remodeling compared to control lean mice after AngII infusion. Adipocyte-specific PDGF-D knockout attenuated hypertensive cardiac remodeling in obese mice. Consistently, adipocyte-specific PDGF-D overexpression transgenic mice (PA-Tg) showed exacerbated cardiac remodeling after AngII infusion without high-fat diet treatment. Mechanistic studies indicated that AngII-stimulated macrophages produce urokinase plasminogen activator (uPA) that activates PDGF-D by splicing full-length PDGF-D into the active PDGF-DD. Moreover, bone marrow specific uPA knockdown decreased active PDGF-DD level in the heart and improved cardiac remodeling in HFD hypertensive mice. Together, our data provide for the first time a new interaction pattern between macrophage and adipocyte, that macrophage-derived uPA activates adipocyte-secreted PDGF-D, which finally accelerates AngII-induced cardiac remodeling in obese mice.

overall_design: mRNA profiles of primary cardiac fibroblasts with or without PDGF-DD treatment.6 samples are analyzed, including 3 replicates of control samples and 3 replicates of PDGF-DD treated samples.

first: Zebei

last: Zhang

first: Chengchao

last: Ruan

first: Yuwen

last: Cheng


title: Implication of Repeat Insertion Domains in the Trans-Activity of the Long non-coding RNA ANRIL [ChIRP-seq]

summary: We performed Chromatin Isolation by RNA Purification (ChIRP-seq) of the lncRNA ANRIL in HEK293 cell line. We identified 3227 genomic regions to be contacted by ANRIL.

overall_design:
Two pools (even and odd) of antisense biotinylated oligos against ANRIL and LacZ negative control were used. Sequencing was done on two independent replicates.
Please note that each processed data file was generated from both even and odd samples, and is linked to the corresponding *Even* sample records.


title: Epigenetic drift during long-term culture of cells in vitro [4C]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. These changes might be directly regulated or caused by gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift”. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) particularly the culture-associated hypomethylation is reversed simultaneously with age-associated and pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpolulations of MSCs at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results indicate that DNAm changes during culture-expansion resembles epigenetic drift.

overall_design: Examination of chromatin interactions in two donors of mesenchymal stromal cells in early (P2 and P3) and late (P7 and P9) passages at four senescence-associated regions (associated with the genes ALOX12, CASR, LTC4S and KRTAP13.3)

first: Julia

last: Franzen

first: Theodoros

last: Georgomanolis

first: Anton

last: Selich

first: Chao-Chung

last: Kuo

first: Reinhard

last: Stöger

first: Lilija

last: Brant

first: Melita

middle: S

last: Mulabdić

first: Eduardo

last: Fernandez-Rebollo

first: Clara

last: Grezella

first: Alina

last: Ostrowska

first: Matthias

last: Begemann

first: Miloš

last: Nikolić

first: Minseung

last: Choi

first: Björn

last: Rath

first: Anthony

middle: D

last: Ho

first: Michael

last: Rothe

first: Axel

last: Schambach

first: Argyris

last: Papantonis


title: Gene expression after TSA treatment in H69 cells

city: Dallas

first: Mingrui

last: zhu

address: 5323 Harry Hines Blvd

department: Pathology

institute: UTSouthwestern Medical Center

summary: Objective of the study is to determine global changes in gene expression after HDAC inhibitor Trichostatin (TSA) treatment in H69 cell line

overall_design: Vehicle (DMSO) and TSA (1uM) treated H69 cells were incubated for 24 hours then RNA was extracted. Triplicates were used for both samples.

first: Esra

last: Akbay

last: Zhu


title: Induction of an Interferon Response Program in EGFR Mutant Lung Cancer by Tyrosine Kinase Inhibitors Positively Associates with Clinical Response

city: Aurora

first: Natalia

last: Gurule

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to analyze rapid transcriptional responses induced by TKIs early in treatment that associate with the range of patient responses observed to oncogene specific inhibitors.

overall_design: RNA-seq was used to define transcriptional changes  that occur in response to EGFR TKI in human lung cancer cell lines PC9, H1650, HCC4006, and H1975 and human 8 matched lung tumor biopsies.

first: Caroline

last: McCoach

first: Trista

last: Hinz

first: Dan

last: Merrick

first: Adriaan

last: Van Bokhoven

first: Jihye

last: Kim

first: Tejas

last: Patil

first: Jacob

last: Calhoun

first: Raphael

last: Nemenoff

first: Aik

last: Tan

first: Robert

last: Doebele

first: Lynn

last: Heasley


title: Targeted inhibition of GFI1/KDM1A combined with BET inhibitor augments lethal activity against AML including post-MPN sAML cells [RNA-seq]

first: Kapil

last: Bhalla

summary: To determine the impact of inhibition of KDM1A/LSD1 through genetic manipulation by CRISPR/Cas9 or inducible shRNA or following treatment with irreversible LSD1 inhibitor INCB059872 on global transcriptomic profile in AML and post-MPN sAML cells. To determine the impact of GFI1 knockdown on global transcriptomic profile in AML cells.

overall_design: OCI-AML5 cells with or without LSD1 knockout by CRISPR/Cas9, depletion of LSD1 or GFI1 by shRNA, or OCI-AML5 cells that were treated with 1000 nM of  irreversible LSD1 inhibitor INCB059872 for 16 hours. Additionally, secondary AML (SET2) and their OTX persister-resistant derivative (SET2 OTX P/R) cells were treated for 16 hours with 250 nM of INCB059872 to determine the effects of LSD1 inhibitor treatment on the global transcriptome profile in parental and BET inhibitor persister-resistant cells. Cells were treated independently and RNA was isolated from biologic replicates and RNA Sequencing was performed.

first: Warren

last: Fiskus


title: Targeted inhibition of GFI1/KDM1A combined with BET inhibitor augments lethal activity against AML including post-MPN sAML cells


title: DEAD-box RNA helicase 27-Mediated MicroRNA Biogenesis Is Essential for Zygote Division and Stem Cell Homeostasis in Arabidopsis

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

summary: Zygote division and stem cell homeostasis are crucial events for plant development. Here, we found that mutations in DEAD-box RNA helicase 27 (RH27) affected zygote division and stem cell homeostasis in Arabidopsis (Arabidopsis thaliana). The strong mutant allele rh27-1 showed a zygote-lethal phenotype, while the weak mutant allele rh27-2 showed defective embryogenesis and compromised stem cell homeostasis in both the shoot apical meristem (SAM) and root apical meristem (RAM). RH27 was expressed in embryos from the zygote stage, and in the SAM and RAM. Cytological analyses revealed that stem cell homeostasis in the SAM and RAM was disrupted in rh27-2. Then, the expression levels of genes related to stem cell homeostasis were elevated in rh27-2, which coincides with down-regulations of their corresponding negative regulatory microRNAs. Furthermore, small RNA-sequencing indicated that the reduction of miRNAs was a global effect in both shoot apices and root tips of rh27-2. Additionally, the accumulation of pri-miRNAs was detected to be decreased. Biochemical studies showed that the nucleus-localized RH27 interacted directly with SERRATE, a component of the microprocessor complex, and DAWDLE, which facilitates the recruitment of substrates to the complex, suggesting that RH27 is a subunit of the microprocessor complex. Overall, this work provides evidences that RH27 regulates zygote division and stem cell homeostasis in Arabidopsis through miRNA biogenesis.

overall_design: Small RNA-sequencing and RNA-sequencing were used to study global effects of RH27 on miRNA accumulation and expressions of pri-miRNAs and miRNA targets,respectively.

first: Xiu-Li

last: Hou

first: Xiu-Feng

last: Song

first: Xiaofeng

last: Cao

first: Chun-Ming

last: Liu


title: RNA Sequencing  Analysis of BMDMs from Wild Type and DRD5-/- mice

city: nan jing

first: liu

last: lu

state: jiang su

address: Chunhua

department: immunology

institute: nanjing medical university

summary: We identified that DRD5 protected against DDS-induced colitis, and DRD5 deficiency in macrophages promoted the development of DSS-induced colitis.The purpose of this experiment was to identify how DRD5 protected against DSS-induced colitis.

overall_design:
BMDMs mRNA profiles of wild type (WT) and drd5-/- mice were generated by deep sequencing, in triplicate, using BGISEQ-500
DA dopamine, D5 dopamine receptor, M1 M1 macrophage, M1DA M1 macrophage and dopamine

first: Shuo

last: Yang

first: Lu

first: Yuqing

last: Wu


title: DREAM of purified normal human mammary epithelial cells

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: DNA methylation alterations have similar patterns in normal aging tissue and in cancer. In this study, we investigated breast tissue-specific age-related DNA methylation alterations and used those methylation sites to identify individuals with outlier phenotypes. Outlier phenotype is identified by unsupervised anomaly detection algorithms and is defined by individuals who have normal tissue age-dependent DNA methylation levels that vary dramatically from the population mean. To identify age-dependent DNA methylation sites, we generated DNA methylation sequencing data for 29 purified normal adjacent human breast epithelia (age range 33-82 years old) using Digital Restriction Enzyme Analysis of Methylation (DREAM). Next, we validated the age-related sites in publicly available DNA methylation (450K array) of 97 normal adjacent TCGA samples. We found that hypermethylation in normal breast tissue is the best predictor of hypermethylation in cancer. Using unsupervised anomaly detection approaches, we found that about 10% of the individuals (39 /427) were outliers for DNA methylation from 6 publicly available DNA methylation datasets (GSE88883, GSE74214, GSE101961, GSE69914(normal), GSE69914(normal-adjacent), TCGA (Firehose Legacy)). We also found that there were significantly more outlier samples in normal-adjacent to cancer (24/139, 17.3%) then in normal samples (15/228, 5.2%). Additionally, we found significant differences between predicted ages based on DNA methylation and the chronological ages among outliers and not-outliers. Additionally, we found that accelerated outliers (older predicted age) were more frequent in normal-adjacent to cancer (14/17, 82%) compared to normal samples from individuals without cancer (3/17, 18%). Furthermore, in matched samples, the epigenome of the outliers in the pre-malignant tissue was as severely altered as in cancer.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of 29 purified normal adjacent human breast epithelia (age range 33-82 years old). Briefly, DREAM is a quantitative mapping of DNA methylation with high resolution on a genome-wide scale. The method is based on sequential cuts of genomic DNA with a pair of neoschizomer endonucleases (SmaI & XmaI) recognizing the same restriction site (CCCGGG) containing a CpG dinucleotide (CG). SmaI cuts first all unmethylated sites at CCC^GGG while the methylation tolerant XmaI follows by cutting the methylated sites at C^CCGGG. The enzymes thus generate distinct methylation-specific signatures at the ends of DNA fragments which are deciphered by next generation sequencing. The methylation level at individual CpG sites is calculated as the ratio of sequencing reads with the methylated signature CCGGG to the total number of reads mapping to the site.

first: Shoghag

last: Panjarian

first: Jozef

last: Madzo

first: Kelsey

last: Keith

first: Carolyn

middle: M

last: Slater

first: Carmen

last: Sapienza

first: Jean-Pierre

last: Issa


title: Discordant regulation of eIF2 kinase GCN2 and mTORC1 during nutrient stress

city: Indianapolis

first: Ronald

last: Wek

state: IN

address: 635 N. Barnhill Dr. MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Here we report Total RNA seq and RiboSeq on MEF cells treated with halofuginone. Halofuginone is a competitive inhibitor of the Prolyl-tRNA synthetase that results in an accumulation of uncharged Prolyl-tRNA upon treatment that leads to an activation of the protein kinase Gcn2.

overall_design: Total RNA Seq and ribosome footpinting in halofuginone and untreated MEF cells

first: Jagannath

last: Misra

first: Michael

last: Holmes

first: Emily

last: Mirek

first: Hyeong-Geug

last: Kim

first: Kenneth

last: Carlson

first: X

last: Dong

first: Tracy

middle: G

last: Anthony


title: Gene expression in pachytene spermatocytes and round spermatids depleted of HDAC3

city: Nanjing

first: Lan

last: Ye

state: Jiangsu

address: B112 Xuehai Building,101 Longmian Avenue, Jiangning district

institute: Nanjing Medical University

summary: This study aims to explore the transcriptomic changes in Stra8-cre/Hdac3fl/- mice at meiotic and postmeiotic stages. Pachytene spermatocytes and round spermatids were isolated from testes of Hdac3fl/+ and Stra8-cre/Hdac3fl/- mice at 7-8 week-old through STA-PUT method. Cells from 6 WT mice or 10 Stra8-cre/Hdac3fl/- mice were pooled for one biological replicate. RNA-seq libraries were prepared in biological triplicates.

overall_design: Total RNA was extracted from pachytene spermatocytes and round spermatids isolated from wild-type and Stra8-cre/Hdac3fl/- using TRIzol reagent. For each group, we have  biological triplicates. Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer's instructions.

first: Z

last: Kang

first: H

last: Yin

first: L


title: RNA-seq Renin cells isolated from Ren1c-YFP mice with aortic coarctation

city: Charlottesville

first: Hirofumi

last: Watanabe

address: 409 Lane Rd, Bldg MR4

institute: University of Virginia School of Medicine

summary: RNA-seq was performed to compare the transcriptome of renin cells to test the effects of renal perfusion pressure changes

overall_design: Evaluation of the transcriptome of renin cells. 3 biological replicates of mice with aortic coarctation and 2 biological replicates of mice with sham surgeries.


title: NRF2/KEAP1 in hepatocytes controls fibro- and carcinogenesis in chronic liver disease

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Background & Aims: Inflammation in chronic liver diseases induces oxidative stress and thus may contribute to progression of liver injury, fibrosis, and carcinogenesis. The KEAP1/NRF2 axis is a major regulator of cellular redox balance. In the present study, we investigated whether the KEAP1/NRF2 system is involved in liver disease progression in human and mice. Methods: The clinical relevance of oxidative stress was investigated in a well-characterized cohort of NAFLD patients (n=63) by liver RNA sequencing and correlated with histological and clinical parameters. For functional analysis hepatocyte-specific NEMO knock-out (NEMO∆hepa) mice were crossed with hepatocyte-specific KEAP1 knock-out (KEAP1∆hepa) mice. Results: Immunohistochemical analysis of human liver sections showed increased oxidative stress and high NRF2 expression in patients with chronic liver disease. RNA sequencing of liver samples in a human pediatric NAFLD cohort revealed a significant increase of NRF2 activation correlating with the grade of inflammation, but not with the grade of steatosis, which could be confirmed in a second adult NASH cohort. In mice, microarray analysis revealed that KEAP1 deletion induces NRF2 target genes involved in glutathione metabolism and xenobiotic stress (e.g., Nqo1). Furthermore, deficiency of one of the most important antioxidants, glutathione (GSH), in NEMO∆hepa livers was rescued after deleting KEAP1. As a consequence, NEMO∆hepa/KEAP1∆hepa livers showed reduced apoptosis compared to NEMO∆hepa livers as well as a dramatic downregulation of genes involved in cell cycle regulation and DNA replication. Consequently, NEMO∆hepa/KEAP1∆hepa compared to NEMOΔhepa livers displayed decreased fibrogenesis, lower tumor incidence, reduced tumor number, and decreased tumor size.  Conclusions: NRF2 activation in NASH patients correlates with the grade of inflammation, but not steatosis. Functional analysis in mice demonstrated that NRF2 activation in chronic liver disease is protective by ameliorating fibrogenesis, initiation and progression of hepatocellular carcinogenesis.

overall_design: Microarray analysis was performed on livers or primary hepatocytes of control, hepatocyte-specific NEMO knockout mice, hepatocyte-specific KEAP1 knockout mice, or hepatocyte-specific NEMO/KEAP1 double knockout mice.

first: Antje

last: Mohs

first: Tobias

last: Otto

first: Mark

middle: V

last: Boekschoten

first: Christian

last: Trautwein


title: Targeted inhibition of GFI1/KDM1A combined with BET inhibitor augments lethal activity against AML including post-MPN sAML cells [ChIP-seq]

first: Kapil

last: Bhalla

first: Warren

last: Fiskus


title: Genome-wide maps of histone H3K9 acetylation in the mouse strains C57BL/6J, MSM/Ms, and their F1 hybrids

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of B1 and B2 SINE families within Mus musculus. Using a novel RNA sequencing method developed here, we detected the expression of SINEs in testes at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs contained transcripts from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses revealed that polymorphic B2 insertions served as a chromatin boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, a total of > 100 polymorphic B2 insertions were bound by CTCF, a well-known chromatin boundary protein. These results suggest that the currently active B2 copies are mobile chromatin boundary elements that can modulate gene expression level, and are likely involved in epigenomic and phenotypic diversification of the mouse species.

overall_design: H3K9ac ChIP-seq experiments and comparison for liver of the two mouse strains.


title: Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190613_174740_sham_cont]

city: Rehovot

first: Tomer

last: Chen

address: P.O.box 26

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

summary: In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposure to PEG, and from roots under 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM for 0, 1, 2, 3 h.

overall_design: WT Arabidopsis thaliana seedlings were exposed to 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM 0, 1, 2, 3 h, and root RNA was extracted sequenced using the MARSeq protocol.

first: Robert

last: Fluhr