title: BCG vaccination of mice elicits transcriptional changes in blood that predict protection against M.tb. challenge

city: Silver Spring

first: Sherry

last: Kurtz

address: 10903 New Hampshire Ave, Bldg 52/72 Rm 5328

institute: US Food and Drug Administration

summary: Although BCG has been used for almost 100 years to immunize against Mycobacterium tuberculosis, TB remains a global public health threat.  Numerous clinical trials are underway studying novel vaccine candidates and strategies to improve or replace BCG, but vaccine development still lacks a well-defined set of immune correlates to predict vaccine-induced protection against tuberculosis.  This study aimed to address this gap by examining transcriptional responses to BCG vaccination in C57BL/6 inbred mice, coupled with protection studies using Diversity Outbred mice.  We evaluated relative gene expression in blood obtained from vaccinated mice, because blood is easily accessible and data can be translated to human studies.  We first determined that the average peak time after vaccination is 14 days for gene expression of a small subset of immune-related genes in inbred mice.  We then performed global transcriptomic analyses using whole blood samples obtained two weeks after mice were vaccinated with BCG.  Using comparative bioinformatic analyses and qRT-PCR validation, we developed a working correlate panel of 18 genes that were highly correlated with administration of BCG but not heat-killed BCG.  We then tested this gene panel using BCG-vaccinated Diversity Outbred mice and revealed associations between the expression of a subset of genes and disease outcomes after aerosol challenge with M. tuberculosis.  These data therefore demonstrate that blood-based transcriptional immune correlates measured within a few weeks after vaccination can be derived to predict protection against M. tuberculosis, even in outbred populations.

overall_design: Comparison of gene expression profiles in whole blood at 14 days after vaccination with PBS or BCG in C57BL/6 mice

first: Patrik

last: Ryden

first: Karen

last: Elkins


title: Targeting KDM4B to disrupt the core regulatory transcription network governed by PAX3-FOXO1 in high-risk rhabdomyosarcoma [ChIP-seq]

status: Public on Sep 06 2022

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma is an aggressive childhood soft tissue sarcoma, mainly driven by the pathognomonic PAX3–FOXO1, which governs a core regulatory circuitry transcription factor (CRC TF) network. Here we show that the histone lysine demethylase KDM4B is a therapeutic vulnerability to the PAX3–FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B significantly delays tumor growth, disrupting the expression of CRC TFs in accordance with the alterations of PAX3–FOXO1-determining super enhancers.  Combination of KDM4B inhibitor with cytotoxic chemotherapy leads to significant tumor regression in preclinical PAX3–FOXO1+ RMS models.  In summary, we have identified a targetable epigenetic modifier required for the functions of PAX3–FOXO1, which may translate to a novel therapeutic approach for the high-risk RMS.

overall_design: Examination of chromatin accessibility, histone modification post QC6352 treatment in RH30.

first: Fang

last: Jie

first: Jin

last: Hongjian

first: Yang

last: Jun


title: RNAseq of parental and persister cells generated human cancer cells

first: Douglas

middle: R

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

type: Expression profiling by high throughput sequencing

summary: Persister cells (PS) were generated by diverse drug treatments of PC9 cells. Transcriptomes of these differently generated drug-persisting cells revealed common gene expression signatures related to metastasis and invasion. To test the impact of ATF4 and BCL2 effector proteins on the gene expression profiles of PS, we also investigated changes in gene expression upon BH3-mimetic treatment after gene knock-down. Enrichment analysis of differentially expressed genes (DEGs) confirmed the overall dependence on BCl-2 effector proteins and ATF4 for our previously identified pathways.

overall_design: 52 Samples of PC9 and HT29 cell lines treated with different treatments

first: Halime

last: Kalkavan

first: Mark

middle: J

last: Chen

first: Jeremy

middle: C

last: Crawford


title: Targeting KDM4B to disrupt the core regulatory transcription network governed by PAX3-FOXO1 in high-risk rhabdomyosarcoma

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

overall_design: Refer to individual Series


title: Transcriptome profiling time course of ZPR1-depleted S.cerevisiae cells

status: Public on Sep 05 2022

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St

institute: Harvard University

summary: The aim of this study was to gain insight into the temporal dynamics of the transcriptome on depletion of the essntial eukaryotic gene ZPR1 in S.cerevisiae.

overall_design: Comparative gene expression analysis of bulk RNA-seq data on ZPR1 depletion in a S.cerevisae stran where is ZPR1 is C-terminally tagged with an auxin-induclible degron (ZPR1-AID). Samples collected at multiple timepooints after addition of auxin derivative, 5-Ph-IAA.

first: Ibrahim

middle: M

last: Sabbarini

first: Dvir

last: Reif

first: Alexander

last: McQuown

first: Anjali

last: Nelliat

first: Jeffrey

last: Prince

first: Britnie

middle: S

last: Membreno

first: Colin

last: Wu

first: Andrew

middle: W

last: Murray


title: Synertistic effects of Arid1a inactivation and oncogenic Kras mutation on chromatin accessbility in mouse embryonic cells (MEFs)

city: Rochester

first: Aram

middle: F.

last: Hezel

state: NY

address: 300 Elmwood Avenue

department: Wilmot Cancer Institute

institute: University of Rochester Medical Center

summary: To explore mechanisms underlying the cooperative effect in the proliferative phenotype, we harvest MEFs of different genotypes (KA, K, A, WT) recombined and un-recombined.

overall_design: Differential chromatin accesbility analysis of ATAC-seq data for recombined WT, A, K and KA MEFs

first: Guo

last: Bing

first: Scott

last: Friedland


title: Effects of ARID1A knockdown on gene expression in human cholangiocyte cell line MMNK1

summary:
To explore transcriptomic mechanisms underlying the proliferative, dedifferentiated phenotypes observed in ARID1A knockdown MMNK1 cell,
We performed RNA-seq analysis on MMNK1 cells infected with sh-ARID1A versus sh-Scramble lentiviruses

overall_design: Comparative gene expression profiling analysis of RNA-seq data between  control and ARID1A knockdown  MMNK1 cells

first: Michael

last: O’Dell

first: Wang

last: Wenjia


title: Geography and molecular anatomy of germ layers in the gastrulating primate embryo

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

country: China

institute: Guangzhou Laboratory

summary: During mammalian embryogenesis, temporal and spatial regulation of gene expression and cell signaling influences lineage specification, the patterning of tissue progenitors and the morphogenesis of embryo. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about early human and non-human primate gastrulation due to the limitation of technical and ethical. Here, we present a morphological and molecular approach that reveals the systematically morphological changes and comprehensive transcriptional landscape of cell types populating the non-human primate embryos during gastrulation.

overall_design: By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on Crab-eating macaque embryo sections at a high resolution of 5-50 cells per sample. We then constructed a comprehensive spatial transcriptome map in gastrulating embryos.

first: Guizhong

last: Cui

first: Wei

last: Si

first: Naihe

last: Jing

first: Guangdun

last: Peng


title: Synertistic effects of Arid1a inactivation and oncogenic Kras mutation on gene expression in mouse embryonic cells (MEFs)

summary:
To explore transcriptomic mechanisms underlying the cooperative effect in the proliferative phenotype, we harvest MEFs of different genotypes (KA, K, A, WT) recombined and un-recombined.
We performed RNA-seq analysis on 5 recombined (Ad-CMV-Cre) cell lines of each genotypic conditions (WT, Arid1a L/L , Kras-LSL-G12D, and Kras-LSL-G12D; Arid1a L/L) as well as 2 or 3 un-recombined (Ad-CMV-GFP) or mock-infected MEF cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for recombined (Ad-CMV-Cre) and non-recombined (Ad-CMV-GFP) or mock-infected MEFs with no, single or double Kras/Arid1a floxed alleles


title: Synergistic effects of Arid1a inactivation and oncogenic Kras mutation in mouse embryonic cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Characteristics of the senescent cells of the chronic kidney disease in mice

city: Tokyo

first: Makoto

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: Institute of Medical Science, University of Tokyo

summary: To investigate the contribution of the senescent cells to the kidney diseases

overall_design: The CKD was introduced by feeding an adenine-rich diet in the p16-tdTomato mice.

first: Sae

last: Aratani

first: Teh-Wei

last: Wang


title: Parallels between oncogene-induced cardiac neoplasia and heart regeneration in zebrafish

city: Fribourg

first: Anna

last: Jazwinska

address: Chemin du Musée 10

country: Switzerland

institute: University of Fribourg

summary: We used a cardiac-specific tamoxifen-dependent Gal4-ERT2/UAS model to achieve uniform but conditionally regulated expression of the oncogene HRASG12V in zebrafish cardiomyocytes. We found that the inhibition of TOR signaling using rapamycin treatment counteracts neoplasic growth. We analyse the transcriptome of neoplasic ventricles after exposure to DMSO and rapamycin and we applied bioinformatic analysis to determine common and distinctive molecular signatures of neoplasia versus regeneration of the heart.

overall_design: Adult zebrafish ventricles of regenerating and neoplasic hearts were isolated for RNA-sequencing

first: Catherine

last: Pfefferli

first: Marylène

last: Bonvin

first: Steve

last: Robatel

first: Julien

last: Perler

first: Désirée

last: König


title: Quantitative Analysis of mid-L4 WT worms after P. aeruginosa PA01 infection for 12 hours

status: Public on Sep 04 2022

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

summary: To identify candidate genes whose expressions were regulated by P. aeruginosa PA01, we used RNA-Seq analysis to study the transcriptomic profiles of mid-L4 worms exposed to P. aeruginosa PA01 for 12 hours. Differential expression analysis was performed by comparing  WT worms exposed to P. aeruginosa PA01 for 12 hours versus worms fed E. coli OP50.

overall_design: The transcriptional profiles of mid-L4 WT worms exposed to P. aeruginosa PA01 or  E. coli OP50 for 12 hours were generated by deep sequence, in quadruplicate, using Illumina Novaseq™.

first: Jian-fan

last: Zhang

first: Wen-qing

last: Yang

first: Cheng-Gang

last: Zou


title: LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing

city: Houston

first: Deqiang

last: Sun

state: TX

address: 2121 W Holcombe Blvd

department: Search Results Web results  Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology

institute: Texas A&M University

type: Methylation profiling by high throughput sequencing

summary: LiBis is a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis improves the number of informative CpGs and the precision to quantify the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.

overall_design: Low input whole genome bisulfite sequencing.

first: Yue

last: Yin

first: Jia

last: Li

first: Jin

first: Minjun

last: Lee

first: Sibo

last: Zhao

first: Linlang

last: Guo

first: Jianfang

first: Mutian

first: Yun

last: Huang

first: Xiao-Nan


title: Mechanism of inert inflammation in an immune checkpoint blockade-resistant tumor subtype bearing transcription elongation defects

city: Cincinnati

first: vishnu

last: modur

state: OH

address: 3333 Burnet Avenue, R7509

institute: Cincinnati Children's Hospital

summary: High baseline CTLs in TEdef+ tumors result from the aberrant activation of the Nucleic Acid Sensing-TBK1-CCL5/CXCL9 signaling cascade, which induces an immunosuppressive microenvironment with increased regulatory T cells and exhausted CTLs.

overall_design: 2 Control, 2 Flavopiridol teated

first: Vishnu

last: Modur

first: Yi

last: Zheng


title: Gene expression profile of hepatocytes and macrophages at single cell level in normal and DDC-injured 1 week liver [scRNA-seq]

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: By employing single-cell transcriptional profiling, we uncovered that mature hepatocytes re-activate reprogramming/progenitor-related genes (RRG) and dedifferentiate to liver progenitor-like cells (LPLC). Because we found macrophages regulated hepatocyte dedifferentiation, We also dissected the transcriptional profiling of hepatocytes in single-cell level during DDC injury after macrophage-depletion via clondronate liposomes. Besides, we uncovered the heterogeneity of liver macrophages in normal and DDC-injured liver via scRNA-seq as well.

overall_design: Single-cell RNA sequencing of hepatocytes and macrophages in liver

first: Lu

first: Lei

last: Cui

first: Ping

last: Lin


title: RNA-sequence analysis of mammary epithelial cells with and without DNp63 using tamoxifen driven conditional deletion of DNp63

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

summary: Several genes involved in oxidative phosphorylation and stem cells and polarity were reduced in DNp63 floxed mice compared to WT

overall_design: Examination of WT (n=2) and  Dnp63 cKO (n=2) mammary epithelial cells after inducing with tamoxifen at puberty (pty)

first: John

last: Tobias


title: MicroRNA-18a prevents senescence of mesenchymal stem cells by targeting CTDSPL

city: Nanjing

first: Bo

address: Sipailou 2#

institute: Southeast University

type: Non-coding RNA profiling by high throughput sequencing

summary: Stem cell therapy requires massive scale homogeneous stem cells under strictly qualification control. However, Prolonged ex vivo expansion impairs the biological functions and results in senescence of mesenchymal stem cells (MSCs). We investigated the function of CTDSPL in premature senescence process of MSCs and clarified that miR-18a-5p played a prominent role in preventing senescence of long-term cultured MSCs and promoting the self-renew ability of MSCs. Inhibition of miR-18a-5p promoted the expression of CTDSPL and induced premature senescence of MSCs. Continuous overexpression of miR-18a-5p improved self-renewal of MSCs by reduced ROS level, increased expression of Oct4 and Nanog, promoted growth rate and differentiation capability. We reported for the first time the dynamic interaction of miR-18a-5p and CTDSPL is crucial for stem cell senescence.

overall_design: To prepare for deep sequencing, four small RNA libraries (UCMSC-P4, UCMSC-P11, CBMSC-P4, CBMSC-P11) were constructed

first: Xianhui

last: Meng


title: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University


first: Yi-Cheng

last: Ma

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H4K5ac and H4K8ac in mid-L4 WT worms exposed to P. aeruginosa PA01 for 12 hours.

overall_design: To identify candidate genes whose expressions were regulated by the histone H4 modifications during P. aeruginosa PA01 exposure, we performed chromatin immunoprecipitation (ChIP) using H4K5ac and H4K8ac antibodies followed by DNA sequencing (ChIP-seq) in mid-L4 WT worms exposed to P. aeruginosa PA01.

first: Jian-fan

last: Zhang

first: Wen-qing

last: Yang

first: Cheng-Gang

last: Zou


title: PRC2 molecule EED is a target of epigenetic therapy of neuroblastoma

status: Public on Sep 03 2022

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Epigenetic modification by polycomb repressive complex (PRC) molecules appears to have a role in tumorigenesis and aggressiveness of neuroblastoma (NB). Embryonic Ectoderm Development (EED) is a member of PRC2 complex and binds the H3K27me3 mark deposited by EZH2, via propagation on adjacent nucleosomes. Here we studied the molecular roles of EED in MYCN-amplified neuroblastoma cells by using EED-knocked down shRNAs, EED-knocked out sgRNAs, and EED small molecule inhibitor EED226. EED suppression profoundly inhibited the NB cell proliferation and flat-and soft agar colony formation. Transcriptome analysis by microarray of the EED-KD NB cells indicated the de-repression of the cell cycle regulated and differentiation-related genes; GSEA analysis results suggested that cell cycle repressed gene sets were strongly upregulated. Further, epigenetic treatment by the combination of EED inhibitor EED226 and HDAC inhibitor valproic acid effectively suppressed NB cell proliferation and colony formation. The combinatory epigenetic treatment up-regulated the cell cycle regulation- and differentiation-related genes.

overall_design: RNA was extracted at 10 days after shEED-expressing lentiviral infection, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Dilibaerguli

last: Shaliman

first: Ryuichi

middle: P

last: Sugino

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: Splicing Factor SRSF1 Promotes Tumorigenesis via Oncogenic Splice-Switching and Predicts Poor Prognosis in Multiple Myeloma

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

summary: Alternative splicing (AS) and its regulation play critical roles in cancer, yet the dysregulation of AS and its molecular bases in multiple myeloma (MM) development have not yet been elucidated. We identified SRSF1 as a key splicing factor in tumor progression, SRSF1 expression was frequently upregulated in MM and correlated with poor survival.We conducted transcriptome comparison of SRSF1-knockdown and control cells highlighted the functional importance of SRSF1 in mediating MM progression through regulating AS, and revealed the upstream and downstream molecular regulation mechanism of SRSF1. Further investigation to clarify molecular mechanisms and to replicate our findings is necessary. Thus, our findings are of high translational relevance and are expected to have a substantial impact on the development of a promising epigenetic approach for investigating targeted therapies for MM with high SRSF1 expression.

overall_design: RNA-seq in LP-1 cells with or without SRSF1 knockdown.

first: Bingzong

last: Li


title: The effect of meflin in the response to TGB-β stimulation in murine lung primary fibroblasts

city: Nagoya

first: Koji

last: Sakamoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Respiratory medicine

institute: Nagoya University

summary: Comparison of global gene expression profilles between fibroblasts from Meflin(islr)-knock out mouse and fibroblasts from wild type mouse under the presence or absence of TGFβ.

overall_design: Primary lung fibroblasts isolated from either Meflin knockout mice or wild type C57BL/6J mice were cultured in the presense or absense with recombinant TGF-β1 (5ng/ml) for 48hr. Four independent experiments were conducted in each group.

first: Yoshio

last: Nakahara


title: Gut microbiomes associated with hepatopancreatic and gonadal transcriptomes and their impact on growth traits in M. rosenbergii

city: Hangzhou

first: Jindong

last: Ren

address: No.198, Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

summary: With the increasing global demand for high-quality protein resources, improving the feed utilization rate and growth rate of aquaculture animals is the main way to solve the shortage of high-quality animal protein for humans. Improving the growth rate of Macrobrachium rosenbergii, the world's second most-produced freshwater prawn, is of particular importance for increasing the supply of high-quality protein to humans. In this study, we found that growth traits, such as body weight and weight gain of M. rosenbergii, were associated with gut microbes by applying 16s sequencing technology, as well as associated with hepatopancreatic and gonadal transcriptomes. By comparing the relative abundance of gut microbes between the male (high weight gain, HiWG) and female (low weight gain, LoWG) animals, we have shown that at the phyla, family and genera level, the abundance of microbes existed significantly difference between both groups. At the genera level, the abundance of Candidatus Hepatoplasma and unidentified Chloroplast lower in the LoWG animals than in the HiWG animals, and Lactobacillus and Ligilactobacillus have opposed trend. The abundance of Candidatus Hepatoplasma and unclassfied Chloroplast was associated with the growth traits in the HiWG group, as well as with the expression of glutathione peroxidase and collagen, which were highly expressed in the hepatopancreas and gonads of HiWG group animals and significantly associated with protein digestion, absorption and metabolism of M. rosenbergii and might promote growth and development. These associations were not detected in the female LoWG group.

overall_design: Gut microbiomes associated with hepatopancreatic and gonadal transcriptomes in M.rosenbergii

first: Hongxiang

last: Xu

first: Bao

last: Lou

first: Demin


title: Sequencing of proximal tubular carnitine-acetyl transferase knockout kidney cortex from mouse

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: We report the comparison of normal vs proximal tubular cell specific CrAT knockout kidney cortex by sequencing analysis

overall_design:
CrAT was deleted in proximal tubular cells of mice using Cre/Lox technology (Ggt -CRE). Mice were aged out to 12-24 months when pathology and mitochondrial lipid "overload" were evident.
RNA was isolated by the TRIzol method, libraries and sequencing were done using a Lexogen/Illumina platform.

first: Claudia

last: Kruger

first: Susan

last: Newman

first: Richard

last: Carmouche


title: Multi-omics analysis reveals gut-brain interactions mediating the anti-obesity effect of Akkermansia muciniphila

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Previous studies have implicated a causal role for the gut bacterium Akkermansia muciniphila in counteracting diet-induced obesity and metabolic dysfunctions. However, a systems level understanding of the molecular mechanisms underlying the anti-obesogenic effect of A. muciniphila is lacking. Using fructose-induced obese mice as a model, we carried out multiomics studies to investigate the molecular cascades mediating the effect of A. muciniphila. We found that A. muciniphila colonization in fructose-induced obese mice triggered significant shifts in gut microbiota composition as well as alterations in numerous gut and plasma metabolites and gene expression in the hypothalamus. Among these, we found that the metabolite oleoyl-ethanolamide in the gut and circulation and hypothalamic oxytocin are the key regulators of gut-brain interactions that underlie the A. muciniphila anti-obesity effect. Our multiomics investigation elucidates the molecular regulators and pathways involved in the communication between A. muciniphila in the gut and hypothalamic neurons that counter fructose-induced obesity .

overall_design: Freshly dissected hypothalami were dissociated with papain (Worthington, Lakewood, NJ, USA) for single cell isolation (Brewer and Torricelli, 2007). Single cells were barcoded using single-cell transcriptomes attached to microparticles (STAMPs) followed by generating cDNA library with the Drop-seq protocol by Macosko et al 2015 (Macosko et al., 2015). Cells were suspended in 0.01% BSA-PBS at a final concentration of 100 cells/μl for as previously described (Arneson et al., 2018). Paired-end sequencing data was generated using Illumina NovaSeq 6000 at a sequencing depth of ~40,000 read pairs per cell, with custom length of 26 for read 1 and 76 for read 2 and 8 bp index read for multiplexing.

first: Sung

last: Ha

first: Insook

last: Ahn

first: Thomas

last: Kowal-safron

first: Justin

last: Yoon

first: Graciel

last: Diamante

first: Ingrid

last: Cely

first: Guanglin

last: Zhang


title: BisDemethoxyCurcumin (BDC) loaded H-Ferritin-Nanocages Mediate Regulation of inflammation in Alzheimer’s Disease Patients

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary: Bisdemethoxycurcumin (BDC) might be inflammation inhibitor in AD. BDC is almost insoluble in water, poorly absorbed by the organism, and rapidly degraded. We developed a nanoformulation of BDC based on H-Ferritin nanocages (HFn).

overall_design: The effect BDC-HFn on AD and control PBMCs was tested to evaluate the transcriptomic profile by RNA-sequencing.

first: Stella

last: Gagliardi

first: Marta

last: Truffi

first: Veronica

last: Tinelli

first: Cecilia

last: Pandini

first: Matteo

last: Cotta Ramusino

first: Giulia

last: Perini

first: Alfredo

last: Costa

first: Sara

last: Negri

first: Serena

last: Mazzucchelli

first: Bonizzi

last: Arianna

first: Leopoldo

last: Sitia

last: Busacca

last: Sevieri

first: Alessandra

last: Ricciardi

first: Davide

last: Prosperi

first: Fabio

last: Corsi

first: Cristina

last: Cereda

first: Carlo

last: Morasso


title: Chromatin accessibility changes in Htr6 KO mouse hippocampus

city: Ashburn

first: Shu-Hsien

last: Sheu

state: VA

address: 19700 Helix Drive

institute: Janelia Research Campus/Howard Hughes Medical Institute

summary: 5-hydroxytryptamine receptor 6 is a cilia-restricted serotonin receptor. Ablation of Htr6 causes defects in learning and memory. The study shows that chromatin accessibilty changes in KO mice may underpin these defects.

overall_design: Comparison between wild-type and KO hippocampus

first: David

last: Clapham

first: Séverine

last: Chaumont-Dubel

first: Andrew

middle: L

last: Lemire

first: Lihua

last: Wang

first: Vincent

last: Dupuy


title: Impact of changing mice housing temperature on glucocorticoids' effects on different adipose tissue depots

city: Dresden

first: Holger

last: Henneicke

address: Fetscherstraße 105

country: Germany

institute: Center for Regenerative Therapies Dresden (CRTD)

summary: Elevated serum concentrations of glucocorticoids (GCs) result in excessive lipid accumulation in white adipose tissue (WAT) as well as dysfunction of thermogenic brown adipose tissue (BAT) – ultimately leading to the development of obesity and metabolic disease. Here, we examined the impact of cold exposure on the adverse metabolic effects of chronic GC exposure on adipose tissue in rodents.

overall_design: Male 10-week-old C57BL/6NRj mice were treated with corticosterone (GC) via drinking water or placebo (Ctrl) for 4 weeks while being maintained at 22°C (room temperature) or 13°C (cold temperature). Gene expression of 3 adipose tissue depots [interscapular BAT (iBAT), gonadal WAT (gWAT), subcutaneous WAT (sWAT)] was analysed via RNA seq.

first: Manuel

last: Gado

first: Annett

last: Heinrich

first: Denise

last: Wiedersich

first: Katrin

last: Sameith

first: Andreas

last: Dahl

first: Vasileia

middle: I

last: Alexaki

first: Michael

last: Swarbrick

first: Ulrike

last: Baschant

first: Ingo

last: Grafe

first: Nikolaos

last: Perakakis

first: Stefan

last: Bornstein

first: Martina

last: Rauner

first: Lorenz

last: Hofbauer


title: Identification of the differentially expressed genes in the mouse embryonic dorsal spinal cord from E10.5 to E12.5

city: Shenzhen

first: Peng

last: Han

address: 1088 Xueyuan Avenue, Nanshan District

department: Department of biology

institute: Southern University of Science and Technology

summary:
To identify differentially expressed genes in the developmental mouse dorsal spinal cord, we characterized the global gene expression profiling of mouse embryonic dorsal spinal cord commissural neurons at E10.5, E11.5 and E12.5.
We used the Affymetrix Mouse Exon 1.0 ST Array platform to analyze the gene expression profiling. We included the gene expression data obtained from dorsal spinal cord commissural neuron at different embryonic stage. 2 Biological replicates were performed.

overall_design: Dorsal spinal cord commissural neurons were labeled with eGFP by crossing Wnt1-cre with Rosa26mTmG mice. Embryos were identified as E0.5 when a copulatory plug was observed at noon. At E10.5, E11.5 and E12.5, spinal cords were dissected and GFP+ dorsal spinal neurons were collected by fluorescence-activated cell sorting (FACS). RNA from different samples were used for microarray analysis.

first: Sheng-Jian

last: Ji

first: Samie

last: Jaffrey


title: Transcriptome analysis of wild-type and Csf2-/- bone marrow-derived macrophages during legionella pneumophila infection

city: philadelphia

first: Sunny

last: Shin

state: Pennsylvania

address: 3610 Hamilton Walk, Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

summary: Pathogens have evolved a wide range of strategies to allow survival and subsequently cause diseases in human, however, it’s still poorly understood how the immune system operates successfully to overcome pathogen-induced disturbance and enable robust immune responses against infection. The intracellular bacteria Legionella pneumophila has the ability to block host translation which causes global protein synthesis blockade in the target cells, but the host can still strongly evoke innate immune responses. We previously found that IL-1 signaling was critical for innate immunity during Legionella infection. Here, we further clarify that IL-1 signaling acts directly on alveolar epithelial cells, which potently drives granulocyte-macrophage colony-stimulating factor (GM-CSF) production by these cells, and importantly, GM-CSF signaling fundamentally promotes inflammatory immune responses in myeloid cells through cell-intrinsic transcriptional regulation via JAK2/STAT5 pathway. Our findings reveal that lung epithelial cells act as a key intermediator to facilitate communication between infected cells and bystander cells which is essential for antimicrobial defense.

overall_design: Comparison of mRNA profiles between WT and Csf2-/- BMDMs with or without legionella pneumophila LP02flaA infection at 12 h by RNA sequencing analysis (two genotypes and two treatments in triplicate, a total of 12 samples)

first: Xin

last: Liu


title: RNA-sequencing in  for Low, high or high density+PTPRK-deleted HeLa cells

status: Public on Sep 02 2022

city: Daejeon

first: Hyun

middle: Ahm

last: Sohn

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

summary: Density-dependent regulation of cell growth is presumed to be caused by cell-cell contact, but the underlying molecular mechanism is not yet clearly defined. Our goal is to identify receptor-type protein tyrosine phosphatase-kappa (PTPRK) is an important regulator of cell contact-dependent growth inhibition and to elucidate the related mechanism regulated by PTPRK with analyzing transcriptome-based datasets generated from different condition of cell density combined with manipulation of R-PTP-kappa expression using siRNA.

overall_design: We analyzed mRNA profiles in HeLa cells with Low density, High-density+siCtrl, High-density+siPTPRK, High+orthovanadate(OVA)

middle: A

first: Young

last: Yeom

first: Dong

last: Lee


title: Single nuclei analyses of supraspinal neurons in the mouse brain

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

summary: The mammalian brain contains numerous neurons distributed across forebrain, midbrain, and hindbrain that project axons to the lower spinal cord and work in concert to control movement and achieve homeostasis. Extensive work has mapped the anatomical location of supraspinal cell types and continues to establish specific physiological functions. The patterns of gene expression that typify and distinguish these disparate populations, however, are mostly unknown. Here we combined retrograde labeling of supraspinal cell nuclei with fluorescence activated nuclei sorting and single nuclei RNA sequencing analyses to transcriptionally profile neurons that project axons from the mouse brain to lumbar spinal cord. We identified fourteen transcriptionally distinct cell types and used a combination of established and newly identified marker genes to assign an anatomical location to each. To validate the putative marker genes, we visualized selected transcripts and confirmed selective expression within lumbar-projecting neurons in discrete supraspinal regions. Finally, we illustrate the potential utility of these data by examining the expression of transcription factors that distinguish different supraspinal cell types and by surveying the expression of receptors for growth and guidance cues that may be present in the spinal cord. Collectively these data establish transcriptional differences between anatomically defined supraspinal populations, identify a new set of marker genes of use in future experiments, and provide insight into potential differences in cellular and physiological activity across the supraspinal connectome.

overall_design: Single nuclei RNA sequencing of neurons in the mouse brain that were retrogradely labeled from the lumbar spinal cord

middle: G

first: Pantelis

last: Tsoulfas

first: Zachary

last: Beine

first: Wang

last: Zimei


title: Morphological and Molecular Defects in Human Three-Dimensional Retinal Organoid Model of X-Linked Juvenile Retinoschisis

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

summary: The goals of this study are to analyze the effects of RS1 mutation on retinal transcriptome profiling during retina differentiation. We used next generation sequencing to analyze the retinal mRNA profiles in a panel of time-course differentiated 3D retinal cups (RCs) from control donor- and XLRS patient-derived iPSCs, as well as 150-day differentiated RCs from CRISPR/Cas9-reparied patient-derived iPSCs. The transcriptomes of control-RCs and patient-RCs considerably diverged along the time course of differentiation, with the difference becoming more pronounced at the later time points. In contrast, analysis of repaired RCs revealed transcriptomes that were highly similar to those of control-RCs and significantly different from those of patient-RCs. Because RS1 is only expressed in later stage of differentiation, we focued on days 90, 120, and 150 post-induction to identify the genes whose expression was reduced at least 2-fold in patient-RCs. Among all of these genes, 326 genes were overexpressed in normal RCs at all of these stages, emphasizing their importance. According to GSEA annotation, nine out of these 326 genes were implicated in eye development. Among these nine genes, the expression of RS1, IQCB1, and OPA1 was rescued in CRISPR repaired RCs. The relative loss of expression became even more prominent in later stages of retinal differentiation. Our transcriptome analysis revealed significant changes in gene expression between patient-derived and control-RCs that become more pronounced at the later stages of development. This implies that RS1 is essential for normal retinal development at the systemic level. These results reflect the progressive nature of the disease phenotypes observed in RS-1-mutant RCs, mirror the observed ciliary phenotype, and reveal potential links of XLRS to other hereditary retinopathies.

overall_design: mRNA profiles of 3D retinal organoids at Day 0, 50, 90, 120, 150 post-differentiation induction from control donor- and XLRS patient-derived iPSCs, as well as from Day 150 3D retinal organoids differentiated from CRISPR/Cas9-corrected patient-derived iPSCs, were generated by deep sequencing using Illumina HiSeq 2000.

first: Ping-Hsing

first: Kang-Chieh

last: Huang

first: Mong-Lien

last: Wang

first: Shih-Hwa

last: Chiou


title: Microarray analysis of long noncoding RNAs in exosomes from SNU-668 Erastin-resistant cells and parental SNU-668 cells

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

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

summary: a microarray analysis of long noncoding RNAs was performed in exosomes from SNU-668 Erastin-resistant cells and parental SNU-668 cells

overall_design: lncRNA profiles of  exosomes from SNU-668 Erastin-resistant cells and parental SNU-668 cells

first: Mingzhe


title: Transcriptomic and proteomic studies of condylar ossification of the temporomandibular joint in porcine embryos

city: BeiJing

first: lei

last: xiang

address: No. 31, Xinjiekou east street, Xicheng district

institute: Jishuitan Hospital

summary: Objective The purpose of this study was to find the key regulatory genes and proteins in condylar ossification of temporomandibular joint (TMJ) by transcriptomics and proteomics in porcine embryos. Method A total of 12 miniature pig embryos (6 in each group) at E45 and E85 days were used in this study. Six embryos for tissue sections (3 in each group) . The remaining six embryos were cut down the condyle along the parallel line between the lowest point of the sigmoid notch and the highest point of the condyle, and each condylar tissue sample was divided into two parts averagely. After RNA extraction, library construction and sequencing, one part tissue was analyzed by mapping to compare the differential expression of mRNA before and after ossification of embryonic condylar tissue. Another tissue was analyzed by protein extraction, enzymolysis and mass spectrometry to compare the differential expression of protein before and after ossification of embryonic condylar tissue. Finally, the differential genes and proteins were analyzed by GO and KEGG enrichment analysis. The differentially expressed genes in transcriptome and proteomic analysis were verified by QPCR. Result A total of 25322 genes were detected by transcriptome analysis, and there were 19584 differential genes between E85 days and E45 days. There are 1592 differential genes were screened to meet the Fold change≥2 or ≤0.5 of which 1086 genes were up-regulated and 506 genes were down-regulated in E85 days compared with E45 days. A total of 4613 proteins were detected by proteomic analysis, there were 419 differential proteins between E85 and E45 days, including 313 up-regulated proteins and 106 down-regulated proteins. A total of 37 differentially expressed genes/proteins were found by cross transcriptome and proteomic analysis. QPCR analysis showed that 13 of 15 genes were consistent with transcriptome analysis. Conclusion Condylar transcriptome and proteomic analysis during the development of temporomandibular joint in miniature pigs revealed the regulatory genes/proteins of condylar ossification. These regulatory genes/proteins can provide basic data for human TMJ development research and disease treatment.

overall_design: Comparative gene expression profiling analysis of mandibular condyle in 45 day old and  85 day old miniature pig embryos.

first: Lei

last: Xiang

first: Yongfeng

last: Li

first: Xuewen

first: HuaWei

first: Ping

last: Chang

first: Xiaodan

last: Mu

first: Tengyue

last: Tianteng

first: Min

last: Hu


title: Embryo/ larval toxicity and key gene expression signatures of maternally transferred hexabromocyclododecane (HBCD) in Pimephales promelas

city: Sasaktoon

first: Susari

last: Malala Irugal Bandaralage

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

summary: Hexabromocyclododecane (HBCD) is a brominated flame retardant that presents a threat to aquatic organisms as it can be maternally transferred and has been reported to hinder development and survival in early-life stage (ELS) fish. However, little is known to date regarding the molecular mechanisms that drive the toxicity of HBCD. This study examined the apical and molecular response patterns of maternally transferred HBCD in fathead minnow (Pimephales promelas) larvae at seven (whole transcriptome) and 14 (apical and physiological) days post-fertilization. The larvae sampled at 7dpf for whole transcriptomics analysis revealed dysregulation of pathways involved in membrane integrity (inhibition of calcium channel) and metabolic processes (downregulation of amino acid, glucose, and lipid biosynthesis), while the larvae reared for 14 days exhibited a significant decrease in survival at the highest treatment condition. These results indicate that maternal transfer of HBCD is of concern in fish, which may act through indirect mechanisms involving the inhibition of membrane transport leading to disruption in metabolic processes, collectively resulting in energy depletion and subsequently mortality.

overall_design: Adult fathead minnows were exposed to solvent control (ethanol-evaporated), 11.5, 36.4, 106 mg hexabromocyclododecane /kg food (wet weight) for 49 days. Fertilized eggs were obtained between day 25 and 42 of the adult dietary HBCD exposure. Fathead minnow larvae were sampled 7 days post-fertilization (pools of 20 larvae per sample) at measured concentrations of <LOD, 0.576, 1.77, 5.89 mg hexabromocyclododecane/ kg (wet weight). mRNA profiles were done on composite samples of whole fathead minnow larvae from the solvent control, low, and medium treatment conditions (the high treatment group was not subjected to this analysis due to significant mortality. Treatment groups have 5 replicates each.

last: Irugal Bandaralage

first: Juan

last: Bertucci

first: Alper

last: Alcaraz

first: Derek

last: Green

first: Anita

last: Masse

first: Jessica

last: Ewald

first: Jiangou

last: Xia

first: Doug

last: Crump

first: Niladri

last: Basu

first: Natacha

last: Hogan

first: Markus

last: Hecker


title: Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice [human]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: We analyzed the expression profiles of human and mouse meningiomas (driven by NF2 loss, YAP1-MAML2, TRAF7/KLF4/SMO1/AKT1, or constitutively active non-fusion YAP1). We found that YAP1-MAML2 meningiomas resemble NF2mutant tumors and constitutively exert de-regulated YAP1 activity that is dependent on the interaction with TEADs.

overall_design: HEK 293 cells were grown in 48 well plates, transfected with indicated RCAS plasmids and total RNA was isolated 48 hours post-transfection

first: Frank

last: Szulzewsky

first: Eric

last: Holland


title: Balanced act of a leading strand DNA polymerase specific domain and its exonuclease domain promotes genome-wide replication fork symmetry

city: new york

first: clemence

last: claussin

state: New York

address: 1275 York Avenue

department: molecular biology

institute: Memorial sloan kettering cancer center

summary: During genome replication, the leading strand DNA polymerase conducts continuous synthesis over long stretches of DNA within each replicon. Processive DNA synthesis supports symmetric progression of sister replication forks and efficient genome duplication. To address the mechanisms underlying leading strand polymerase-mediated synthesis, we examine one of its conserved domains, referred to as POPS, in the budding yeast Pol2 enzyme. We provide evidence that POPS supports replication fork symmetry and efficient genome replication via balancing the function of the Pol2 exonuclease domain. We found that the defective growth, slow S phase progression, and impaired genome synthesis associated with a POPS mutation were rescued by abolishing the Pol2 exonuclease activity. The suppressive effects further extended to the increased DNA re-arrangements in the POPS mutant and its negative genetic interactions with mutants of other genome maintenance factors. Significantly, our single molecule replicon-seq data demonstrate that the POPS mutant exhibited genome-wide replication fork asymmetry, and this defect was improved by eliminating the Pol2 exonuclease activity, thus providing a basis for its rescuing of a range of POPS mutant phenotypes. Collectively, these data suggest a model in which balanced activity between a unique Pol2 catalytic domain, and its exonuclease domain facilitates replication fork symmetry and genome maintenance.

overall_design: MCM4 was fused to Miccrococcal nuclease ( MNase) to generate DNA double strand break at the site of replisomes. DNA ends are repaired and MinION compatible DNA adaptors are ligated. Full length molecules are sequenced. Because cells have been released from a G1 arrest in presence of BrdU, we can select for replicon reads (reads that contain BrdU) informatically using DNAscent.

first: Xiangzhou

last: Meng

first: Clémence

last: Claussin

first: Gemma

last: Regan-Mochrie

first: Lestyn

last: Whitehouse

first: Xiaolan

last: Zhao


title: Micheliolide exerts effects in MPNs by inhibiting STAT3/5 activation via covalently binding to STAT3/5 proteins

city: Tianjin

first: Huijun

last: Huang

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
The JAK1/2 inhibitor ruxolitinib is a cornerstone of management for some subsets of BCR-ABL negative myeloproliferative neoplasms (MPNs), but some patients respond suboptimally to ruxolitinib.Here, we evaluated the efficacy of micheliolide (MCL) alone or in combination with ruxolitinib in JAK2V617F mutated MPN cell lines, MPN patient primary samples and Jak2V617F knock-in mouse model and found that MCL was able to exert effective therapeutic effects in MPNs.
To gain insights of the molecular mechanisms by which MCL exerts effects, we then performed gene expression profiling analysis using data obtained from RNA-seq of UKE1 cells following treatment with MCL and/or ruxolitinib.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for UKE1 cells which were pre-stimulated by TNF-α to mimic the pro-inflammatory micro-environment in vivo, and subsequently treated with MCL, ruxolitinib, or MCL combined with ruxolitinib, respectively.

first: Jinqin

last: Liu

first: Zhijian

last: Xiao


title: Microarray analysis of long noncoding RNAs in primary human keratinocytes in response to CaCl2 stimulation

first: Ming

last: Ma

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

summary: A microarray analysis of long noncoding RNAs was performed in primary human keratinocytes in response to CaCl2 stimulation

overall_design: lncRNA profiles of primary human keratinocytes in response to CaCl2 stimulation over time.

first: Chunxiao

last: Li


title: Transcriptional profilling of liver from C57BL/6 wildtype and PPARα-knockout mice treated with PFOA and GenX after 20 weeks of high-fat diet

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Perfluoroalkyl substances (PFAS) are man-made chemicals with suspected endocrine-disrupting properties. Exposure to perfluorooctanoic acid (PFOA) has been linked to disturbed metabolism via the liver, although the exact mechanism is not clear. Moreover, information on the metabolic effects of the new PFAS alternative GenX is limited. We tested whether low-dose exposure to PFOA and GenX induces metabolic disturbances, including NAFLD, dyslipidemia, and glucose tolerance in mice and studied the involvement of PPARα. To this end, male C57BL/6J wildtype and PPARα−/− mice were given 0.05 or 0.3 mg/kg bw/day PFOA, or 0.3 mg/kg bw/day GenX next to a high-fat diet for 20 weeks. RNA sequencing was performed on liver, next to thorough assesment of metabolic parameters. RNA sequencing revealed that whereas the effects of GenX are entirely dependent on PPARα, effects of PFOA are mostly dependent on PPARα. In the absence of PPARα, the involvement of PXR/CAR becomes more prominent. Exposure to high-dose PFOA in mice decreased body weights and increased liver weights in wildtype and PPARα−/− mice. High-dose but not low-dose PFOA reduced plasma triglycerides and cholesterol, which for triglycerides, showed PPARα dependency. PFOA and GenX increased hepatic triglycerides in a PPARα-dependent manner. Overall, we show that long-term and low-dose exposure to PFOA and GenX disrupts lipid metabolism in mice. Whereas the effects of PFOA are mediated by multiple nuclear receptors, effects of GenX are entirely mediated by PPARα. Our data underscore the potential of PFAS to disrupt metabolism by altering signaling pathways in the liver.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from livers of male C57BL/6 wildtype and PPARα-knockout mice treated with 0.05 mg/kg bw/day or 0.3 mg/kg bw/day PFOA, or 0.3 mg/kg bw/day next to a high-fat diet for 20 weeks (n=4/group).

first: Brecht

last: Attema

first: Aafke

last: Janssen

first: Deborah

last: Rijkers

first: Evert

last: van Schothorst

first: Sander

last: Kersten


title: Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice

first: Sonali

last: Arora

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

overall_design: Refer to individual Series


title: 10X single-cell RNA-sequencing profiling of hepatic non-parenchymal cells from LPS or PBS-administrated Hlj1 knockout and littermate wild-type mice.

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

summary: Hlj1 knockout mice survive better than wild-type mice when injected with a lethal dose of lipopolysaccharide (LPS). As the liver is the major source for production of inflammatory cytokines and is also responsible for bacterial and toxin clearance when hosts are exposed to pathogens, we asked whether Hlj1 participated in immune modulation in the liver.  We isolated and sequenced each hepatic non-parenchymal cells from these mice, and identified Hlj1 as the key regulator to enhance IFN-g-related signaling in NK cells.

overall_design: Hlj1 wild-type (WT) and Hlj1 whole-body knockout (KO) mice are intraperitoneally injected with 20 mg/kg LPS or PBS as control and sacrificed 8 hours post injection. Largest liver lobe of n=3 mice from same group are pooled together and grinded to isolate and purify non-parenchymal cells, which were prepared for sc-RNA sequencing using the 10X chromium platform.

first: Wei-Jia

last: Luo

first: Chia-Ching

last: Chang

first: Kang-Yi

last: Su


title: Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism

city: Manchester

first: Matthew

last: Hepworth

address: AV Hill Building

country: United Kingdom

institute: University of Manchester


title: Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism [2]

summary: IgA+ Plasma Cells were sort-purified from the small intestinal lamina prorpia of C57BL/6 mice at four Zeitgeber time points (ZT0, 6, 12 and 18). RNA extracted from these samples was subjected to bulk RNA seq to identify time of day differences in IgA+ PC gene expression.

overall_design: Each sample represents IgA+ PC sort-purified from the small intestine of one indivisual animal. Main comparisons are transcriptional signatueres over the course of a circadian day (ZT0, 6, 12 and 18).

first: Hugo

last: Penny


title: High resolution definition of the Staphylococcus aureus WalKR regulon

status: Public on Sep 01 2022

city: Melbourne

first: Tim

last: Stinear

state: Victoria

address: 792 Elizabeth St, Melbourne

country: Australia

institute: University of Melbourne


title: Single Cell RNA Sequencing Analysis of MCL Patient Samples

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: Mantle cell lymphoma (MCL) is a rare, highly heterogeneous type of B-cell non-Hodgkin’s lymphoma (NHL) driven by multiple genetic mutations disrupting cell cycle regulation and DNA damage response. Despite advances in therapy, novel treatment approaches are needed especially for highly proliferative MCL which has a particularly progressive clinical course even in the era of Bruton’s tyrosine kinase therapy. The sumoylation pathway is known to be upregulated in many cancers including lymphoid malignancies. However, little is currently known about the role of the sumoylation pathway and its oncogenic potential in MCL. We found extensive upregulation of the sumoylation pathway in MCL, particularly at the level of the E1 enzymes SAE1 and SAE2, with elevated expression levels of sumoylation enzyme components showing a worse prognosis and a strong positive correlation with cell cycle associated genes. Targeting the sumoylation pathway with TAK-981, a first in class sumoylation inhibitor currently being investigated in a clinical study of B-cell NHL in combination with rituximab (NCT04074330), resulted in potent loss of sumoylation in MCL cells with significant activity in in-vitro and in vivo models of MCL, including ibrutinib resistance cases. We found mitotic dysregulation to be an important, although not all encompassing mechanism of cell death upon loss of sumoylation of TAK-981 in MCL cells. We uncovered a diverse sumoylation program upon mitosis entry that was significantly reduced with TAK-981. Centromeric localization of the well known sumoylation substrate topoisomeraseIIA (TopIIA) was significantly abrogated upon mitosis entry, likely contributing at least in part to the mitotic dysregulation seen in MCL cells. This mechanism is highly relevant as TopIIA is significantly upregulated in MCL with SAE1/2 overexpression. Our study, in addition to the recently described immunomodulatory activity of TAK-981, not only validates SAE1/2 as a therapeutic target in MCL but also opens the door to further mechanistic work to uncover how to best use desumoylation therapy to treat MCL and other lymphoid malignancies.

overall_design: 4 Samples were collected from 4 patients.  No reference or control groups are included.


title: Model Establishment of Mice with Oxaliplatin-induced Hepatic Sinusoidal Obstruction Syndrome

city: Wuhan

first: xinwei

last: CHENG

state: Hubei province

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital, Tongji Medical college, Huazhong University of Science and Technology

summary: To further explore to mechanisms of oxaliplatin-induced hepatic sinusodial obstruction syndrome, we established a mouse model of OXA-induced HSOS and the difference of mRNA expression level between normal mice and model mice was detected.

overall_design: Two-condition experiment, control vs model mice. Biological replicates: 4 control replicates, 4 HSOS model replicates.

first: Chen

last: Zhu

first: Xinwei

last: Cheng


title: Genome-wide reduction in chromatin accessibility and unique transcription factor footprints in endothelial cells and fibroblasts in scleroderma skin

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: We assessed genome-wide chromatin accessibility and transcription factor footprinting in endothelial cells and fibroblasts isolated from skin biopsies from healthy subjects and diffuse cutaneous scleroderma patients.

overall_design: ATAC-seq analysis of endothelial cells and fibroblasts in healthy controls and diffuse cutaneous systemic sclerosis patients

middle: H

first: Pei

last: Tsou


title: Epigenome programming by H3.3K27M mutation creates a dependence of pediatric glioma on SMARCA4

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Patients with diffuse midline gliomas-H3K27-altered (DMG) display a dismal prognosis. However, the molecular mechanisms underlying DMG tumorigenesis remain poorly defined. Here we show that SMARCA4, the catalytic subunit of mammalian SWI/SNF chromatin remodeling complex, is essential for the proliferation, migration and invasion of DMG cells and tumor growth in patient-derived DMG xenograft models. SMARCA4 co-localizes with SOX10 at gene regulatory elements (GRE) to control the expression of genes involved in cell growth and extracellular matrix (ECM). Moreover, SMARCA4 chromatin binding is reduced upon depletion of SOX10 or H3.3K27M, a mutation occurring in about 60% DMG tumors. Furthermore, the SMARCA4 occupancy at enhancers marked by both SOX10 and H3K27 acetylation is reduced the most upon depleting the H3.3K27M mutation. Taken together, our results support a model in which epigenome reprogramming by H3.3K27M creates a dependence on SMARCA4-mediated chromatin remodeling to drive gene expression and the pathogenesis of H3.3K27M DMG.

overall_design: The CUT&RUN experiments were conducted in WT, BRG1 KO, SOX10 KO, H3.3K27M KO DIPG6/17 cells. The markers performed by CUT&RUN methods in DIPG cells included BRG1, SOX10, H3K4me3, H3K27Ac and H3.3K27M.  For the regulation of gene expression, we performed total RNA-seq experiments in WT, BRG1 KO DIPG6/17 cells.

first: Yan

last: Mo

first: Shoufu

last: Duan

first: Xu

last: Hua


title: High resolution definition of the Staphylococcus aureus WalKR regulon [ChIP-seq]

summary: Here, we use a panel of defined walKR mutants and functional genomics including ChIP-seq to confirm a high-resolution consensus WalR DNA-binding motif and characterise a 61-gene direct regulon

overall_design: FLAG-tagged bacterial DNA-binding proteins under inducible expression in Staphylococcus aureus, to faciltate  immunoprecipitation DNA-sequencing (ChIP-seq)

first: Liam

last: Sharkey

first: Ian

last: Monk

first: Torsten

last: Seemann


title: On-treatment transcriptional profiling in HER2+ inflammatory breast cancer

city: Boston

first: Beth

last: Overmoyer

state: MA

address: 450 Brookline Avenue

department: Susan F. Smith Center for Women’s Cancers

institute: Dana-Farber Cancer Institute

summary: Inflammatory breast cancer (IBC) is a rare and understudied disease, with 40% of cases presenting with HER2-positive IBC. Within a cohort of newly diagnosed patients with HER2-positive IBC, we sought to (i) assess the pathologic complete response (pCR) rate of short-term neoadjuvant dual-HER2-blockade and paclitaxel, (ii) define baseline and on-treatment transcriptional profiles of tumor biopsies that are associated with pCR, and (iii) identify biologic pathways that may explain the effect of neoadjuvant therapy on pathologic tumor response.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of tumor biopsies

first: Sonia

last: Pernas


title: Novel Regulators and Developmental Pathways of Pituitary Thyrotrope Subpopulations

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

address: 101 Nicolls Road

institute: Stony Brook University

summary: The pituitary gland regulates growth, metabolism, reproduction, the stress response, uterine contractions, lactation, and water retention.  It secretes polypeptide hormones in response to hypothalamic input, end organ feedback, and diurnal cues.  The mechanisms by which pituitary stem cells are recruited to proliferate, maintain quiescence or differentiate into specific cell types, especially thyrotropes, are not well understood.  We utilized single-cell RNA sequencing in juvenile P7 mouse pituitary cells to identify transcription factors in pituitary stem and endocrine populations, with a focus on thyrotrope subpopulations.  We first identified common gene regulatory networks activated in proliferating stem and proliferating endocrine cells.  We ascertained Shox2 and Sox14 as candidate regulators of pars distalis and pars tuberalis thyrotropes, respectively, and subsequently found reduced hormone expression in Sox14-knockout pars tuberalis thyrotropes.  We further discovered dual-identity cells expressing both POU1F1 and NR5A1 and demonstrated that approximately one-third of pars distalis thyrotropes are descended from NR5A1-expressing cells, typically considered gonadotrope progenitors.  We have therefore used single-cell transcriptomics to identify novel developmental mechanisms regulating the specification and hormone expression in thyrotrope subpopulations.

overall_design: We performed scRNAseq of 7-day-old (P7) murine pituitary cells in two concurrently processed pools using Tshb-Cre; Rosa26-Eyfp FACS-purified pituitary cells combined with control (Cre-negative) unsorted total pituitary cells to capture all pituitary populations with increased proportion of rare Tshb-lineage populations.  We also selected P7 pituitary glands to capture increased proportions of stem cells which are more abundant at young ages.

middle: Y

first: Lucy

last: Menage

first: Karine

last: Rizzoti

first: Greg

last: Hamilton

first: Typhanie

last: Dumontet

first: Kaitlin

last: Basham

first: Alexandre

middle: Z

last: Daly

first: Michelle

last: Brinkmeier

first: Mathias

last: Treier

first: John

last: Cobb

first: Alessio

last: Delogu

first: Robin

last: Lovell-Badge

first: Gary

middle: D

last: Hammer

first: Sally

last: Camper


title: A novel repressor for expression of a type 6 protein secretion system links nitrogen signaling with beneficial plant-microbe interactions

city: Bremen

first: Xun

last: Jiang

state: Bremen

address: Leobener Straße 5

department: Department of Microbe-Plant Interactions

institute: University of Bremen

summary:
To investigate the regulon of the novel transcriptional regulator TssR discovered in our study
We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type Azoarcus olearius sp. BH72 and tssR deleted mutant cultured under microaerobic conditions with additional ammonium

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and BHΔtssR cultured under non-nitrogen-fixing conditions


title: Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice [mouse]

first: Sonali

last: Arora

overall_design: Gene expression data from mouse RCAS-YAP1-MAML2-v2 or RCAS-NLS-2SA-YAP1-derived meningioma-like tumors (either extra-cranial, extra-axial, or intra-ventricular tumors).

first: Frank

last: Szulzewsky

first: Eric

middle: C

last: Holland


title: Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism [1]

first: Matthew

last: Hepworth

summary: IgA+ Plasma Cells were sort-purified from the small intestinal lamina prorpia of mice with a B cell lineage-intrinsic deletion of Arntl (Mb1 Cre+/- x Arntl fl/fl) or Cre negative littermate controls (also deisgnated WT and KO), at two Zeitgeber time points (ZT0 and ZT12). RNA extracted from these samples was subjected to bulk RNA seq to identify time of day differences and to compare role of Arntl expression in this context.

overall_design: Each sample represents IgA+ PC sort-purified from the small intestine of one indivisual animal. Main comparisons are transcriptional signatueres at ZT 0 vs ZT12 (time of day) and in WT (Mb1 Cre-/- x Arntl fl/fl) vs KO (Mb1Cre+/- x Arntl fl/fl) cells.

first: Hugo

last: Penny

middle: R


title: Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs (NHEJ)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Mesenchymal Stromal Cells (MSCs) have been employed in vitro to support HSPC expansion and in vivo to promote Hematopoietic Stem and Progenitor Cells (HSPCs) engraftment. Based on these studies, we developed an MSC-based co-culture system to optimize transplantation outcome of CRISPR-Cas9 gene-edited (GE) human HSPCs. We show that bone marrow (BM)-MSCs produce several hematopoietic supportive and anti-inflammatory factors capable to alleviate the proliferation arrest and mitigate the apoptotic and inflammatory programs activated in GE-HSPCs, improving their expansion and clonogenic potential in vitro. The use of BM-MSCs resulted in superior human engraftment and increased clonal output of GE-HSPCs contributing to the early phase of hematological reconstitution in the peripheral blood of transplanted mice. In conclusion, our work poses the biological bases for a novel clinical use of BM-MSCs to promote engraftment of GE-HSPCs and improve their transplantation outcome.

overall_design: CRISPR-Cas9 gene-edited (GE)-HSPCs cultured in presence or not with Mesenchymal Stromal Cells (MSCs) and transplanted into NSG mice. Non-Homologous End Joining (NHEJ) tracking performed on samples from peripheral blood (PB) and bone marrow (BM) of xenotransplanted mice.

first: Stefania

last: Crippa

first: Anastasia

last: Conti

first: Valentina

last: Vavassori

first: Ivan

last: Merelli

first: Raffaella

last: Di Micco

first: Maria

middle: E

last: Bernardo


title: SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis.We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing.SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT，PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis.We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.

first: Junjie

last: Zhou

first: Wenhao

last: Chen

first: Qianwen

last: He

first: Dong


title: Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs.


city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary: ChIP-seq for the SDC-3 subunit of the dosage compensation complex in wild-type N2 C. elegans and Hi-C in C' elegans strains with deleted rex and extra rex sites

overall_design: ChIP-Seq and Hi-C

first: Will

middle: S

last: Kruesi

first: Nicholas

middle: J

last: Fuda

first: Miki

last: Okada

first: Katjusa

last: Brejc


title: Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs (BAR-Seq)

first: Stefano

overall_design: CRISPR-Cas9 gene-edited (GE)-HSPCs cultured in presence or not with Mesenchymal Stromal Cells (MSCs) and transplanted into NSG mice. BAR-Seq clonal tracking performed on samples from peripheral blood (PB) and bone marrow (BM) of xenotransplanted mice.


title: Effect of LSD1 inhibitor B35 on gene expression of A549  cells

city: Shengyang

first: 海蓝

last: 黄

state: Liaoning

address: No.103,Wenhua Street, Shenhe District

institute: Shenyang Pharmaceutical University

summary: To investigate the antitumor mechanism of LSD1 inhibitor B35 on NSCLC, we collected  A549 cells treated with B35(2μM) for 72 hours, then we  performed gene expression profiling analysis using data obtained from RNA-seq of control cells or B35 treatment group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells under control or treated with LSD1 inhibitor B35

first: Hailan

last: Hunag

first: Yanting

last: Gu


title: Evaluation of human group 2 innate lymphoid cells (ILC2) in Dengue Fever

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

institute: University of Oxford

summary: Transcriptomic profiling of blood ILC2 from dengue fever patient groups and comparator healthy controls

overall_design: Peripheral blood mononuclear cells (PBMCs) were separated from healthy, patients with dengue fever (DF) and dengue hemorrhagic fever (DHF) and ILC2 cells were isolated by fluorescence-activated cell sorting

first: Clare

last: Hardman

first: Neelika

last: Malavige

first: Graham

last: Ogg


title: High resolution definition of the Staphylococcus aureus WalKR regulon [RNA-seq]

first: Tim

last: Stinear

first: Liam

last: Sharkey

first: Ian

last: Monk

first: Torsten

last: Seemann


title: mRNA sequencing of primary tumors resected from mice

city: La Jolla

first: Katherine

last: Birmingham

state: Ca

address: 2880, Torrey Pines Scenic Drive

department: Bioengineering

institute: University of California San Diego

summary: Mice were injected with MDAMB231 cells (weakly adherent, strongly adherent, or unsorted control) that were allowed to grow into a tumor for 6 weeks. After 6 weeks, the mice were sacrificed and the tumors were resected. mRNA sequencing was performed on dissociated cells from the tumors.

overall_design: Examination of mRNA sequencing of tumors from strongly adherent, weakly adherent, and unsorted MDAMB231 cells.

first: Jeremy

last: Tuler

first: Adam

last: Engler

first: Benjamin

last: Yeoman


title: Comparative single-cell genomics uncovers evolutionarily conserved features and therapeutic targets in triple-negative breast cancer fibroblasts

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

summary: We performed scRNA-seq analysis of fibroblasts from murine and human TNBCs. We observed three CAF subtypes in mouse TNBC: two transcriptionally distinct CAFs that were found intermingled and adjacent to tumor cells, and distal CAFs that were located further away from tumor cells. All three CAFs appear to evolve from normal resident fibroblasts/pericytes by activation of Pdgf and Tgfb receptors in fibroblasts in parallel with reciprocal upregulation of ligands in tumor cells and other tumor microenvironment cells. Additionally, extracellular matrix, glycolytic and mitochondrial respiratory genes were strongly upregulated in all three CAFs. Murine pancreatic CAFs displayed matching subtypes. Human TNBCs displayed three analogous CAF subtypes, although only a subset of marker genes are conserved. Finally, the upregulation of specific extracellular matrix genes in different CAF subtypes provides a basis for developing selective CAF-targeted therapeutics.

overall_design: scRNAseq was performed on a total of thirteen samples: three human samples and ten mouse samples. The human tissue samples of triple negative breast tumors were provided by the NCI Cooperative Human Tissue Network. The murine breast  tumor samples were harvested from mammary glands of two transgenic mouse models: a) MMTV-PyMT and b) C3(1)-Tag SV40. The pancreatic tumor came from the Ptf1⍺-CreERTM; LSL- KRASG12D strain.  .

first: Ana

middle: P

last: Delgado

first: Scott

last: Powers


title: Parental and persister cells generated human cancer cells

city: Memphis

first: Douglas

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Gene expression of PBMCs is altered during TB infection.

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

summary: Total RNA from PBMCs isolated from TB patients and healthy individuals was subjected to RNASeq analysis. The samples among two groups were compared to analyze differentially expressed genes.

overall_design: Transcriptome from 6 TB patients and 6 healthy individuals were compared by RNASeq.

first: Ranjeet

last: Mahla

first: Akhilesh


title: Global transcriptomic analysis of cells infected with Ebola virus (EBOV)

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University


title: ChIP-Seq of H3K27ac in Wild Type (WT),  and Actb-/- (KO) Mouse Embryonic Fibroblasts

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Genome-wide ChIP-Seq of H3K27ac in WT and β-actin KO MEFs to assess the role of nulcear actin in regulating histone acetylation

overall_design: ChIP-Seq was performed for 6 samples (3 replicates of KO cells, 2 replicates of WT cells and one input control)

first: Syed

last: Mahmood

first: Nadine

last: ElSaid


title: Whole transcriptome sequencing of 3T3L1 cells treated with butyrylation inhibitor LTK-14A

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: Study of the major pathways and genes affected by the butyrylation inhibitor LTK-14A in 3T3L1 cells

overall_design: Comparison of gene expression in 3T3TL1 cells made to undergo differentiation in presence of LTK-14A with gene expression patttern of 3T3L1 cells differentiating in the absence of any inhibitor and in presence of DMSO as solvent control

first: Tapas

middle: K

last: Kundu

first: Aditya

last: Bhattacharya

first: Madavan

last: Vasudevan


title: Next Generation Sequencing Analysis of Pparafl/fl and PparaΔIE intestinal transcriptomes

city: Bethesda

first: Yuhong

last: Luo

state: MD

address: 37 Convent Dr

department: NCI

institute: NATIONAL INSTITUTES OF HEALTH

summary: Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic diseases globally and nonalcoholic steatohepatitis is its progressive stage with limited therapeutic options. Here a role for intestinal peroxisome proliferator-activated receptor α (PPARα)-fatty acid binding protein 1 (FABP1) in obesity-associated metabolic syndrome, fatty liver and nonalcoholic steatohepatitis via modulating dietary fat absorption was uncovered. Intestinal PPARα is highly activated accompanied by marked upregulation of FABP1 by high-fat diet (HFD) in mice and obese humans. Intestine-specific PPARα or FABP1 disruption in mice decreases HFD-induced obesity, fatty liver and nonalcoholic steatohepatitis and intestinal PPARα disruption fails to further decrease obesity and NASH. Chemical PPARα antagonism improves metabolic disorders depending on the presence of intestinal PPARα or FABP1. Translationally, GW6471 decreases human PPARα-driven intestinal fatty acid uptake and therapeutically improves obesity in PPARA-humanized, but not Ppara-null, mice. These results suggest that intestinal PPARα-FABP1 axis could be a therapeutic target for NASH.

overall_design: Bulk RNA-seq of RNA isolated from the intestine of Chow- or HFD-fed Pparafl/fl and PparaΔIE mice.

first: Tingting

last: Yan

first: Frank

last: Gonzalez


title: Neutrophil extracellular traps induce glomerular endothelial cell dysfunction and pyroptosis in diabetic kidney disease

city: Chongiqng

first: Fengfan

last: Zheng

address: No.1 Youyi Street, Yuzhong District, Chongqing, China

institute: Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

summary: Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease. Neutrophil extracellular traps (NETs) are a network structure composed of loose chromatin and embedded with multiple proteins. Here, we observed increased NETs deposition in the glomeruli of DKD patients and diabetic mice (streptozotocin-induced or db/db mice). After degrading NETs with DNase I, diabetic mice exhibited attenuated glomerulopathy and glomerular endothelial cell (GEC) injury. We also observed alleviated glomerulopathy and GEC injury in peptidylarginine deiminase 4 (PAD4)-knockout mice with streptozotocin-induced diabetes. In vitro, NET-induced GEC pyroptosis was characterized by pore formation in the cell membrane, dysregulation of multiple genes involved in cell membrane function, and high expression of pyroptosis-related proteins. Strengthening the GEC surface charge by oleylamine significantly inhibited NET-induced GEC pyroptosis. These results indicate that NET-induced alterations in GEC charge are associated with GEC pyroptosis in the pathogenesis of DKD and suggest that NETs are a potential therapeutic target for DKD.

overall_design: mRNA profiles of human renal glomerular endothelial cells (HRGECs) treated with neutrophil extracellular traps (NETs) or vehicle control, and the experiments were repeated five times.

first: Linqiang

last: Ma

first: Xuan

last: Li


title: LncRNA Gm26917 promotes macrophage differentiation by enhancing Annexin A1 ubiquitination in LPS-induced acute liver injury

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

summary: Our studies demonstrated that Gm26917 localized in the cytoplasm of hepatic macrophages and globally regulated expressions of inflammatory genes and differentiation of macrophages. In vivo study showed that lentivirus-mediated gene silencing of Gm26917 attenuated liver inflammation and protected mice from LPS-induced ALI. Furthermore, mechanistic study showed that 3’- truncation of Gm26917 interacts with N-terminus of Annexin A1, a negative regulator of NF-κB signaling pathway. We also found that Gm26917 knockdown suppressed NF-κB activity by decreasing the ubiquitination of Annexin A1 and its interaction with NEMO. Besides, expression of Gm26917 in inflammatory macrophage was regulated by transcription factor forkhead box M1 (FOXM1). LPS treatment could dramatically increase the binding of FOXM1 to the promoter region of Gm26917 in macrophages. In sum, our findings suggest that lncRNA Gm26917 silencing protected against LPS-induced liver injury by regulating TLR4/NF-κB signaling pathway in macrophages.

overall_design:
the transcriptome profile of wild type (WT) and LPS-treated mice
the transcriptome profile of lentivirus-shRNA-NC and lentivirus-shRNA-Gm26917-treated mice peritoneal macrophage

first: Qing

last: Zhao

first: Wei

last: Shao


title: Transcriptomes analysis of ercc2/xpd mutant zebrafish

city: Wuhan

first: Ruilin

last: Zhang

address: 185 Donghu Road

institute: Wuhan University

summary: BioProject accession(PRJNA762494).Next Generation Sequencing Facilitates Quantitative analysis  of  transcriptomes to reveal transcriptional changes in ercc2/xpd mutant zerbafish.

overall_design: Gene expresion profiles in ercc2/xpd mutants and siblings at 5 and 7 days post fertilization (dpf) were generated by deep sequencing, in triplicate,using Illumina Hiseq 4000.

first: Jinmin


title: mRNA sequencing of skins isolated from B6;129S4-Npytm2Rpa/J homozygous mice and wildtype litter mates reveals transcriptomic changes indicative of skin inflammation associated with Npy overexpression.

city: Birmingham

first: Melissa

last: Harris

state: AL

address: 1300 University Blvd, CH464

department: Biology

institute: University of Alabama at Birmingham

summary: Neuropeptide Y (NPY) is a pleiotropic peptide produced in the central nervous system and peripheral organs. Despite conjectures that NPY may have a role in skin physiology and pathology, the effects of NPY in this organ remain poorly understood. We reported that a knock-in mouse with entopic NPY overexpression exhibits significantly elevated NPY in the skin, accompanied by premature and progressive hair graying secondary to depletion of melanocyte stem cells within hair follicles. However, the question remains as to whether NPY overexpression in the skin can induce non-melanocyte pathology. In this study, we employed this mouse to investigate consequences of skin-specific overexpression of NPY. Our findings show that chronic NPY overexpression in the skin induces dermal fibrosis and epidermal hyperkeratosis. Additionally, NPY overexpression induces significant accumulation of macrophages and T-regs in the dermis. RNA sequencing of whole skin from NPY-overexpressing mice further reveals NPY-mediated transcriptional changes consistent with inflammatory processes and inflammation-associated skin changes. Together, these results provide long-awaited evidence of NPY’s involvement in skin pathology, providing a background for future precise definition of its role in the regulation of cutaneous homeostasis.

overall_design: Examination of mRNA isolated from whole skin of 22-week-old homozygous B6;129S4-Npytm2Rpa/J mice (NPY tet/tet) and their wildtype siblings (NPY +/+).

middle: L

first: Joseph

middle: W

last: Palmer


title: Wild type and probiotic feeding transcriptome of pelodiscus sinensis

city: hangzhou

first: Shujie

last: Xu

state: zhejiang

address: yuhang rd 866

institute: Zhejiang University

summary: In recent years, the scale culture of Chinese soft-shelled turtle has developed rapidly. However, diseases in aquaculture are the main problems affecting the rapid and healthy cultivation. Strengthening the immunity of Chinese soft-shelled turtles is extremely important to control the infection of pathogenic bacteria. Bacillus has attracted attention as a probiotic supplement in aquatic feeds.In our previous studies, we found that the addition of Bacillus subtilis B10 to diets could increase survival rate, daily weight gain (DG) and feed conversion ratio (FCR) of Chinese soft-shelled turtles, improving the activities of digestive enzyme and optimizing the microbial communities of intestinal in Chinese soft-shelled turtle.However, the study on the mechanism of Bacillus subtilis B10 in Chinese soft-shelled turtle culture remains rare. Therefore, in this study, we used Bacillus subtilis B10 to feed the turtle, and used RNA-seq to explore its mechanism.

overall_design: liver mRNA profiles of pelodiscus sinensis.The control group and treatment group were fed the normal diet and the diet supplemented with Bacillus subtilis B10, respectively.Sample name (C: control; T: treatment; M: male; F: female)


title: Global transcriptomic analysis of hepatocyte cells infected with Ebola virus (EBOV)

city: Boston

first: Carlos

last: Villacorta-Martin

summary: We performed transcriptomic analysis of a Ebola virus (EBOV) infected hepatocyte cells. We utilized primary human hepatocytes (PHHs), iPSC-derived hepatocytes (iHeps), and immortalized hepatocarcinoma cell line Huh7 cells. Cells were infected with a multiplicity of infection of 10 and harvested after 1 day. Corresponding Mock infected samples were also included in this study.

overall_design: Global transcriptomic analysis of 2 donors of PHHs, 3 donors of iHeps, and Huh7 cells were infected with EBOV and harvested 1 day later for analysis. Corresponding mock infected samples were included for each cell type and donor. Triplicate replicates (n=3) were submitted for each donor and cell type (PHH = 6; iHep = 9; Huh7 = 3).

first: Whitney

last: Manhart

first: Gustavo

last: Mostoslavsky


title: Small RNA sequencing of the 8 to 30-nucleotide window in homo sapiens

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

institute: IRCM

summary: RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have challenged this dogma by preserving ribosomal RNA (rRNA) in our samples and by lowering the minimal RNA size window of our small RNA-Seq analyses to 8 nt

overall_design: Analyzing the content of the RNA size window between 8 and 30 nt of 2 different biological samples from Homo sapiens by small RNA-Seq.

first: Patrick

last: Provost

first: Charles

last: Beauparlant

first: Marine

last: Lambert

first: Abderrahim

last: Benmoussa


summary: We performed transcriptomic analysis of a time course of Ebola virus (EBOV) iPSC-derived hepatocytes. Mock infected and EBOV infected hepatocytes were harvested 1, 2, 3, and 7 days post-infection for analysis. Hepatocytes were infected with EBOV at a multiplicity of infection of 10.

overall_design: Global transcriptomic analysis of iPSC-derived hepatocytes infected with Ebola virus (EBOV) and harvested at 1, 2, 3, and 7 days post-infection. Corresponding, uninfected cells were harvested at matching time points. Duplicate samples (n=2) were submitted for analysis.


title: Reverse Remodelling of the Lung Vasculature after Hypoxia

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Pulmonary hypertension (PH) is a life-threatening disease, characterized by excessive pulmonary vascular remodeling, leading to elevated pulmonary arterial pressure and right heart hypertrophy. PH is caused, among other factors, by chronic hypoxia, leading to hyper-proliferation of pulmonary arterial smooth muscle cells (PASMC) and apoptosis-resistant pulmonary microvascular endothelial cells (PMVEC). Upon re-exposure to normoxia, chronic hypoxia-induced PH in mice is reversible.   In this study, we aim to identify novel candidate genes involved in pulmonary vascular remodeling specifically in the pulmonary vasculature.

overall_design: C57BL/6J mice were exposed to normoxia, chronic hypoxia, or chronic hypoxia with subsequent re-exposure to normoxia for different time points. Lung vasculature was extracted using laser-microdissection and subjected to microarray analysis. In total, vessels from lungs of 76 animals (23 controls – hypoxia, and 8-12 per time point) were analyzed by dual-color hybridizations in a balanced dye-swap design.

first: Friederieke

last: Weisel

first: Christine

last: Veith

first: Norbert

last: Weismann


title: ATRX histone binding and helicase activities have distinct roles in neuronal differentiation

city: Philadelphia

first: Anna

last: Bieluszewska

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: We have identified the distinct effects on neuronal differentiation of two different mutations of ATRX. We generated E14 mouse embryonic stem cell lines with mutations in the histone binding domain of ATRX (PHDmut) or in the helicase domain (K1584R). Neurodifferentiation is both delayed and compromised in PHDmut and K1584R, and manifest differently from complete ATRX loss. We performed ATRX ChIP-seq which showed changes in occupancy of ATRX in PHDmut and K1584R. Our CUT&RUN and RNA-Seq reveal that mutations or deficiency of ATRX result in separate patterns of dysregulation in gene expression and PRC2 binding, suggesting different roles of each ATRX domain in neuronal differentiation

overall_design: CUT&RUN, ChIP, and RNA-Seq was performed on E14 mouse embryonic stem cells (mESCs) and on mESCs differentiated to neural progenitor cells.

first: Bieluszewska

last: Anna

first: Wulfridge

last: Phillip

first: Ren

last: Wenqing

first: Sarma

last: Kavitha


title: PBMCs from healthy donors and CTCL patient control vs SEB stimulation

city: Beijing

first: Xiangjun

last: Liu

address: No.8 Xishiku Street

institute: Peking University First Hospital

summary: Transcriptional profiling of peripheral blood mononuclear cells from healthy donors and leukemic CTCL patients upon recombinant SEB treament.

overall_design: Two-condition experiment 1) CTCL PBMC samples: control vs SEB (100ng/mL or 500ng/mL); 2) Healthy Donors PBMC samples: control vs SEB (100ng/mL or 500ng/mL);

first: Yang

last: Wang


title: Competitive Endogenous RNA Landscape in Epstein-Barr Virus Associated Nasopharyngeal Carcinoma

city: Fuzhou

first: xiandong

last: lin

state: fujian

address: No. 420 Fuma Road, Jinan District

institute: Fujian Cancer Hospital and Fujian Medical University Cancer Hospital

summary: In this study, we investigated the role of microRNAs and circular RNAs in Nasopharyngeal Carcinoma (NPC) by constructing a circRNA-miRNA-mRNA co-expression network and performing differential expression analysis on mRNAs, miRNAs, and circRNAs. By comparing the expression profile of non-cancerous immortalized nasopharyngeal epithelial cell lines and NPC cell lines, we identified differentially expressed coding and non-coding RNAs. By leveraging coexpression and miRNA target prediction tools, we constructed a ceRNA network composed of mRNAs, miRNAs, and circRNAs.

overall_design: We report the bulk RNA-seq expression of mRNA, miRNA, and circRNA in nasopharyngeal epithelial cell lines and nasopharyngeal carcinoma cell lines, including the Epstein-barr virus associated subtype. We also report the expression of mRNA, miRNA, and circRNA in two metastatic and two non-metastatic nasopharyngeal carcinoma patient samples.

first: Xiandong

last: Lin

first: Steven

first: Keyu

first: Tao

last: Huang


title: Next-Generation Sequencing Facilitates Quantitative Analysis of WT, Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- Embryonic Stem Cells Transcriptomes

city: Nanjing

first: Yaru

last: zhu

address: Xuefu Road

institute: Nanjing University

summary: Polycomb repressive complexes (PRC) are epigenetic transcriptional repressors by establishing facultative heterochromatin repressive domains and play an essential role in numerous developmental processes. PRC1, which contains the E3 ligases RING1A/B and deposits H2AK119ub, forms six biochemically subcomplexes (PRC1.1-PRC1.6) based on the assembled PCGF protein (PCGF1–PCGF6), and has been involved in the maintenance of embryonic stem (ES) cell state. More recent evidence indicates that PCGF family participates in the self-renewal and pluripotent maintenance. However, it is still enigmatic that how the PCGF family engaged in the controlling process. Here, we generate the Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- ES cells using CRISPR/Cas9 technique and CRE-LoxP recombination system to discover the central determinants in PCGF family-related biological process.

overall_design: Gene expression profiling of WT (control), Ring1a-/-, Ring1b-/-, Ring1a/b-/-, Pcgf1/3/5/6-/- and Pcgf1/2/3/4/5/6-/- embryonic stem cells.

first: Zhu

last: Yaru

first: Dong

last: Lixia

first: Qin

last: Jinzhong


title: EZH2 inhibition in glioblastoma stem cells is associated with increased expression of neuronal genes and the neuronal developmental regulators ZIC2, ZNF423 and MAFB

city: Glasgow

first: Katherine

last: West

address: University of Glasgow

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary: Here we use two GBM stem cell lines, representing the classical/pro-neural and mesenchymal GBM subtypes, to investigate the effects of three different EZH2 inhibitors on GBM stem cell survival and gene expression: EPZ6438, GSK343 and UNC1999. RNA-seq analysis revealed that all three EZH2 inhibitors led to increased expression of genes related to neurogenesis and/or neuronal structure in both GBM stem cell lines. Chromatin immunoprecipitation (ChIP-Seq) was used to identify potential direct targets of the histone methylation activity of EZH2 that might be driving the increase in neuronal gene expression.

overall_design: Two glioblastoma stem cell lines were treated with various EZH2 inhibitors. RNAseq and ChIP-seq were performed in order to investigate the molecular changes.

first: Adam

middle: G

first: Bnar

middle: A

last: Kader


title: S-palmitoylation of PCSK9 induces sorafenib resistance in liver cancer by activating PI3K/AKT signaling pathway

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed PCSK9 knockdown or treated with PCSK9 inhibitors in HepG2 cells along with RNA sequencing.

overall_design: RNA sequencing in HepG2 cells with shControl, shPCSK9, DMSO and PCSK9 inhibitors.

first: H

first: X

last: Jin


title: Daphnane diterpenoids as potent and tolerable importin-b1 inhibitors to treat castration-resistant prostate cancer

city: Guangzhou

first: Jialuo

address: 132# Waihuandong Road, Guangzhou University City

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: RNA seq comparative analysis of XX, XY, and XXTet3-/- mutant mouse embryonic stem cells versus XX, XY, and XXTet3-/- mutant epiblast-like cells

city: San Francisco

first: Barbara

last: Panning

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

summary:
In XXTet3-/- mESCs DNA methylation levels are higher than XX wildtype levels.  We sought to determine if changes in cytosine modifications observed in XXTet3-/- mESCs impacted gene expression, we performed RNA-seq. 104 genes were up regulated in the mutant XX mESCs relative to wild type controls, and 86 were down regulated
To ask whether the XX-specific nuclear enrichment of TET3 is necessary for a developmental transition, we differentiated WT XX and XXTet3-/- mESCs into epiblast-like cells (EpiLCs).  Comparison of WT XX and XXTet3-/- EpiLC RNA-seq showed that 404 genes exhibited increased expression and 499 exhibited decreased expression in mutant cells.  GO term analysis showed gene expression changes affecting several LIF and BMP signaling pathways. However, despite these changes in signaling pathway driven expression, the expression of mESC markers went down and mEpiLC markers went up comparably upon differentiation WT XX and XXTet3-/- mESCs, suggesting that many key transcriptional changes that characterize this transition can occur without TET3.

overall_design: Comparative RNA seq analysis to determine if TET3 is necessary for the developmental transition of mESC to EpiLCs

first: Elizabeth

last: Martin

first: Jie

last: Wue

first: Melanie

last: Oakes


title: RNA-seq in RAW264.7 cells after silence of Synbindin in response to LPS

first: Luoyan

last: Ai

state: Shanghai

address: 145 Middle Shandong Road

department: Division of Gastroenterology and Hepatology

institute: Shanghai Jiao Tong University

summary: RAW264.7 cells were transfected with Synbindin siRNA for 48hours, then 100ng/ml LPS were treated cells for 4 hours. Before and after LPS stimulation, cells were collected and RNA were extracted for RNA-seq.

overall_design: mRNA profiles of RAW264.7 cells after Synbindin silence upon LPS stimulation  were generated by deep sequencing, in triplicate,using illumina Hiseq.

first: Antao

last: Xu