title: The hyperconnected 3D clique at the Ets1 locus is required for T cell function (ATAC-Seq)

first: Golnaz

last: Vahedi

overall_design: ATAC-Seq

first: Aditi

last: Chandra

first: Sora

last: Yoon

first: Michael

last: Michieletto

first: Naomi

last: Goldman

first: Emily

last: Ferrari

first: Leonel

last: Joannas

first: Jorge

last: Henao-Mejia


title: Transcriptomes in Human neuroblastoma cell line SH-SY5Y under oxidative stress conditions

status: Public on Jun 20 2023

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

type: Expression profiling by high throughput sequencing

summary: The SH-SY5Y Human neuroblastoma cell line was subcloned from the SK-N-SH cell line, which has been isolated from a bone marrow biopsy of a 4 year-old female patient. To examine the overall distribution of gene expression under stress condition in human neuronal cells, we investigated changes in the transcriptome profiles in the SH-SY5Y cells exposed with sodium arsenite which causes oxidative stress. We detected changes in the expression levels for several genes including FOS and Jun, which are well-known stress-dependent upregulated genes.

overall_design: rRNA-depleted RNA-seq of control and Arsenite-treated SH-SY5Y cells

first: Ken-ichi

last: Takayama

first: Satoshi

last: Inoue


title: scRNA-sequencing from HPV-positive head and neck squamous cell carcinomas

city: Houston

first: Xiuning

last: Le

address: 1515 Holcombe Blvd

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: We report single cell transcriptome data from HPV-positive head and neck squamous cell carcinoma patients

overall_design: Examination of transcriptome and cell-composition differences in HPV-positive head and neck cancer cancer using 10X Genomics platform


title: Multi-omic signatures of Chronic Beryllium Disease bronchoalveolar lavage cells relate to T cell function and innate immunity [Methylation]

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

type: Methylation profiling by genome tiling array

summary: We performed DNA methylation profiling between Chronic Beryllium Disease, beryllium-sensitized, and healthy control bronchoalveolar cells, and integration with gene expression and proteomic data

overall_design: Bronchoalveolar lavage cells were collected from 30 Chronic Beryllium Disease, 30 Beryllium Sensitized, and 12 healthy control lungs

first: Iain

middle: R

last: Konigsberg

first: Li

last: Li

middle: V

first: Lisa

middle: A

last: Maier


title: Tumor-localized catalases fail to alter tumor growth or transcriptional profiles in mice

status: Public on Jun 21 2023

city: Cambridge

first: K Dane

last: Wittrup

state: MA

department: Biological Engineering, Chemical Engineering, Koch Institute of Integrative Cancer Research

institute: Massachusetts Institute of Technology

summary: Catalase is an antioxidant enzyme that catalyzes the rapid conversion of hydrogen peroxide to water and oxygen. Use of catalase as a cancer therapeutic has been proposed to reduce oxidative stress and hypoxia in the tumor microenvironment, both activities which are hypothesized to reduce tumor growth. Furthermore, exposing murine tumors to exogenous catalase was previously reported to have therapeutic benefit. We studied the therapeutic effect of tumor-localized catalases with the aim to further elucidate the mechanism of action. To do this, we engineered two approaches to maximize intratumoral catalase exposure: 1) an injected extracellular catalase with enhanced tumor retention, and 2) tumor cell lines that over-express intracellular catalase. Both approaches were characterized for functionality and tested for therapeutic efficacy and mechanism in murine syngeneic tumor models. We did not observe a significant difference in tumor growth or survival between catalase-treated and untreated mice when either approach was used. Finally, bulk RNA sequencing of tumors was performed, comparing the gene expression of catalase-treated and untreated tumors. Gene expression analysis revealed very few differentially expressed genes as a result of exposure to catalase and notably, we did not observe changes consistent with an altered state of hypoxia or oxidative stress. In conclusion, we observe that sustained intratumoral catalase neither has therapeutic benefit nor triggers significant differential expression of genes associated with the anticipated therapeutic mechanism.

overall_design: RNA-sequencing was performed on tumors (CT26 and 4T1)  treated with or without extracellular or intracellular catalase

first: Allison

last: Sheen

first: Yash

last: Agarwal

first: Keith

last: Ming Hong Cheah

first: Sarah

middle: C

last: Cowles

first: Jordan

last: Stinson

first: Joseph

last: Palmeri

first: Hadley

middle: D

last: Sikes

first: K


title: Transcriptional impact of eepR mutation in Serratia marcescens

city: Pittsburgh

first: Robert

middle: MQ

last: Shanks

state: PA

address: EEI 1020, 203 Lothrop st.

department: Ophthalmology

institute: University of Pittsburgh

summary: The EepR protein is a two-component response regulator protein in the bacterium Serratia marcescens.  Mutation of the eepR gene results in pleiotropic changes including reduced expression of secondary metabolites and proteases.

overall_design: Four biological replicates were analyzed for each of 2 genotypes (each of the three biological replicates is a combination of three biological replicates)

first: Nicholas

last: Stella

middle: M


title: Impact of PRRX1 knockdown on the transcriptome of normal human lung fibroblasts (NHLF) in the presence or the absence of TGF-β

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: To assess the role of PRRX1 in TGF-β-induced lung fibroblast activation, we transfected in human NHLF with PRRX1 or control siRNAs and then exposed these cells to TGF- β (1 ng/mL). RNA samples were harvested 48 hours after TGF-β exposition. Two independent experiments were carried out.

overall_design: 2 independent experiments performed in a one color design, corresponding to 8 conditions (siControl#1, siControl#1+TGF-β, siControl#2,  siControl#2+TGF-β, PRRX1siRNA#1, PRRX1siRNA#1 +TGF-β, PRRX1 siRNA#2, PRRX1siRNA#2 +TGF-β) for a total of 16 samples.

first: Mailleux

last: N.

first: Mari

last: B.

first: Lebrigand

last: K.

first: Mounier

last: Carine


title: RNA editing using the flap endonuclease 1 guided by hairpin DNA probes

city: Nanjing,China

first: kun

last: tian

address: School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing,  China.

country: China

institute: China Pharmaceutical University

summary: Here we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, called the HpSGN system, for both DNA and RNA editing without sequence limitation.To investigate the mRNA on/off target cleavage effective of the HpSGN system,we co-transformed HepG2 (liver hepatocellular cells) with plasmids encoding FEN1 with NES and two groups of hpDNAs targeting the mRNA of AFP (Alpha Fetoprotein) gene and CDK9 (Cyclin-dependent kinase 9) gene, respectively. RNA-seq was used to examine the on/off taget cleavage effective.We proved the HpSGN system can knock down specific mRNAs in human cells at a level of ~25%.At the same time,it indicated that a degree of off-targets occur in HpSGN-treated cells.

overall_design: Examination the on/off target cleavage effect of the HpSGN system.

first: Kun

last: Tian


title: ChIP-seq for TCF4 in human medial ganglionic eminence-like organoids (hMGEOs) derived from ihtc-03 cell line.

status: Public on Jun 19 2023

city: nanjing

first: yuanyuan

last: wang

address: 818 Tianyuan E Rd, Nanjing, JIANGSU

institute: nanjing medical university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To depict the gene regulatory network of TCF4 in interneuron development, We performed chromatin immunoprecipitation-sequencing (ChIP seq) on human medial ganglionic eminence-like organoids (hMGEOs) to identify genome-wide TCF4 binding sites. This study provides compelling evidence to support the biological rationale linking TCF4 to the developing cortical interneuron.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TCF4 in hMGEOs derived from ihtc-03 cell line. we identify genome-wide TCF4 binding sites in hMGEOs against the input.

first: Mingyan

last: Lin

first: Yuanyuan

last: Wang

first: Liya

last: Liu


title: Blood exsosomal miRNAs of liver disease patients

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

summary: Aiming to develop circulatin biomarkers for liver disease, including  progression of fibrosis/inflammation.

overall_design: 40 liver disease patients

first: Y-h

first: Yoshiki

last: Murakami


title: Ablation of collagen XII disturbs joint extracellular matrix organization and causes patellar subluxation

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

summary: Collagen XII, belonging to the fibril-associated collagens, is a homotrimeric secreted extracellular matrix (ECM) protein encoded by the COL12A1 gene. Mutations in the human COL12A1 gene cause an Ehlers-Danlos/myopathy overlap syndrome leading to skeletal abnormalities and muscle weakness. Here, we studied the role of collagen XII in joint pathophysiology by analyzing collagen XII deficient mice and human patients. We found that collagen XII is widely expressed across multiple connective tissue of the developing joint. Lack of collagen XII in mice destabilizes tendons and the femoral trochlear groove to induce patellar subluxation in the patellofemoral joint. These changes are associated with an ECM damage response in tendon and secondary quadriceps muscle degeneration. Moreover, patellar subluxation was also identified as a clinical feature of human patients with collagen XII deficiency. The results provide an explanation for joint hyperlaxity in mice and human patients with collagen XII deficiency.

overall_design: Examination of the single cell transcriptome in joints with collagen XII deficiency


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [RNA-Seq II]

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

summary: The extravillous trophoblast (EVT) cell lineage is a key feature of placentation and critical for spiralartery remodeling and successful pregnancy. Our knowledge of transcriptional regulation driving EVT cell development is limited. Here, we mapped the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem (TS) cells and their transition into the differentiated EVT cell lineage. We identified that chromatin accessibility in intergenic regions was more extensive in EVT cells than in TS cells in the stem state, which is indicative of increased enhancer-driven gene regulation. Using reference epigenome annotation, we noted that 18% of the chromatin landscape in EVT cells was uncharted. We linked regulatory regions to their cognate target genes and characterized the three-dimensional organization of the TS cell functional genome by Hi-C. Integrational analysis of chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enabled identification of transcription factors and regulatory mechanisms associated with EVT cell lineage development. Subsequent analyses elucidated functional roles forTFAP2C,EPAS1,SNAI1, andDLX6in the regulation of EVT cell lineage development.EPAS1was identified as an upstream regulator of EVT cell transcription factors, includingSNAI1andDLX6, and was found to be upregulated in idiopathic recurrent pregnancy loss. Collectively, we have revealed activation of a dynamic regulatory network that provides a framework for understanding EVT cell specification in trophoblast cell lineage development and human placentation.

overall_design: RNA-Seq

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

middle: S

first: Ayelen

last: Moreno-Irusta

first: Ross

middle: P

last: McNally

first: Emily

last: Wesley

first: Khursheed

last: Iqbal

first: Warren

last: Cheung

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Courtney

last: Marsh

first: Michael

middle: J

last: Soares

first: Elin

last: Grundberg


title: Blood exsosomal miRNAs of patients with normal livers and liver disease patients

first: Y-H.

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

overall_design: Refer to individual Series


title: Transcriptomic profiling reveals a role for pro-survival and stress responsive genes in suppressing fly parkin phenotypes.

city: Bethesda

first: Richard

last: Youle

state: MD

address: 35 Convent Drive, 2C917

department: Surgical Neurology Branch

institute: National Institute of Neurological Disorders and Stroke, NIH

summary: For examining the gene expression changes due to loss of the innate immunity gene STING in a parkin mutant fly background, we performed RNA-sequencing to compare the transcriptomes of the stingRG5, park25, and stingRG5; park25 mutant flies, using the shared background stock w1118 as a wild-type control. There were significant differences in the expression patterns of stress-repsonsive genes in the double mutants, compared to either single mutant strain alone. These underlying changes to the transcriptional landscape in sting-/- flies necessitates further study to better understand the role of stress-responsive genes in mitigating mitochondrial and oxidative damage during development or disease.

overall_design: Total fly lysates (10 flies each, with 2-3 biological replicas per group) were analysed with RNA-Seq, DESeq2, and GSEA for gene expression changes in mutant alleles (park25, stingRG5, double) compared to wild-type w1118 controls

first: Andrew

middle: T

last: Moehlman

first: Gil

last: Kanfer


title: ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts [TT-Seq]

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit Pol II termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. ZC3H4, in turn, directly connects to the ZCCHC8 component of the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay.

overall_design: ARS2, Cleavage and polyadenylation complex subunit CPSF73 (CPSF3), Integrator complex subunit INTS11 and RNA exosome subunit RRP40 (EXOSC3) were knocked down in HeLa cells using siRNA. The corresponding control was the non-tageting EGFP siRNA knockdown. Two biological replicates were generated for transient transcriptome (TT)-seq.

first: Jérôme

middle: O

last: Rouvière

first: Anna

last: Salerno-Kochan

first: William

last: Garland

first: Yuhui

last: Dou

first: Om

last: Rathore

first: Ewa

last: Šmidová Molska

first: Guifen

last: Wu

first: Manfred

last: Schmid

first: Andrii

last: Bugai

first: Lis

last: Jakobsen

first: Kristina

last: Žumer

first: Patrick

last: Cramer

first: Jens

last: Andersen

first: Elena

last: Conti

first: Torben

middle: H

last: ensen


first: Y-H.

last: Taguchi

summary:
Blood exsosomal miRNAs of patients with normal livers, to be compared with liver diseas patients
Aiming to develop circulatin biomarkers for liver disease, including  progresson of fibrosis/inflammation. This data set should be uasd as control samples to be compared with liver disease patients.

overall_design: 72 patients with normal livers were analysed. No replidate studies were performed.

first: Y-h

first: Yoshiki

last: Murakami


title: Blood exosomal miRNAs of liver disease patients and healthy controls

type: Non-coding RNA profiling by high throughput sequencing

summary: Aiming to develop circulation biomarkers for liver disease, including  progression of fibrosis/inflammation.

overall_design: 16 CCC patients, 20 HCC patients, 11 healthy controls


title: ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts

city: Aarhus

first: Jerome

last: Rouviere

address: Universitetsbyen 81

overall_design: The ARS2 and ZC3H4 transcription termination factors were knocked down in HeLa cells using siRNA in presence or absence of ectopic expression of ARS2-WT or ZnF-mutant. The corresponding controls was the non-tageting EGFP siRNA knockdown. Two biological replicates were generated for each RNA-seq.

first: Jérôme

last: Rouvière

first: Anna

first: Søren

last: Lykke-Andersen

last: Molska

last: Jensen


title: Genome-wide DNA methylation study in penile cancer

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Genome-wide DNA methylation profile in penile carcinoma to uncover molecular markers

overall_design: DNA from frozen penile tissue was isolated using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA), and RNA was extracted using RNeasy (Qiagen). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer RNA 6000 LabChip kit (Agilent Technologies, Santa Clara, CA, USA). HPV status was established for all PeCa via Linear Array HPV Test Genotyping (Roche Molecular Diagnostics, Branchburg, NJ, USA). Furthermore, primers binding to the L1 region of the HPV virus (primers pair GP5+/GP6+) were also used

first: Hellen

last: Kuasne

last: Albuquerque Marchi

first: Silvia

last: Rogatto


title: METTL14 Regulates Chromatin Bivalent Domains in Mouse Embryonic Stem Cells [RNA-seq]

city: Shanghai

first: Hongjie

last: Shen

state: Shanghai

address: No.130, Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: METTL14 (methyltransferase-like 14) is an RNA binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation of mRNA. Recent studies identified a function for METTL3 in heterochromatin and transcription, but the role of METTL14 in these contexts remains unclear. Here we show that METTL14 binds and regulates mouse embryonic stem cell bivalent domains, which are marked with tri-methylation at lysine 27 of histone H3 (H3K27me3) and tri-methylation at lysine 4 of histone H3 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels at bivalent regions, resulting in the resolution of the bivalency and in increased transcription. We demonstrate that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. Instead, METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the histone 3 lysine 27 (H3K27) methyltransferase complex PRC2 and the histone 3 lysine 4 (H3K4) demethylases KDM5B to chromatin. Our findings identify a METTL3-independent function of METTL14, important for maintaining the bivalent domains in mESCs, thus revealing a new mechanism of bivalent domain regulation in mammals.

overall_design: Examination of total RNA in METTL14 WT,METTL14 KO mESCs.

first: Mandi

last: Mu

first: Wenqi

last: Xu

first: Yang

last: Shi


title: Overlapping role of c-Jun N-terminal kinase (JNK) 1 and 2 in imidazole ketone erastin-induced ferroptosis

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Ferroptosis is an iron-dependent form of non-apoptotic cell death characterized by the generation of excess reactive oxygen species (ROS) and lipid peroxidation. However, it remains largely unknown whether signaling pathways, such as the ROS-activated mitogen-activated protein kinase (MAPK) pathways, affect ferroptosis. The c-Jun N-terminal kinase (JNK), a MAPK signaling molecule that plays an essential role in apoptosis, is activated in response to various stimuli, including oxidative stress. In this study, we examined the functional role of JNK in cell death induced by imidazole ketone erastin (IKE), a potent ferroptosis inducer, using gene knockout technology. We found that JNK1/2 double-knockout cells, but not JNK1 or JNK2 single-knockout cells, were much more tolerant to IKE-induced cell death compared to control cells. We further demonstrated that IKE-induced increase in CTH and HMOX1, key genes in ferroptosis, in control cells was substantially suppressed by the depletion of JNK1 and JNK2. These results suggested that JNK1 and JNK2 play an important, overlapping role in ferroptosis. Our findings advance our understanding of the JNK pathway, which could contribute to future pharmacological developments in ferroptosis-related diseases such as cancer and neurodegeneration.

overall_design: Comaprison between wild type parental cells and the JNK1/2-double knockout cells at four different time points (0, 4, 8, and 12 h) after treatment with IKE(Imidazole ketone erastin).

first: Ravdandorj

last: Odongoo

first: I

middle: K

last: Gunarta

first: Purev

last: Erdenebaatar

first: Ryusuke

last: Suzuki

first: Makiko

last: Meguro-Horike

first: Yoshio

last: Endo

first: Toshihiro

last: Fujii

first: Rikiro

last: Fukunaga

first: Katsuji

last: Yoshioka


title: Genome-wide screening reveals the key genes that are responsible for trametinib-induced apoptosis

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: To explore the geness that are responsible for trametinib-induced apoptosis, we performed Genome-scale CRISPR-Cas9 knockout screening in GSU with 0.015% DMSO or 15 nM trametinib for 14 days. We found that TP53 is critical for executing trametinib-induced apoptosis.

overall_design: GeCKO Library screen in GSU with vehicle or tramrtinib for 14 days.

first: Xiang

last: Wang

first: Jing-Yu


title: Single cell transcriptomic expression profiling by single cell RNA sequencing for human induced pluripotent stem cells (iPSCs) derived cortical organoids

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: The pupose of this study is to explore the single cell transcriptome profiling changes of cortical organoids differentiated from POLG patient iPSCs compoared to control organoids.

overall_design:
Examination of singel cell transcriptomic profile in iPSC-derived cortical organoids
NOTE FROM SUBMITTER: According to the local law, the raw fastq data can not be uploaded due to the sensitivity of the data.

first: Kristina

middle: X

first: Anbin

last: Chen


title: Identification of DraRS in C. difficile, a two-component regulatory system that responds to lipid II interacting antibiotics

status: Public on Jun 17 2023

city: Iowa City

first: Anthony

last: Pannullo

state: IA

address: 30 N Dubuque St

department: Microbiology

institute: University of Iowa

summary: Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 220,000 infections, 12,000 deaths, and upwards of $1 billion in medical costs in the US each year. C. difficile is highly resistant to a variety of antibiotics, but we have a poor understanding of how C. difficile senses and responds to antibiotic stress, and how such sensory systems affect clinical outcomes. There has been recent interest in using a daptomycin analog, Surotomycin, to treat C. difficile infections. We have identified a spontaneous C. difficile mutant that displays increased daptomycin resistance. We performed whole-genome sequencing that this mutant possessed a nonsense mutation, S605*, in draS which encodes a putative sensor histidine kinase of a two-component system (TCS). The draSS605* mutant has approximately a 4-8-fold increase in daptomycin MIC compared to WT. We found that expression of constitutively active DraRD54E in WT increases daptomycin resistance 8-16-fold and increases bacitracin resistance ~4-fold. We found that a selection of lipid II inhibiting compounds leads to increased activity of the luciferase-based reporter, PdraR-sLucopt including vancomycin, bacitracin, ramoplanin, and daptomycin. Using RNA-seq we identified the DraRS regulon. Interestingly, we found that DraRS can induce expression of the previously identified hex locus required for synthesis of a novel glycolipid produced in C. difficile. Our data suggest that induction of the hex locus by DraR explains some, but not all, of the DraR-induced daptomycin and bacitracin resistance.

overall_design: RNA-seq experiments, controls and experimental conditions all done in biological triplicate

first: Pannullo

middle: G

last: Anthony

first: Zbylicki

last: Brianne

first: Ellermeier

last: Craig


title: Effects of imeglimin and metformin on islets of db/db mice

city: Maebashi

first: Jun

last: Shirakawa

address: 3-39-15 Showa-machi

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

summary: To investigate the effects of imeglimin and metformin on islet cells in db/db mice, we isolated pancreatic islets from db/db mice treated with/without imeglimin and metformin or db/+ mice.

overall_design: Total RNA samples of islets from db/+ mice (db-1, -2, -3), db/db mice (db/db-Ctrl1, 2, 3), or imeglimin and metformin-treated db/db mice (db/db-ImeMet1, 2, 3) were subjected to RNA-Seq.

first: Kuniyuki

last: Nishiyama

first: Masato

last: Ono

first: Takahiro

last: Tsuno

first: Ryota

last: Inoue

first: Ayako

last: Fukunaka

first: Tomoko

last: Okuyama

first: Mayu

last: Kyohara

first: Yu

last: Togashi

first: Setsuko

last: Fukushima

first: Takuto

last: Atsumi

first: Aoi

last: Sato

first: Asuka

last: Tsurumoto

first: Chisato

last: Sakai

last: Fujitani

first: Yasuo

last: Terauchi

first: Shuichi

last: Ito


title: CD4+ T cells have different gene profiles between Ogt-KD and control mice after EAE

status: Public on Jun 18 2023

city: Tianjin

first: Junwei

last: Hao

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: To investigate whether the level of O-GlcNAc could affect CD4+ T cell function after EAE, we performed RNA-sequencing analysis on splenic CD4+ T cells. The downregulation of OGT in CD4+ T cells led to changes in gene expression profile in CD4+ T cells with a 2-fold threshold. Next, Gene Ontology (GO) analysis was performed to compare differentially expressed genes in Ogt-KD and control mice. These results indicated that OGT was involved in the regulation of multiple important cellular events.

overall_design: CD4+ T cells were isolated from the splenic single-cell suspension of 3 Ogt-KD and 3 control EAE mice at acute phase for RNA-seq analysis.


title: RNA-seq analysis of  gene expression in wild type and rli2 RNAi seedlings

first: Shi-Xia

last: Yu

address: Dongchuan Road, Shanghai Minhang District No. 800

institute: Shanghai Jiaotong University

summary: To investigate the differential gene expression between wild type and rli2 RNAi, we collected samples of the seedlings from WT and rli2 RNAi plants with three biological replicates to perform RNA-seq assay.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and rli2 RNAi seedlings.

first: Wen-Hui

last: Lin

first: Li-Qin

last: Hu


first: Søren

last: Lykke-Andersen


title: The essential chaperone DNAJC17 activates HSP70 to coordinate RNA splicing and G2-M progression

city: San Francisco

first: Amit

last: Sabnis

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

summary: Molecular chaperones including the heat-shock protein 70-kilodalton (HSP70) family and the J-domain containing protein (JDP) co-chaperones maintain homeostatic balance in eukaryotic cells through regulation of the proteome.  The expansive JDP family helps direct specific HSP70 functions, and yet loss of single JDP-encoding genes is widely tolerated by mammalian cells, suggesting a high degree of redundancy.  Using a genetic screen of DJPs in human cancer cell lines, we found the RNA recognition motif (RRM) containing DNAJC17 to be pan-essential.  Knockdown of DNAJC17 leads to relatively few conserved changes in the abundance of individual mRNAs, but instead deranges gene expression through exon skipping, primarily of genes involved in cell cycle progression.  Concordant with cell viability experiments, the C-terminal portions of DNAJC17 are dispensable for restoring splicing and G2-M progression. Our findings identify essential cellular JDPs and suggest that diversification in JDP structure extends the HSP70-JDP system to control divergent processes such as RNA splicing.

overall_design:
Two pediatric cancer cell lines, Rh30 and ES8, were transduced with dCas9-KRAB and then with sgRNA targeting the 5'UTR of DNAJC17 or non-targeting control.
As an additional control, we included Rh30 and ES8 cells transduced with a cDNA stably expressing a DNAJC17 lacking the C-terminal RRM (DRRM) that underwent knockdown of endogenous DNAJC17.
Cells were selected in puromycin for 72 hours following sgRNA transduction prior to lysis and RNA extraction. Each experimental condition was tested in triplicate.

first: David

last: Allegakoen


title: Phenotypic Screening Following Transcriptomic Deconvolution to Identify Transcription Factors Mediating Axon Growth Induced by a Kinase Inhibitor

city: Port Washington

first: Jeffrey

middle: Adam

last: Lowell

state: New York

address: 74A Firwood Road

institute: Northwell Health

summary: After injury to the central nervous system (CNS), both neuron-intrinsic limitations on regenerative responses and inhibitory factors in the injured CNS environment restrict regenerative axon growth. Instances of successful axon regrowth offer opportunities to identify features that differentiate these situations from that of the normal adult CNS. One such opportunity is provided by the kinase inhibitor RO48, which dramatically enhances neurite outgrowth of neurons in vitro and substantially increased contralateral sprouting of corticospinal tract neurons when infused intraventricularly following unilateral pyramidotomy. The authors present here a transcriptomic deconvolution of RO48-associated axon growth, with the goal of identifying transcriptional regulators associated with axon growth in the CNS. Through the use of RNA sequencing (RNA-seq) and transcription factor binding site enrichment analysis, the authors identified a list of transcription factors putatively driving differential gene expression during RO48-induced neurite outgrowth of rat hippocampal neurons in vitro. The 82 transcription factor motifs identified in this way included some with known association to axon growth regulation, such as Jun, Klf4, Myc, Atf4, Stat3, and Nfatc2, and many with no known association to axon growth. A phenotypic loss-of-function screen was carried out to evaluate these transcription factors for their roles in neurite outgrowth; this screen identified several potential outgrowth regulators. Subsequent validation suggests that the Forkhead box (Fox) family transcription factor Foxp2 restricts neurite outgrowth, while FoxO subfamily members Foxo1 and Foxo3a promote neurite outgrowth. The authors’ combined transcriptomic-phenotypic screening strategy therefore allowed identification of novel transcriptional regulators of neurite outgrowth downstream of a multitarget kinase inhibitor.

overall_design: Rat embryonic hippocampal neurons treated in culture for two days with either DMSO or RO48, an experimental kinase inhibitor shown to promote neurite outgrowth. We then performed gene expression profiling analysising using data obtained from RNA-seq of treated cells after 48 hours of treatment.

first: Vance

last: Lemmon

first: John

last: Bixby


title: RNA-Seq of p57Kip2 wild type and p57Kip2 knockout sorted Hopx-GFP+ intestinal stem cells

city: Toulouse

first: Arnaud

last: Besson

address: 118 route de Narbonne

department: MCD UMR5077

institute: Centre de Biologie Integrative - CNRS

summary: The goal was to identify the changes in transcriptome profiling (RNA-Seq) caused by p57(CDKN1C) knockout in a population of Hopx+ cells sorted from dissociated intestinal crypts of E18.5 murine embryos

overall_design: Hopx+ cells were sorted from 5 p57 wild type and 5 p57 knockout E18.5 intestines

first: Justine

last: Creff


title: ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts [RNA-Seq]

overall_design: ARS2, Cleavage and polyadenylation complex subunit CPSF73 and Integrator complex subunit INTS11 were knocked down in HeLa cells using siRNA. The corresponding control was the non-tageting EGFP siRNA knockdown. Two biological replicates were generated for RNA-seq.

first: Jérôme

last: Rouvière

first: Anna

last: Salerno-Kochan

first: William

last: Garland

first: Yuhui

last: Dou

first: Om

last: Rathore

first: Ewa

last: Molska

first: Guifen

last: Wu

first: Manfred

last: Schmid

first: Andrii

last: Bugai

first: Lis

last: Jakobsen

first: Kristina

last: Žumer

first: Patrick

last: Cramer

first: Jens

last: Andersen

first: Elena

last: Conti

first: Torben

last: Jensen


title: Differential and cooperative effects of IL-25 and IL-33 on T helper cells contribute to cryptococcal virulence and brain infection

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

summary: Cryptococcal disease pathogenesis is associated with the induction of type 2 immune response which is largely mediated by adaptive T helper cells. Recently, epithelial cell-derived IL-33 and IL-25 are recognized as key mediators in driving pathogenic type 2 inflammation during C. neoformans infection. Although IL-25 and IL-33 exhibit a combinatorial and closely related function, the differential effect of these cytokines in the regulation of host immune response against C. neoformans infection is still elusive. We observed a predominantly increase of IL-25/IL-33 responsive Th cells within the lung after infection, especially at the chronic infection phase. The ex vivo stimulation of cryptococcal-specific Th cells demonstrated combinatorial effect of IL-25 and IL-33 in promoting the production of type 2 cytokines. A comparative transcriptomic analysis revealed coordinatel effects of these cytokines in promoting activation, survival, and homeostasis of adaptive Th cells during C. neoformans infection. The expression of type 2 cytokines and chemokine was absent in Th cells of Il17rb-/- mice, indicating the requirement of IL-25-mediated Th2-type immune responses during C. neoformans infection. Further analysis of the degree of virulence indicated a positive correlation between the frequency of IL-17RB/ST2-expressing Th cells and cryptococcal brain dissemination in vivo.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of IL-25 and IL-33 treated effector CD4+ T helper cell isolated from the lung of BALB/c and Il17rb-/- m

first: Adithap

last: Hansakon

first: Siranart

last: Jeerawattanawart


title: METTL14 Regulates Chromatin Bivalent Domains in Mouse Embryonic Stem Cells.

first: Hongjie

last: Shen

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

overall_design: Refer to individual Series


title: A human maternal-fetus interface transcriptome atlas

first: Xiaoya

last: Zhao

state: -- None selected --

address: No. 910, Hengshan Rd

institute: School of Medicine, Shanghai Jiaotong University

summary: Trophoblasts undergos dynamic differentiation and self-renewal during pregnancy. Expecially, EVTs anchor the placenta to the uterus to ensure pregnancy success, and its invasive excessiveness is a probable consequence of ruptured tubal ectopic pregnancy (REP), that resulting in maternal infertile and/or even deaths. We present REP, abortive tubal ectopic pregnancy (AEP)and intrauterine pregnancy (IP) atlas by integrating single-cell RNA-seq. We define cell subtypes within EVTs and each of the feature genes. Further, we utilize monocle3 and RNA velocty to identify the developmental trajectories of EVT subsets. CellPhoneDB and cell-chat unravel secretion of CSF1 by falloppian tubal secretory epithelial cells directly interact with CSF1R of EVT to strengthens the invasive ability.

overall_design: Expression profiling by high throughput sequencing

first: X

middle: Y

first: Q

last: Zhu

first: J

last: Zhang

first: M

middle: Q

last: Li


title: Single cell transcriptomics of yound and aged naked mole-rat (NMR) epidermal cells

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Study the global transcriptional heterogeneity of young and aged NMR epidermis using scRNA-seq,

overall_design: Dorsal skin of 3 young (mean age: 1.1 years) and 3 aged (mean age: 11.3 years) NMR were collected. After a short enzymatic epidermis-dermis digestion and separation, epidermal cells were mechanically dissociated and directly loaded into the chromium controller (10x Genomics) without any FACS-sorting. All the experiments were processed at the same time and mainly analysed using Seurat and Monocle pipelines.

first: Romain

last: Fontaine

first: Aleksandra

last: Savina

first: Selim

last: Aractingi


title: RNAseq of primary preadipocytes and adipocytes isolated from 3 months-old mice

city: Doha

first: Borbala

last: Mifsud

address: LAS Building, Education City

country: Qatar

institute: Hamad Bin Khalifa University

summary: Preadipocytes and adipocytes were isolated from the epididymal fat pads of three months old hemizygous Zfp423GFP/+ male mice.

overall_design: Gene expression profiling was performed using 6 RNA-seq replicates for each cell type.

first: Sandovici

last: Ionel


title: Single-Cell Transcriptome Atlas of Human Mesenchymal Stem Cells

city: SHANGHAI

first: Grayson

last: Gong

state: SHANGHAI

address: xinjunhuan road

institute: OEBIO

summary: The heterogeneity of mesenchymal stem cells (MSCs) remains incompletely inventoried, which often hampers reproducibility in clinical applications and basic research. Advanced single-cell RNA sequencing (scRNAseq) is a robust tool for dissecting cellular heterogeneity, while the comprehensive single-cell atlas still has not been achieved for human MSCs.Using massively parallel multiplexing scRNAseq, we constructed this atlas of >130,000 single-MSC transcriptomes across multiple tissues and donors to decipher their heterogeneity. The most widely clinical-utilized tissue-resources for MSCs were collected, including normal bone marrow (n=3), adipose (n=3), umbilical cord (n=2), and dermis (n=3).Based on this high-quality data, we identified the 7 tissue-specific and 5 conserved MSC subpopulations with distinct gene-expression signatures from multiple tissue origins, which has not been achieved previously. We noticed that extracellular matrix hugely contributes to MSC heterogeneity. Notably, tissue-specific MSC subpopulations exhibited hugely heterogeneous on ECM-associated immune regulation, antigen processing/presentation, and senescence, which also contributed to inter-donor and intra-tissue heterogeneity. The variable dynamics of ECM-associated genes depicted the discrete trajectory patterns across multiple tissues. Additionally, the conserved and tissue-specific transcriptomic-regulons and protein-protein interactions were identified, representing common or tissue-specific MSC potentially functional roles. Furthermore, we also discovered that the umbilical-cord-specific subpopulation possessed advantages in immunosuppressive properties.In summary, our work provides timely and exciting insights into MSC heterogeneity on multiple levels. In addition to resource value, this MSC atlas taxonomy provides a comprehensive understanding of cellular heterogeneity, revealing the potential improvements in MSC-based therapeutic efficacy.

overall_design: Examination of 11 MSC samples from 4 tissues using single-cell RNAseq

first: Zheng

last: Wang


title: MCF10A cells expressing empty vector, siRNA-resistant wild-type and siRNA-resistant catalytically dead TIP60 treated with control or TIP60 siRNA

city: Singapore

first: Shreshtha

middle: Sailesh

last: Bhatia

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: Alternative splicing of RNA transcripts can result in a multitude of variations from the genome. Since splicing can occur co-transcriptionally, chromatin structure has been reported to affect the choice of a splice site. TIP60 is a haploinsufficient tumor suppressor gene that is frequently downregulated in cancers. Since TIP60 is a writer of histone and non-histone modifications, we investigated TIP60’s role in modulating alternative splicing. RNA sequencing was performed in TIP60-depleted MCF10A cells and with cells rescued with wild-type or catalytically inactive TIP60. The majority of the differential splicing events were skipped exon events, including exon 25 skipping event of ITGA6. To identify the splicing factor that regulates this event, a siRNA screen of 77 splicing factors was employed. TIP60 depletion results in an increase in the ITGA6 isoform that lacks exon 25 and the siRNA screen identified ESRP2 to regulate splicing of ITGA6 exon 25. This study suggests that alternative splicing of ITGA6 exon 25 is regulated by the TIP60-ESRP2 axis.

overall_design: RNA-Seq of MCF10A cells stably expressing empty vector (MSCV), siRNA-resistant wild-type (*WT-TIP60) and siRNA-resistant catalytically dead (*KD-TIP60) TIP60 treated with control or TIP60 siRNA

first: Sudhakar

last: Jha


title: Multi-omic signatures of Chronic Beryllium Disease bronchoalveolar lavage cells relate to T cell function and innate immunity

city: Aurora

first: Ivana

last: Yang

institute: University of Colorado - Anschutz Medical Campus


title: Promoter Capture Hi-C of day 0 (D0) and day 7 (D7) 3T3-L1 cells before and after adipogenic treatment

summary: 3T3-L1 preadipocytes were differentiated into mature adipocytes using adipogenic differentiation media. Promoter Capture Hi-C at D0 (two days post confluency) and D7 of adipocyte differentiation was performed to analyse regulatory interactions.

overall_design: Promoter CHi-C analysis of D0 and D7 3T3-L1 cells before and after adipogenic differentiation was performed on 3 replicates each


title: Single-cell sequencing of brain macrophages after focused-ultrasound blood-brain barrier opening

city: New York

first: Elisa

last: Konofagou

state: NY

address: 630 West 168th Street, P&S 19th Fl. Rm. 418

department: Biomedical Engineering

institute: Columbia University

summary: Focused Ultrasound (FUS) combined with microbubbles (FUS+MB) to transiently open the blood brain barrier (BBB) has shown promise as an immunotherapeutic in models of neurodegenerative disorders - resulting in significantly reduced pathological load and improved cognition. Preliminary histology and bulk tissue analysis of FUS+MB have indicated brain macrophage changes as a potential mechanism of the immunotherapy. However, prior to this study the temporal effect of FUS+MB on the two dominant brain macrophage populations - microglia and central nervous system associated macrophages (CAM) has not been reported.    In this study, we establish that FUS+MB triggers a biphasic process involving both microglia and CAM. In the Phase I, 24h after treatment, microglia and resident CAM exhibit an early response signature, characterized by the upregulation of recruitment-associated chemokine and cytokines. In Phase II, 72h after treatment, CAM population size increases dramatically and both cell types exhibit a late response signature, characterized by upregulation of interferon genes indicative of cellular activation and immune response. Next, cell cycle analysis and immunohistochemistry indicate that microglia exhibit increased proliferation across both phases but CAM do not. Finally, the brain macrophage population size is correlated with the ultrasound-induced cavitation dose, indicating a dose-dependent response to treatment. The findings presented herein not only provide insight into the mechanism of the FUS+MB immunomodulatory effects but also into a mechanism of brain macrophage response that is capable of ameliorating neurological disease.

overall_design: Examination of transcriptomic changes in FUS+MB brain macrophages from 24h and 72h after treatment as compared to sham and naive samples.

first: Alina

middle: R

last: Kline-Schoder

first: Sana

last: Chintamen


title: Effect of HES1 and HES4 on gene expression in A549 cells

first: Jing

last: He

address: No. 160 Pujian Road

institute: Renji Hospital

summary: RNA-seq analysis in shHES1 and shHES4 A549 cells

overall_design: To reveal the differentially regulated genes in A549, we conducted shHES1 and shHES4 cells for RNA-seq analysis.


title: The deubiquitylating enzyme USP35 restricts regulated cell death to promote survival of renal clear cell carcinoma

city: Dalian

first: Han

last: Liu

state: Liaoning

address: 9 West sec. Lvshun South Road

institute: Dalian Medical University

summary: The ubiquitin proteasome system governs a wide spectrum of cellular events and offers therapeutic opportunities for pharmacological intervention in cancer treatment. Renal clear cell carcinoma represents the predominant histological subtype and accounts for the majority of cancer death related to kidney malignancies. Through a systematic survey in the association of human ubiquitin-specific proteases with patient prognosis of renal clear cell carcinoma and subsequent phenotypic validation, we uncovered the tumor-promoting role of USP35. Biochemical characterizations confirmed the stabilizing effects of USP35 towards multiple members of the IAP family in an enzymatic activity-dependent manner. USP35 silencing led to reduced expression levels of IAP proteins, which were accompanied with increased cellular apoptosis. Further transcriptomic analysis revealed that USP35 knockdown altered expression levels of NRF2 downstream transcripts, which were conferred by compromised NRF2 abundance. USP35 functions to maintain NRF2 levels by catalyzing its deubiquitylation and thus antagonizing degradation. NRF2 reduction imposed by USP35 silencing rendered renal clear cell carcinoma cells increased sensitivity to ferroptosis induction. Finally, induced USP35 knockdown markedly attenuated xenograft formation of renal clear cell carcinoma in nude mice. Hence, our findings identify a number of USP35 substrates and reveal the protecting role of USP35 against both apoptosis and ferroptosis in renal clear cell carcinoma.

overall_design: Gene expression profiling analysis with RNA-seq data of renal clear cell carcinoma 769-P cells following induced USP35 knockdown

first: Shanshan

first: Taushu


title: Effect of overexpression of NFAT5 on gene expression during TMZ resistance of U87 and U251 cells.

first: zhenyue

last: gao

address: Qixiangtai road 22

department: School of Basic Medical Sciences

institute: Tianjin Medical University

summary: To investigate the mechanism of NFAT5 resistance to TMZ in gliomas, we performed mRNA sequencing analysis of NFAT5-overexpressing U251 and U87 cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87 and U251 cells and its NFAT5 overexpression derivatives.

first: Yu

last: Ren


title: Alcohol-Induced Alterations in Sperm Noncoding RNAs Persist After One Month Cessation and Correlate with Indicators of Epididymal Mitochondrial Dysfunction II

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

summary: Background Chronic preconception paternal alcohol use modifies the sperm epigenome, inducing fetoplacental growth defects in the offspring of exposed males. A crucial outstanding question in the field of paternal epigenetic inheritance concerns the resilience of the male reproductive tract and the germline's capacity to recover and correct sperm-inherited epigenetic errors after stressor withdrawal. Objectives  We set out to determine if measures of the sperm-inherited epigenetic program revert to match the control treatment one month after withdrawing daily alcohol treatments. Materials and Methods  Using a voluntary access model, we exposed C57Bl6/J males to 10% alcohol for ten weeks, withdrew alcohol treatment for four weeks, and used RNA sequencing to examine gene expression patterns in the caput section of the epididymis. We then compared the abundance of sperm small RNA species between treatments.   Results  In the caput section of the epididymis, chronic alcohol exposures induced changes in the transcriptional control of genetic pathways related to mitochondrial function, oxidative phosphorylation, the generalized stress response (EIF2 signaling), and Sirtuin signaling. Subsequent analysis identified region-specific, alcohol-induced changes in mitochondrial DNA copy number across the epididymis, which correlated with increases in the mitochondrial DNA content of alcohol-exposed sperm. Notably, in the corpus section of the epididymis, increases in mitochondrial DNA copy number persisted one month after alcohol cessation. Analysis of sperm noncoding RNAs between Control and Alcohol-Exposed males one month after alcohol withdrawal revealed a ~100-fold increase in mir-196a, a microRNA induced as part of the Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2)-driven cellular antioxidant response.  Discussion and Conclusion Our data reveal that alcohol-induced epididymal mitochondrial dysfunction and differences in sperm noncoding RNA content persist after alcohol withdrawal. Further, differences in mir-196a and sperm mitochondrial DNA copy number may serve as viable biomarkers of adverse alterations in the sperm- inherited epigenetic program.

overall_design: RNA seq on EtOH treated and EtOH ceased isolated caput portions of the epididymis

first: Alexis

middle: N

last: Roach

first: Sanat

last: Bahdsalve

first: Sam

last: Higgins

first: Destani

last: Derrico

first: Kara

last: Thomas

first: Ali

last: Basel

middle: C


title: Transcriptomic profiling of FDH cells expressing wild-type or Site 4 mutant IL-3 receptor

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: RNA was extracted after treatment of FDH cells expressing wild-type or Site 4 mutant IL-3 receptor with IL-3 and the transcriptome was characterised using RNA sequencing.

overall_design: FDH cells expressing wild-type IL3Ra or IL3Ra P248L and bc were incubated with 100 ng/ml IL-3 for 2 and 5 days. RNA was extracted from 10^6 cells/condition using the Ambion mirVana miRNA isolation kit with phenol and RNA-seq was performed.

first: Winnie

middle: L

last: Kan


title: Transcriptomic and ChIP-Seq analyses reveal an important role for the ABI4 during BR response in Arabidopsis

city: Shanghai

first: Xiaolei

address: Chenhua Road 3888

institute: Chinese Academy of Sciences

summary: Brassinosteroids (BRs) are growth-promoting steroid hormones in plants. BRs affect plant growth by regulating panels of downstream genes. Much effort has been made to establish BR-regulated gene expression networks, but these published expression networks poorly overlap. To address this, here we build an optimal BR-regulated gene expression network. 7- and 24-day-old seedlings of constitutive photomorphogenesis and dwarfism (cpd) mutant and bri1-701 (brassinosteroid-insensitive 1) brl1 (BRI1-like receptor genes 1) brl3 (BRI1-like receptor genes 3) triple mutant seedlings were treated with brassinolide (BL), and RNA sequencing (RNA-seq) was used to detect differentially expressed genes (DEGs). By this approach, we generated a transcriptomic database of 4498 DEGs and identified 110 transcription factors specifically respond to BR at different stage. Moreover, we found that among the identified BR-responsive transcription factors, ABSCISIC ACID-INSENSlTIVE4 (ABI4), an ethylene response factor (ERF) transcription factor, inhibits BR-regulated growth. Compared to wild-type plants, the abi4-102 mutant was less sensitive to brassinazole (BRZ) and more sensitive to BR. Next, we performed a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) assay and found that ABI4 directly binds to the BAK1 (BRI1 Associated receptor Kinase 1) promoter and inhibits transcription. These results provide new insights into BR-responsive gene functions in regulating plant growth at different stages and may serve as a basis for predicting gene function, selecting candidate genes, and improving the understanding of BR regulatory pathways.

overall_design: mRNA profiles of 7-and 24-day old cpd  and bri1-701 brl1 brl3 arabidopsis seedlings treated with or without brassinolide (BL) were generated by deep sequencing, in triplicate.

first: Jianming

last: Li


title: CAGE-seq of day 0 (D0) and day 7 (D7) 3T3-L1 cells before and after adipogenic treatment

first: Borbala

last: Mifsud

summary: 3T3-L1 preadipocytes were differentiated into mature adipocytes using adipogenic differentiation media. Total RNA was isolated at D0 (two days post confluency) and D7 of adipocyte differentiation. nAnT-iCAGE sequencing was performed to analyse transcriptional start sites.

overall_design: CAGE-seq analysis of D0 and D7 3T3-L1 cells before and after adipogenic differentiation was performed on 4 replicates each

first: Sandovici

last: Ionel


title: Plasma circRNA sequencing in normal subjects and patients with atrial fibrillation

city: Nanjing

first: Minglong

last: Chen

state: Jiangsu

address: 300#, Guangzhou Road

department: Cardiology

institute: The First Affiliated Hospital of Nanjing Medical University

summary:
Purpose: The aim of this study was to evaluate the difference of plasma circRNA between patients with atrial fibrillation and normal subjects by high-throughput sequencing results.

Methods: Total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.Then, 200 ng RNA was sequenced with high throughput, and then pathway and go analysis were used for comprehensive analysis.Finally, RT-PCR method was used to validate in large sample population

Results: High throughput sequencing results showed that there were significant differences in plasma circRNA expression between patients with atrial fibrillation and non-atrial fibrillation, and 2 optional circRNA in 12 randomly selected circRNA differences were found to be significant in the population

Conclusions:It is the first time that we have used high-throughput sequencing to study the difference of plasma circrna between patients with atrial fibrillation and normal people. The results of sequencing show that the expression of circrna is quite different between the two groups of people. Therefore, we believe that circRNA may play an important role in the occurrence and development of atrial fibrillation.

overall_design: Five normal subjects and five patients with atrial fibrillation

first: Qi

last: Jiang

first: Yongping

last: Lin


city: shanghai

first: xiaomeng

last: cheng

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan University

summary: We depleted TIMM13 using short interfering RNA (siRNA) in A549 lung cancer cells, and found that silencing of TIMM13 could significantly inhibit A549 cell proliferation. Thus, we conducted RNA-seq in the A549 cells transduced with either nontargeting siRNA or two distinct TIMM13-specific siRNAs. We observed widespread gene expression change in A549 cells upon TIMM13 knockdown.

overall_design: Knockdown TIMM13 in A549 lung cancer cell line by two independent siRNAs, to investigate the mechanism of TIMM13 in regulation of cell proliferation.

first: Zhaozhao

last: Zhao

first: Ting

last: Ni


title: mRNA expression of Schwann cell precursor cells from embryonic rats

status: Public on Jun 16 2023

city: Hachioji

first: Junji

last: Yamauchi

state: Tokyo

address: 1432-1 Horinouchi

institute: The University of Pharmacy and Life Science

summary: To investigate an RNA population of rat Schwann cell precursor cells

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of Schwann cell precursor cells

first: Yuki

last: Miyamoto


title: CBX8 promotes LUAD growth and metastasis through transcriptional repression of CDKN2C and SCEL

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

summary: CBX8 promotes LUAD cell proliferation and migration through downregulating the expression of CDKN2C and SCEL.The mRNAs from A549 cells expressing control shRNAs or CBX8 shRNAs were extracted and subjected to RNA-seq.

overall_design: Examination of gene expression changes in CBX8 knockdown and control A549 cells.

first: Lihong

last: Yang

first: Xuanyuan


title: Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner [Fasted]

city: Philadelphia

first: Nathaniel

last: Snyder

state: Pennsylvania

address: 3500 N Broad St, 455 Merb

institute: Temple University

summary: As part of the investigation in the endogenous role of Acot2 in skeletal muscle, we performed RNAseq analysis on Quadriceps muscle from control (Loxp/Loxp) mice and micew  with striated muscle specific knockout of Acot2 (muscle creatine kinase promoter)

overall_design: RNAseq was performed on Quad in mice after an overnight fasted (14 hrs); tissue harvested 9 - 10:30am

first: Carmen

last: Bekeova

first: Erin

last: Seifert


title: Urotensin II/GPR14 Pathway Regulates Chronic Itch in Mice

city: Kaifeng City, Henan Province

first: Hua

state: Henan Province

address: Jinming Campus of Henan University

institute: Henan University

summary: In order to analyze the regulatory effects of UII and GPR14 on gene transcription in Mc903-induced atopic dermatitis skin, ear skin collected from MC903 chronic itch mouse model on day 13 was used for in-depth analysis and sequencing of skin gene expression. The effect of GSK1562590 on the expression of pruritus and inflammatory factors in dermatitis was detected by RNA-seq.

overall_design: Mice were evenly divided into two groups according to body weight. MC903 was applied to the left ear and anhydrous ethanol was applied to the right ear for seven consecutive days. On the 8th day after the success of the model, mc903 was applied to the left ear of mice and anhydrous ethanol was applied to the right ear, and then the mice were treated with equilibrium treatment for 1 hour. After 1 hour, the mice were treated with gavage immediately. The inhibitor group was given GSK1562590(5mg/kg, dose 100ul); The positive control group only applied the same volume of vehicle. Immediately after the drug was applied, mice were subjected to behavioral video 60mim. After the MC903 chronic pruria model was completed, mouse ear skin was extracted for RNA-seq.

first: RenKai

last: Zhu

first: Wenhao

last: Zhang

first: Weiwei

first: Xinrong

last: Yan

first: Chunxu

last: Shan

first: Shanghai

last: Xue

first: Ruizhen

last: Wang

first: Xiaolong

last: Dai

first: Ciara

last: Larkin

first: Jiafu

first: Jianghui

last: Meng


title: Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner [HFD]

overall_design: RNAseq was performed on Quad in mice fed 60% high fat diet for 7 days (Research Diets D12492); Quad was harvested in the morning (9-10:30am)


title: Circle-seq of skin samples from SD rats irradiated with different fractional electron beam radiation

city: Chengdu

first: Bin

last: Shi

address: Yulin Street

institute: Sichuan University

summary: To investigate circular DNA alterations in response to radiation in skin and further study the function of circular DNA

overall_design: We purify and sequence circular DNA via Circle-seq from skin samples of SD rats irradiated with different fractional electron beam radiation (control, 5 Gy X 2 (low dose group) and 5 Gy X 4 (high dose group), respectively).

first: Shuyu


title: Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner [Chow fed]

first: Nathaniel

overall_design: RNAseq was performed on Quad in mice fed regular chow diet (Purina 5001); Quad was harvested in the morning (9-10:30am)


title: Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner

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

overall_design: Refer to individual Series


title: Targeted alveolar regeneration with Frizzled-specific agonists

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary: Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, wherein Wnt-dependent epithelial and stromal progenitors are intermingled, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Moreover, Fzd5 was uniquely required for alveolar epithelial stem cell activity. However, by developing an expanded repertoire of Fzd-Lrp agonists (FLAgs), we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. Fzd5 and Fzd6 FLAgs stimulated supra-physiological alveolar epithelial stem cell activity in mice following lung injury, but only Fzd6 FLAg promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.

overall_design: Cells  grown with Wnt agonist CHIR99201 (LGK_CHIR99201)  for 19 days and then Wnt is withdrawn for 24 hours (24hourwithdrawal) and 48 hours (48hourwithdrawal). We also withdrew CHIR99201 and replaced it with Wnt (LGK974_WNT), Fzd5 agonist (LGK974_FZD5_Agonist) and Fzd6 agonist (LGK974_FZD6_Agonist).

first: R


title: Heterogeneity of therapy-resistant CML cells

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary:
Purpose: We previously demonstrated that immunophenotypically CD34-CD38- TKI resistant LSC/LIC population was clearly heterogeneous. The goal of this study is to explore more about the drug-resistant LSC/LICs
Methods: CML patient cells were treated for 7 days with imatinib and live cells were subjected to scRNA-sequencing
Results: scRNA-seq reveals heterogeneity in the therapy resistant cells. Distinct expression profiles, yet with an interrelated continuumsuggest the existence of a depply-quiescent persister population within resistant cells.
Conclusions: In this study  using single cell transcriptomics and single cell metabolomics analyses we identify and characterize a deeply-quiescent/persister CML LSC/LIC population subset of CML patient cells which is highly dependent on FAO for their metabolomic requierements

overall_design: Single cell transcriptomics of imatinib resistant CML LSC/LICs

first: Nyam-Osor

last: Chimge

first: Michael

last: Kahn


title: Identification of KPNA2 targets by RNA-Seq in osteosarcoma

city: Changzhou

first: Sheng

last: Zhou

address: 29 Xinlong Lane

institute: The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University

summary: Despite recent advances, the poor outcomes in osteosarcoma suggest that novel therapeutic targets are needed. Karyopherin alpha 2 (KPNA2) is a nuclear import factor, which functions as an oncogene in many cancers. However, the role of KPNA2 in osteosarcoma and its mechanism of action are still unclear. To identify gene signatures that play a role in metastasis, we performed RNA-Seq of gene expression profiling on U2OS cells treated with siKPNA2 and siNC (in triplicate for each group).

overall_design: U2OS cells were treated with siKPNA2 and siNC (in triplicate for each group).

first: Ruiping

last: Liu


title: RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic and fructo-oligosaccharides

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

institute: Tianshui normal university

summary:
Purpose:Our data significantly advance understanding of Probiotics and Fructooligosaccharide regulatory mechanism  in  ileum of Taiping chicken
Methods: Using RNA-seq analysis to study the gene expression in ileum tissue after Taiping chicken was given Probiotics and Fructooligosaccharide
Results: A total of 164,629,826 and 149,883,266  raw reads were generated from the CT and MP_ FOS, respectively . After removing the interference data, about 164,028,872 and 149,364,852 clean reads were obtained
Conclusions: through high-throughput sequencing of the six libraries from ileum of Taiping chicken, the expression level of mRNA has significant changes after  given probiotics

overall_design: Control group (CT), birds were fed a corn-soybean basal diet , Probiotics and Fructooligosaccharide group (MP_ FOS), birds were given a basal diet supplemented with  2 mL of probiotics per litre of water and 1 mL of  Fructooligosaccharide per litre of water


title: Low input RNA transcriptomic analysis of spleen and lymph node Fibroblastic Reticular Cells (FRCs) in a murine model of Diffuse Large B-cell Lymphoma (DLBCL)

city: London

first: Alan

last: Ramsay

state: -- Select One --

address: Great Maze Pond

country: United Kingdom

institute: King's College London

summary:
Purpose: analyze the transcriptomic changes occurring in spleen (SP) and lymph node (LN) stromal cells in a murine model of DLBCL.

Purpose: analyze the transcriptomic changes occurring in FRCs in DLBCL

overall_design:
mRNA was extracted from flow sorted FRCs (gating on CD45-, CD31-, PDPN+ cells) isolated from spleen and lymph nodes of lymphoma I{mu}BCL6 and age-matched WT mice

Human samples: mRNA was isolated from healthy LN FRCs (p3)  left untreated or conditioned with human DLBCL cells (cell lines or primary tumor cells)  for 48 hours using transwell (pore size 0.4µm). Primary FRCs directly isolated from DLBCL biopsies were also analyzed (p1)

first: Benedetta

last: Apollonio

first: Peter

last: Jarvis

first: Domenico

last: Cozzetto


title: Molecular analysis in SADBE-induced ACD (Allergic contact dermatitis) model

city: Guangzhou

first: Xueting

address: Changgangdong 250

institute: The Second Affiliated Hospital of Guangzhou Medical University

summary: The mechanisms underlying pruritus of SADBE induced ACD (Allergic contact dermatitis) remain poorly understood,due to limited clinical data and animal studies. In this study, we investigated whether there are certain key signaling molecules downstream of the recently identified peptides mediating itch in the spinal cord. We investigated the changes in the trascriptome by performing RNAseq of cervical spinal cords in control and SADBE induced ACD model. Our study represents the detailed analysis of transcriptomes of spinal cord in chronic itch model with biologic replicates, generated by RNA-seq technology.

overall_design: six mice (3 controls and 3 ACD) were sacrificed. Cervical spinal cord isolation is followed by RNA extraction of single samples, library preparation and sequencing.

first: Yanmei

first: De

first: Yuhuan

last: Wen

first: Ailin

last: Tao


title: Single cell transcriptomic of lymph node stromal cells  in a murine model of DLBCL

summary: Purpose: analyze the transcriptomic changes occurring in LN stromal cells in a murine model of DLBCL

overall_design: mRNA was extracted from flow sorted FRCs isolated from spleen and LN


title: The 31 pairs of FF (fresh frozen) andFFPE (Formalin-fixed paraffin-embedded) data for the application of 95GC to FFPE in 2019.

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

summary: The study aimed to apply 95GC, originally developed using fresh‑frozen (FF) tissues, to formalin‑fixed paraffin‑embedded (FFPE) tissues, because FFPE tissues are routinely prepared and are readily available. Although we previously reported the applicability of 72GC to FFPE tissues (DOI: 10.1016/j.clbc.2013.11.006), the present study aimed to improve the accuracy of 95GC for FFPE tissues using the reference robust multiarray average (refRMA) method, optimized for FFPE tissues. Therefore, a 95GC RS (Recurrence Score) was first developed and then the accuracy of the newly developed 95GC algorithm for FFPE tissues was evaluated using the 95GC RS. These 31 pairs of FF and FFPE data are included in the concordance analysis of 95GC high/low results between FF and FFPE (Figure 3B). A long time passed, and now it is unclear how these 31 cases were distributed among the analysis.    *Note: This old data has been updated multiple times by the other members.  Then, there are some differences from the original paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper.  PMID: 31638234  DOI: 10.3892/or.2019.7358

overall_design: RNA was extracted from 31 pairs of FF (fresh frozen) and FFPE (Formalin-fixed paraffin-embedded) tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.

first: Ryo

last: Tsunashima

first: Yasuto

last: Naoi


title: Transcriptomic analysis of human Fibroblastic Reticular Cells (FRCs) cells in Diffuse Large B-cell Lymphoma (DLBCL)

summary: Purpose: analyze the transcriptomic changes occurring in FRCs in DLBCL

overall_design: mRNA was isolated from healthy LN FRCs (p3)  left untreated or conditioned with human DLBCL cells (cell lines or primary tumor cells)  for 48 hours using transwell (pore size 0.4µm). Primary FRCs directly isolated from DLBCL biopsies were also analyzed (p1)


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [16A, 16C]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (16A_210810, 16C_210408, 16C_210415).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

last: Berube

first: Huaming

last: Chen

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: Title: RNA-seq analysis of mRNA profiles in the livers of HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice fed with an MCD for 3 weeks.

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
ionPurpose: The goal of this study is to investigate how HuR regulates NASH progression.
Methods: The hepatic mRNA profiles of HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice (n=3 for each group) fed with an MCD for 3 weeks were generated by deep sequencing using an Illumina Novaseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of hepatic mRNA profiles in HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice fed with an MCD for 3 weeks, generated by RNA-seq technology. Our results show that 353 genes were upregulated and 422 genes were downregulated. Gene Ontology (GO) analysis showed that genes related to leukocyte migration, leukocyte chemotaxis, cell chemotaxis, neutrophil migration and Fc receptor signaling pathway were significantly decreased, which contributes to the protective effects of NASH progression in HKO mice.

overall_design: The hepatic mRNA profiles in HuR flox/flox and hepatocyte-specific HuR knockout (HKO) mice (n=3 for each group) fed with an MCD for 3 weeks were generated by deep sequencing using Illumina Novaseq platform.

first: Xinzhi

last: Li


title: Effect of conditional knockout of Prkci (atypical PKC iota/lambda coding gene) in mouse enterocytes reveals robust innate immunity transcriptomic response

status: Public on Jun 15 2023

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Atypical PKCiota/lambda is a key effector of the PAR polarity complex which is considered a master determinant of  apico-basal polarity in single-layered epithelial cells. In polarized epithelial cells aPKC is exquisitely localized by the PAR6 partner to a belt nearby the tight junctions. Surprisingly, tissue specific knock out of the transgenic floxed version with villin-CRE showed a chronic inflammation phenotype. The observations were made in three different independent transgenic mouse lines and published by three different groups including ours  (PMID: 27226486; PMID: 30552022; PMID: 21744423 ), which is reassuring for reproducibility. An additional  double KO in both aPKC isoforms further confirmed the results (PMID: 30552022 ). The animals were viable and there was not strong diarrheal or constipation phenotype characteristic of polarity defects in intestinal epithelia. With few exceptions such as ezrin localization, apical polarity markers were generally well polarized. There were changes in cytokine expression by epithelial cells and infiltration of CD8+ T cells (PMID: 27226486; PMID: 30552022).  The goal of the study was to get an unbiased catalog of the transcriptional changes induced by aPKC iota/lambda defect in intestinal epithelial cells to understand the ontology of  gene expression downstream of the PAR polarity complex. The results are consistent with broad changes in NF-kB and IFN dependent transcriptional pathways, possibly mediated by ROCK and Med17 downstream of aPKCiota/lambda (PMID: 2722648; PMID: 33596087). This study was published in PMID: 33596087.

overall_design: Mouse intestine was extracted from Prkci flox/flox (control, samples 784(M)  787(F)  794(M)) and co-housed endogamic Prkci flox/flox x Villin-CRE (experimental conditional KO, 826(M)  861(F)  867(M)) according to IACUC-approved protocol. Immediately after euthanasia, 10 cm segments of jejunum-ileum were cut.  Several washes of the lumen were performed using PBS supplemented with 10 mM glucose, 30 mM EDTA, 5 mM DTT to remove debris and mucus. Following washes, each segment of intestine was clamped with the same ice-cold  solution for 20 minutes. Intestinal mucosae were  squeezed by exerting gentle pressure  with tweezers and  drained by releasing one clamp into sample tube. After a quick spin down, RNA inhibitor (Qiagen inc., Germantown, MD) was immediately added to the pellet. This procedure was repeated at least 5 times until microscopic visualization of the cell suspension showed mostly epithelial cell clumps. Total RNA was extracted using 1 mL TRIzol® Reagent and vigorously homogenized several times using 3 ml syringe (needles 18G11/2 and 20G11/2). Samples were then incubated at room temperature to permit complete dissociation of the nucleoprotein complex before adding chloroform (0.2 mL/mL phenol). Total RNA was then precipitated with isopropanol from the aqueous phase followed by 10 minutes centrifugation 12,000g at 4°C. Pellets were washed with 75% Ethanol, centrifuged for 5 minutes at 7500g, air-dried and finally resuspended in RNase-free water. All RNA samples were subjected to DNase Treatment and Removal Reagents following manufacturer’s instructions (Ambion by Life Technologies provided by Thermofisher Scientific, Waltham, MA). RNA samples were then stored at -80C and submitted for poly-A selection and Illumina NextSeq/NovaSeq NGS technology RNAseq.

first: Pedro

middle: J

last: Salas

first: Anastasia

last: Mashukova

first: Radia

last: Forteza

first: Viraj

last: Shah


title: Integrated extracellular microRNA profiling for uterine sarcomas

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: MicroRNAs stably exist in the peripheral blood and can be potential biomarkers. In this study, we evaluated the serum miRNA profiles of patients with uterine sarcomas.

overall_design: Serum samples of 30 women, which consist of leiomyosarcoma, adenosarcoma, endometrial stromal sarcoma (ESS), uterine smooth muscle tumors of uncertain malignant potential (STUMP), and leiomyoma, were used. Serum miRNA profiles were investigated using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

first: Akira

last: Yokoi

first: Juntaro

last: Matsuzaki

first: Yusuke

last: Yamamoto

first: Kenta

last: Takahashi

first: Mitsuya

last: Ishikawa

first: Junpei

last: Kawauchi

first: Satoko

last: Takizawa

first: Yoshiaki

last: Aoki

first: Ken

last: Kato

first: Tomoyasu

first: Takahiro

last: Ochiya


title: Role of Carboxylesterase 1 in THP-1 Human  Macrophages Under Basal Conditions or Treated with LPS+IFN Gamma (M1) OR with IL4 (M2)

city: Starkville

first: Oluwabori

last: Adekanye

state: MS

address: 240 Wise Center drive

institute: Mississippi State University

summary: Macrophages are one of the major immune cell types responsible for maintaining the innate immunity of the host. They can be polarized into one of the two sub populations in vitro. M1 which is bactericidal and pro inflammatory, and M2 which is anti inflammatory and active in tissue repair. Carboxylesterases are members of the serine hydrolase superfamily. They can hydrolyze ester-containing compounds into alcohol- and carboxylic acid-containing products. About six isoforms have been identified in humans, and CES1 and CES2 are the most studied and best characterized. CES1 is a triacylglycerol hydrolase. Triacylglycerols are primarily found in cytoplasmic lipid droplets and are the major form of fat storage in the cells. Hydrolysis of triacylglycerol liberates free fatty acids that are crucial for cellular metabolic activities.  Liberated fatty acids such as polyunsaturated fatty acids (PUFA) become substrates for enzymes that produce eicosanoids, while other fatty acids act as ligands for membrane receptors and nuclear receptors, such as toll-like receptor 4 (TLR4) and PPAR gamma respectively. We sought to understand how the inactivation of CES1 in the human THP-1 macrophage cell line would impact lipid metabolism and macrophage phenotype under resting conditions and following stimulation. Control and CES1 knockdown (KD) THP-1 monocytic cells were differentiated into macrophages with 20 nM PMA over 72 h, then rested for 24 h prior to being treated with either 1-ug/mL LPS + 100-ng/mL interferon gamma (M1) or 100-ng/mL IL-4 (M2) for 24 h, or they were left untreated (M0) for the same length of time. Total RNA was extracted using QIAshredder (QIAGEN) and sent to Novogene Inc (Sacramento, CA) for library construction, RNA sequencing and data processing. Our data present a transcriptomic snapshot when CES1 is knocked down in THP-1 macrophages during the resting state and polarized state.

overall_design:
To investigate the role of cabroxylestesrase 1 in naïve (M0), M1, and M2 THP-1 macrophages
Carboxylesterase 1 gene was stably knocked down with shRNA using a lentivirus system, and its level of expression was verified to be at least 85% reduced.
We perfomed comparative gene expression profiling of the control and knocked down (CES1KD) macrophages using three experimental groups. Experimental groups were defined as follows: resting (M0), LPS + interferon gamma (M1), and IL4 (M2), each analyzed in quadruplicate.

first: Abdolsamad

last: Borazjani

first: Matthew

last: Ross


title: Hfq LiRIP-seq in Salmonella

city: Shanghai

first: Fang

last: Liu

address: Life Science Research Building 320 Yueyang Road, Xuhui District

institute: Institut Pasteur of Shanghai, Chinese Academy of Sciences

summary: We have developed a novel approach named LiRIP-seq to profile the global RNA-RNA interactome in Salmonella enterica. By pulse expressing T4 RNA ligase from an inducible pBAD promoter, LiRIP-seq enables in vivo proximity ligation of Hfq-bound RNAs to their interaction partners. This is followed by enrichment of ligation products (RNA chimeras) using Hfq-coIP and subsequent RNA-seq analysis.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Salmonella  wild type or hfq::3xFLAG tagged strains carrying the plasmid pYC582 or empty vector were grown in LB medium at 37 °C. T4 RNA ligase was induced for 30 min by addition of L-arabinose when the culture reached the indicated OD600 (0.3, 1.5, 2.0+2.5h). RNA-RNA interactomes were profiled by  Hfq-coIP and subsequent RNA-seq analysis.


title: Migration speed of captured breast cancer subpopulations correlates with metastatic fitness

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous breast cancer cell populations, based on their migratory ability alone. We show that captured fast cell subpopulations retain higher migration speed and focal adhesion dynamics over many generations due to a motility-related transcriptomic profile. Upregulated genes in fast selected cells encoded integrin subunits, proto-cadherins and numerous other genes associated with cell migration. Dysregulation of several of these genes correlated with poor survival outcomes in patients, while primary tumors established from fast cells generated a higher number of circulating tumor cells and soft tissue metastases in vivo. Subpopulations of cells selected for a highly migratory phenotype demonstrated an increased fitness for metastasis.

overall_design: We compare parental cells to captured cells. We have 2 batches of 3 technical replicates for the 2 biological replicates. 12 samples in total.

first: Nicolas

last: Desjardins-Lecavalier

last: Annis

first: Alexander

last: Nowakowski

last: Kiepas

first: Loïc

last: Binan

first: Joannie

last: Roy

first: Graziana

last: Modica

first: Steven

last: Hébert

first: Peter

last: Siegel

first: Santiago

last: Costantino


title: Responsiveness to vedolizumab therapy in ulcerative colitis is associated with alterations in immune cell-cell communications

first: Eunice

last: Choi

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Ulcerative colitis (UC) is a major subtype of inflammatory bowel disease (IBD), a spectrum of chronic intestinal disorders caused by dysregulated immune responses to gut microbiota. Although transcriptional and functional changes in a number of immune cell types have been implicated in the pathogenesis of IBD, the cellular interactions and signals that drive these changes have been less well-studied. Moreover, the precise mechanisms of action underlying many biologic therapies, including the anti-47 integrin antagonist vedolizumab, remain incompletely understood. Our study aimed to explore possible additional mechanisms through which vedolizumab acts.

overall_design: We performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) on peripheral blood and colon immune cells derived from patients with ulcerative colitis treated with the anti-47 integrin antagonist vedolizumab. We applied a previously published computational approach, NicheNet, to predict immune cell-cell interactions, revealing putative ligand-receptor pairs and key transcriptional changes downstream of these cell-cell communications (CCC).

first: Duong

last: Han

first: Chiang

last: Natalie

first: Choi

last: Eunice

first: Patel

last: Shefali

first: Olvera

last: Jocelyn

first: Liu

last: Yi

first: Lhsuan

last: Yun

first: Yao

last: Priscilla

first: Hsu

last: Paul

first: Wong

last: William

first: Indralingam

last: Cynthia

first: Tsai

last: Matthew

first: Boland

last: Brigid

first: Wang

last: Wei

first: Chang

last: John


title: Induction of leaf curling in cassava plants by the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae)

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: Certain phytophagous insects can induce leaf curling in their host plants that may provide protected and nutrient-rich habitats. However, the mechanisms of this induction remain poorly understood. The cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), is a serious pest of the cassava and causes leaf curling. To reveal the mechanisms of leaf-curl induction, we first inoculated varying numbers of mealybugs in different locations, namely, the apical meristem and the stem, on cassava seedlings. Second, we performed transcriptome analysis using the total RNA extracted from leaves. The results showed that a single insect was able to induce leaf curling, but the intensity and frequency of the leaf curling were positively correlated with the number of insects. Furthermore, the leaf curling occurred when the mealybugs fed on or close to the apical meristem but not when they fed on the stem. Transcriptome analysis identified a total of 3,931 differentially expressed genes (DEGs) from intact plants and the plants inoculated with mealybugs at different time points. GO analysis of the biological processes revealed that the DEGs contained a series of factors for leaf development of the adaxial–abaxial axis, and auxin biosynthesis and polarity. This suggests that alterations in these functions may cause leaf curling.

overall_design: To investigate the effects of P. manihoti on deformation, varying numbers of second and third instar nymphs of P. manihoti were inoculated into the cassava plants. We inoculated 1, 5, or 10 nymphs into the top of the plants and placed the plants individually in a plastic container (80 mm × 80 mm × 205 mm) with a fine mesh plastic screen on the top and bottom. Eight plants were used for each treatment. The occurrence of deformation was checked every 2–3 days. The first and second leaves from the top stems of the control and inoculated plants were collected at 1, 3, 5, and 10 d after inoculation for RNA-seq analysis.

first: Shun-ichiro

last: Takano

first: Yoshinori

last: Utsumi

first: Atsushi

last: Nagano

first: Satoshi

last: Takahashi

first: Akihiro

last: Ezoe

first: Motoaki

last: Seki

first: Thi

last: Le

first: Keiji

last: Takasu


title: Dynamics of N6-methyladenosine modification during aging and their potential roles in the degeneration of intervertebral disc

city: Chongqing

first: Libangxi

last: Liu

address: 183 Xinqiao Main Street Shapingba, Chongqing 400037, People’s  Republic of China

institute: Department of Orthopedics Xinqiao Hospital, Army Medical University

summary: N6-methyladenosine (m6A) modification, as one of the epigenetic modification of mRNAs, has been found implicating in various musculoskeletal disorders including IDD. However, the m6A dynamics in the progression of aging related IDD remain largely unknown. The purpose of this study was to investigate the m6A methylome of nucleus pulpous (NP) tissues from intervertebral disc (IVD) at different ages of rats.

overall_design: IVD tissues were obtained from rats at different ages, including 2, 10, and 20 months. Subsequently, methylated RNA immunoprecipitation next generation sequencing (MeRIP-seq) and RNA-seq were conducted to identify differences in m6A methylomes and gene expression in NP tissues, and bioinformatics analysis was used to determine the relationship between them.

first: Hong

last: Sun

first: Chencheng

last: Feng


title: Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

institute: CNRGH

summary: Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection. Here we profile human PBMCs in different conditions using single-cell RNA sequencing.

overall_design: We performed single-cell gene expression profiling on 6 different samples for resting, stimulated, fresh and frozen PBMC samples.

first: Céline

last: Derbois

first: Marie-Ange

last: Palomares

first: Jean-François

last: Deleuze

last: Cabannes


title: Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion zone

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

summary: Functional modifications shape the ability of populations to cope with anthropogenic environmental changes. These modifications are mediated by complex interactions between transmitted and non-transmitted changes which limit their prediction. To study how these changes are intertwined with evolutionary processes in a case of persistent anthropogenic environmental change, we characterized population structure, genetic diversity and individual response on gene expression of the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant. We detected lower effective population size in populations most exposed to ionizing radiation that is not compensated by migrations from surrounding areas. We also highlight a decreased body condition of frogs living in the most contaminated area, a peculiar transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. Population most exposed to ionizing radiation in the Chernobyl exclusion zone experience both genetic drift and functional changes that collectively point towards deleterious effects of ionizing radiation on tree frogs and potential difficulty to adapt to this novel environment.

overall_design: Sampling of 87 Hyla Orientalis individuals along a gradient of radioactive contamination in the chernobyl exlusion zone and in Slavutich, and performed RNAseq  analysis to study gene expression and SNP polymorphisms

first: Olivier

last: Armant

first: Clément

last: Car

first: Sandrine

last: Frelon

first: Luc

last: Camoin


title: Sirtuin 2 inhibition selectively induces senescence in ATRX-deficient malignant gliomas by modulating chromatin landscapes genome-wide [RNA-Seq]

city: Houston

first: Prit Benny

last: Malgulwar

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

institute: U.T. M.D. ANDERSON CANCER CENTER

summary:
To investigate the effect of SIRT2 inhibition on global transcriptomics  profile, we inhibited Sirt2 using small molecules (AGK2)
Our analysis reports phenotype-reversal of gliomas as well as induction of terminal differentiation program.

overall_design: Comparative gene expression profiling analysis of RNA-seqdata for murine neuroprogenitor cells (Tp53-/- and Atrx-/- ) and HDAC inhibitiors (AGK2)

first: Prit

middle: B

first: Jason

middle: T

last: Huse


title: Sirtuin 2 inhibition selectively induces senescence in ATRX-deficient malignant gliomas by modulating chromatin landscapes genome-wide [ChIP-Seq]

summary:
To investigate the effect of SIRT2 inhibition on global epigenome profile, we inhibited SIRT2 using AGK2 and performed ChIP-seq analysis for enhnacers, transcription and repressor histone marks
Our analysis reports global epigenome changes that is responsible for phenotype-reversal of gliomas as well as induction of terminal differentiation program.

overall_design: Comparative epigenome profiling analysis of ChIP-seq-seq data for murine neuroprogenitor cells (Tp53-/- and Atrx-/- ) and HDAC inhibitiors (AGK2)


title: Transcriptome-wide profiling of RNA N4-cytidine acetylation in Arabidopsis thaliana and Oryza sativa

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

summary:
Using acRIP-seq, we present transcriptome-wide atlases of ac4C in Arabidopsis thaliana and Oryza sativa. Analysis of ac4C distribution reveals ac4C is enriched near translation start sites in rice while near translation start sites and end sites in Arabidopsis. Further analysis shows ac4C contributes to RNA stability, splicing and translation.
We then performed NaCNBH3 treatment and RNA-seq to measure C to T mutation and RNC-seq to measure translation efficiency in Arabidopsis.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: This series includes samples for ac4C-seq: control and treated samples from Arabidopsis and rice, samples for acRIP-seq: two biological replicates for ac4C IP, IgG control and input samples and samples for RNC-seq: Input (mRNA) and Ribosome associated (RNC-mRNA) samples from Arabidopsis, Input (mRNA) and Ribosome associated (RNC-mRNA) samples from wild type rice and osnat10.

first: Bin

last: Li

first: Donghao

first: Linjun

last: Cai


title: Effects of BRAF and ERK inhibition on papillary and anaplastic thyroid cancer

city: Aurora

first: Rebecca

middle: E

last: Schweppe

state: Colorado

department: Endocrinology

institute: The University of Colorado Anschutz Medical Campus

summary: To investigate the effects of combined BRAF inhibition (dabrafenib) and ERK inhibition (ulixertinib) on papillary and anaplastic thyroid cancer transcriptional reprogramming

overall_design: Comparative gene expression profiling analysis of RNA-sequencing data for CUTC5 and CUTC60 cells treated with vehicle, dabrafenib, ulixertinib, or the combination

first: Hannah

last: Hicks

first: Nikita

last: Pozdeyev


title: Nutritional Requirements of Human Induced Pluripotent Stem Cells

city: Chicago

first: Davi

middle: Marco

last: Lyra Leite

state: Illinois

address: 320 E Superior St 8-450

institute: Northwestern University

summary: To investigate transcriptome changes on five different hiPSC lines cultured in standard DMEM/F12 and a novel basal media called BMEM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 19c3, 21c10, 22c10, 23c1, and 26c3 human induced pluripotent stem cell lines cultured in DMEM/F12 (control) or BMEM, with three independent biological replicates (derived from different passages) for each sample.

last: Lyra-Leite

first: Raymond

last: Copley

first: Paul

middle: W

last: Burridge


title: Genome-wide maps of transcription in PNPO overexpression(OE) and wildtype(WT) cells in Multiple Myeloma

city: Jiangsu Nanjing

first: Deng

middle: Zhen

last: Dong

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

summary: We found different genes change between WT and OE cells.

overall_design: Examination of 2 different genes changes in 2 cell types.

first: Zhendong

last: Deng