title: Metasilicate-based alkaline mineral water maintains intestinal homeostasis through GLP2-dependent gut-brain-microbiome system: providing new potential therapy for irritable bowel syndrome

status: Public on Mar 31 2023

city: Haerbin

first: Chen

last: Jian

state: China

address: College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P.R. China

country: China

institute: Northeast Agricultural University

type: Expression profiling by high throughput sequencing

summary: To explore the difference in gene expression in the small intestine of weaned piglets who metasilicate-based alkaline mineral water or basic water.

overall_design: Comparative gene expression profiling analysis of drinking metasilicate-based alkaline mineral water treatment piglet and Control group piglets.

first: Jian

last: Chen

first: Bi-Chen

last: Zhao

first: Mu-Zi

last: Li

first: Xiang-Wen

last: Xu

first: Xue-Yan

last: Dai

first: Ya-Ru

first: Jin-Long


title: Impact of the Voltage-Gated Calcium Channel Antagonist Nimodipinedipine on the Development of Oligodendrocyte Precursor Cells

status: Public on Mar 30 2023

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

country: Germany

institute: University Hospital Erlangen

summary:
We investigated the effects of nimodipine, a L-type voltage-gated calcium channel antagonist, on the expression profile of myelin genes in the oligodendrocyte precursor cell (OPC) line Oli-Neu.
We  performed gene expression profiling analysis using data obtained from RNA-seq of four biological replicates for treatment and four replicates for control condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Oli-Neu cells under treatment with Nimodipine or control vehicle.

first: Michael

last: Enders

first: Arif

last: Ekici

first: Stefanie

last: Kuerten


title: Gene expression of leaders and laggers MiaPaCa-2 pancreatic cancer cells during perineural invasion

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

summary: To investigate the mechanisms of cancer cell migration during perineural invasion in pancreatic cancer, we injected fluorescently labelled MiaPaCA-2 cells in the sciatic nerves  and collected the leader and lagger cells.

overall_design: We re-injected half of leader cells after in vitro growth and recollected leader cells. The cycle of harvesting, growth in vitro, and sciatic nerve injection was repeated serially 4 times. We then performed gene expression profiling analysis using data obtained from RNA-seq of Lag-1, Lead-1-4 (numbers representing the passage number) and from non-injected MiaPaCa2.

first: Marcadis

last: Andrea

first: Wong

last: Richard

first: Deborde

last: Sylvie


title: miRNA159b shows reduced expression in rdr1 mutant Arabidopsis thaliana

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report that RDR1 mutation in A. thaliana causes reduced expression of miRNA159b.

overall_design: NGS was carried out to investigated  the differential expression of sRNAs in rdr1 mutant A. thaliana.

first: Ved

last: Prakash

first: Tamas

last: Dalmay

first: Supriya

last: Chakraborty


title: A Deep Learning based Efficacy Prediction System for Drug Discovery [Perillen]

city: 北京

first: zhu

last: jie

address: 北京市海淀区学院路38号

institute: 北京大学医学部

summary: Target protein-based drug and research compound discovery has been undeniably successful strategy in life science research, yet many diseases and biological processes lack obvious targets to enable these approaches. Here, to overcome this major challenge we have developed a deep-learning based efficacy prediction system (DLEPS) to identify potent agents to treat diverse diseases; DLEPS was trained using L1000 project chemical induced “changes of transcriptional profiles” (CTP) data as input. Strikingly, we found that the CTPs for previously unexamined molecules were precisely predicted (0.74 Pearson correlation coefficient). We used DLEPS to examine 4 disorders, and experimentally validated that perillen, chikusetsusaponin IV, trametinib, and liquiritin confer disease-relevant impacts against obesity, hyperuricemia, NASH, and COVID-19, respectively. Importantly, DLEPS also uncovered the biological insight that the MEK-ERK signaling pathway should be understood as a target for developing anti-NASH agents. Beyond illustrating that DLEPS is an effective tool for drug repurposing and development with diverse diseases (including those lacking targets), our study shows how diverse transcriptomics datasets can be harnessed to identify inhibitors and activator chemicals that can expand the scope of biological investigations well beyond mutant-bases analyses.

overall_design: mRNA profiles of kidney tissue after 14 days treatment at 10mg/kg/day of Perillen or vehicle in hyperuricemia mice.

first: Mingjing

last: Gao

first: Xin

last: Wang

first: Jingxiang

first: Zhengwei

last: Xie


title: A Deep Learning based Efficacy Prediction System for Drug Discovery [Trametinib]

address: 北京市海淀区学院路38号

overall_design: mRNA  profiles of liver tissue after 14 days treatment at 0.1mg/kg of Trametinib or vehicle in MCD mice.

first: Jie

last: Zhu


title: mRNA sequence analysis of eutopic and ectopic endometrium in the same patients with adenomyosis

city: Shenyang

first: Jingwen

last: Shi

address: 36 Sanhao Street, Heping District, Shenyang City

institute: Shengjing hospital of China medical university

summary: In this study, we explored differences in gene expression between the eutopic and ectopic endometrium in the same patients with adenomyosis

overall_design: The pathological specimens of patients with adenomyosis were obtained from Shengjing Hospital. This study was approved by the ethics committee of Shengjing hospital (serial number: 2022PS696K). The patients were informed and provided with written informed consents for this study. The patients underwent total hysterectomy due to adenomyosis or cervical intraepithelial neoplasia (CIN). However, the pathological findings confirmed adenomyosis in all cases. Clinical data, including age and fertility status, coexisting with adenomyosis, are available. RNA samples of eutopic and ectopic endometrium were extracted from the patients’ specimens and mRNA sequence analysis was performed.

first: Ying

last: Huang


title: Single cell transcriptomic profiling of tau pathophysiology in a novel 3D neural-glial coculture model

city: Boston

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

summary: We report the development of a novel 3D human induced pluipotent stem cell derived neural-glial coculture model of tauopathy and identify pathways associated with pathogenesis by 10X 3' V3 single cell RNA sequencing.

overall_design: 3D human induced pluripotent stem cell derived neurons exposed to oligomeric tau and glial cells were co-cultured with and without PU-H71 drug treatment. 10X 3' V3 single-cell RNA sequencing was performed at 1, 2, and 3 week timepoints.

first: Hannah

middle: D

last: Rickner

middle: S


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [trios]

city: Granada

first: Martin

last: Munoz-Lopez

state: GRANADA

address: C/ Ilustración

country: Spain

institute: GENYO

type: Genome variation profiling by high throughput sequencing

summary: We did not detected de novo endogenous LINE-1 insertions in human offsprings

overall_design: We searched for de novo LINE-1 insertions in human offsprings by analyzing trios (parents and a child) using the methodology RC-seq

last: Muñoz-Lopez

first: Jose

middle: L

last: Garcia-Perez


title: Differential expression profiles and functional analysis of circulating small extracellular vesicle-derived lncRNA in children with fulminant myocarditis

city: Jinan

first: Bo

last: Han

address: huaiyin，jingwu

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Fulminant myocarditis (FM) is the most serious type of childhood myocarditis. However, the molecular mechanism underlying the pathogenesis of FM has not been fully elucidated. Studies have shown that small extracellular vesicles (sEVs) play important roles in many diseases, but any potential role of sEVs in pediatric FM has not been reported. Here, the differential expression profiles of lncRNAs in plasma sEVs were studied in five children with FM and five healthy children using whole transcriptome sequencing, followed by functional analysis and screening of immune-related target genes. A total of 68 up-regulated and 11 down-regulated differentially expressed sEVs-lncRNAs were identified. Functional analysis showed that the differentially-expressed sEVs-lncRNAs were mainly involved in immune processes, apoptosis, and protein efflux. Further analysis of immune-related target genes revealed that differentially expressed sEVs-lncRNAs were closely related to immune activation, immune cell migration and cytokine pathway signal transduction in FM. Thus, sEVs-lncRNAs may play an important role in the pathogenesis of FM in children

overall_design: Examination of small extracellular vesicles in plasma from 5 children with fulminant myocarditis and 5 normal children.

first: Mengjie

last: Ma

first: Siyu

last: Chen

first: Xinyue

last: Zhang


title: Effect of CVA6 infection on gene expression in RD cells

city: Beijing

first: Cong

middle: cong

address: 155 Changbai Road

institute: Chinese Center For Disease Control and Prevention

summary:
To investigate the effect of a particular gene on CVA6 replication, we established a CVA6-infected RD cell line.
We then performed gene expression analysis using RNA-seq data of cells from the infected and uninfected groups.

overall_design: Gene expression profiling analysis of RNA-seq data from CVA6-infected RD cells.

first: Congcong


title: Transcriptomic analysis of photoperiod regulated dormancy induction in grapevine.

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

institute: South Dakota State University

summary: Transcriptomics study of F2 siblings with different dormancy responsiveness due to photoperiod subjected to long day and short day.  F2 040 and F2 110 genotypes were previously described as part of a larger F2 population (Fennell et al., 2005, Acta Hort 689:533-539).  The F2 040 and 110 genotypes exhibit photoperiod responsive characteristics similar to the Seyval and V. riparia grandparent, respectively (Fennell et al., 2015, doi: 10.3389/fpls.2015.00834)

overall_design: Spur-pruned grapevines were grown under long days until shoots reached 12-15 nodes and then randomized into a continued long (LD, 15 h) or short photoperiod (13 h) for 28 or 42 days (George et al. 2018, J.Prot:187:13-24). Buds were harvested from nodes 3 to 12 on the shoot at 28 or 42 days of LD or SD.  Three replications (10 vines per replicate) were harvested for each photoperiod treatment.

first: Padmapriya

last: Swaminathan

middle: Y


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [placenta]

summary: We detected de novo endogenous LINE-1 insertions in extraembryonic tissues (chorion frondosum)

overall_design: We searched for de novo LINE-1 insertions by RC-seq in extraembryonic tissues (amnion, chorion leave, chorion frondosum), using blood from newborns and mothers as controls


title: Transcriptome analysis reveals key genes and pathways that the nuclear receptor PPARα acts on vascular aging

first: ye

last: Liu

address: You'anmenwai

institute: Capital Medical University

summary: Our research is helpful to understand the physiological and pathological level changes caused by the  nuclear transcriptional receptor PPARα acts on vascular aging, to find the mechanism of the signaling pathway downstream of PPARα in VSMCs, and to determine which signaling pathway is mediated by PPARα

overall_design: In this study, we harvested the entire aortas from 2-, 28- month-old Ppara△SMC and Pparafl/fl mice. The young control group, young knockout-aortas group, aged aortas, and aged knockout-aortas  (5 samples each) were subjected to RNA sequencing.

first: Ye

first: Aijuan

last: Qu


title: Recruitment of dendritic cell progenitors to foci of influenza A virus infection sustains immunity

city: London

first: Carlos

last: Minutti

address: 1 Midland Road

institute: Francis Crick Institute

summary: RNAseq on DC precursors from mouse BM

overall_design: Mouse pre-cDCs were isolated from the BM and RNA-seq analysis was performed to interrogate the expression of different chemokine receptors

first: Mar

last: Cabeza-Cabrerizo

middle: M

first: Mariana

last: Pereira da Costa

first: Caetano

last: Reis e Sousa


title: A Deep Learning based Efficacy Prediction System for Drug Discovery [Chikusetsusaponin IV]

first: zhu

last: jie

address: 北京市海淀区学院路38号

overall_design: mRNA  profiles of subcutaneous fatty tissue after 35 days treatment at 20mg/kg of Chikusetsusaponin IV or vehicle in HFD mice.

first: Jingxiang

last: Wang

first: Jie

last: Zhu

first: Bingbing

last: Guo

first: Jiarui

first: Ruimao

last: Zheng

first: Zhengwei

last: Xie


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [somatic tissues]

first: Martin

last: Munoz-Lopez

summary: We did not detected de novo endogenous LINE-1 insertions in human somatic tissues

overall_design: We searched for de novo LINE-1 insertions by RC-seq in pairs of human muscle-bain tissues

last: Muñoz-Lopez

first: Jose

last: Garcia-Perez


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [hEMB]

summary: Using single-cell genomics, we demonstrated that endogenous LINE-1s are mobilized in human pre-implantation embryos

overall_design: We isolated single cells from the Inner Cell Mass of human pre-implantation embryos that reach the blastocyst stage, amplified their genomes using Multiple Displacement Amplification (MDA), and analyzed the presence of new LINE-1 insertions using the methodology Retrotransposon Capture Sequencing (RC-Seq)


title: Human T cell characterisation

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

summary: Characterisation of human CD4+ cells to gain more insights into regulatory processes.

overall_design: human T cells treated and control

first: Markus

last: Kleinewietfeld

last: Hamad

first: Beatriz

last: Fernandes Côrte-Real


title: A Deep Learning based Efficacy Prediction System for Drug Discovery

address: 北京市海淀区学院路38号

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

overall_design: Refer to individual Series


title: Effect of depletion of FUS on gene expression during in sunitinib-resistance cell lines

city: shanghai

first: jie

last: wang

address: 700 Moyu North Road

department: Department of Urology

institute: Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University

summary: To investigate the function FUS in the regulation of sunitinib-resistance， we used lentiviral transduction to knock down FUS expression in the  sunitinib-resistant RCC cells.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cell lines with sh-FUS and sh-control.

first: Linhui

first: Bing

last: Liu


title: Effect of Sphingomyelin d18:1/14:0 (S14) on gene expression in macrophages

city: Bonn

first: Friederike

middle: Sophie

last: Gorki

address: Venusberg-Campus 1

institute: Institute of Innate Immunity

summary: We compared the effect of Sphingomyelin d18:1/14:0 (S14) and Lipopolysaccharide (LPS) on the gene expression in mouse macrophages at different timepoints

overall_design: RNA-Seq analysis was performed on bone marrow-derived macrophages (isolated from B57BL/6J wild-type mice; n=4) stimulated for 3 h or 18 h with S14 or LPS or left untreated as control.


title: Optimised linear amplification method for whole transcriptome analysis from low quantity RNA isolated from archival FFPE tissue

city: Sharjah

first: Rifat

last: Hamoudi

address: University city

country: United Arab Emirates

institute: University of Sharjah

summary: The study described a comprehensive high-fidelity method to successfully amplify low starting amounts of RNA extracted from FFPE tissue obtained from bronchial biopsies. Both amplified and unamplified RNA resulted in comparable gene expression for lung cancer and asthma samples.

overall_design: FFPE samples from bronchial biopsies collected from lung cancer, asthma and asthmatic lung cancer patients were processed for RNA extraction using Recover all kit. Small amounts of RNA were amplified using in house developed random nanomer-based T3 and T7 amplification described in the study. Both amplified and unamplified RNA were subjected to whole transcriptome analysis using Ion Ampliseq human gene expression panel (Thermo Fisher Scientific, USA) and Ion S5XL sequencer.

first: Poorna

last: Bhamidimarri

first: Laila

last: Salameh

first: Amena

last: Mahdami

first: Hanan

last: Abdulla

first: Bassam

last: Mahboub


title: Gene expression analysis of WT Th17 versus STAT4 deficient Th17 cells from EAE mice

city: Birmingham

first: Laurie

middle: E

last: Harrington

state: AL

address: 845 19th Street S, BBRB 471

department: CDIB

institute: UAB

summary: The purpose of this study is to compare transcriptional profiles of WT and STAT4-deficient Th17 cultured cells from mice with experimental autoimmune encephalomyelitis (EAE) using RNA sequencing.  WT and STAT4 deficient splenocytes from EAE immunized mice were cultured with MOG peptide under Th17 conditions for three days, and then total RNA was extracted from CD4 T cells for sequencing.  Differential gene expression was determined using the DESeq2 algorithm.  These data reveal a previously unrecognized role for STAT4 in Th17 gene expression and function.

overall_design: Age and sex matched mice between 8 and 12 weeks of age were induced for EAE by subcutaneous immunization with 50 μg MOG35−55 peptide (Biosynthesis) emulsified in CFA (150 μg Mycobacterium tuberculosis; Difco) and intraperitoneal (i.p.) administration of pertussis toxin (200 ng; List Biological Laboratories) on days 0 and 2. On day 10 post-immunization, 1x10^8 splenocytes were cultured with complete RPMI 1640 with 10ug/mL MOG35-55 peptide, 2.5ng/ml TGFb (Peprotech), 20ng/ml IL-6 (Peprotech), 10ng/mL IL-23 (Biolegend) and 10ug/mL anti-IFNγ (clone XMG1.2, Bio X Cell) and 10ug/ml anti-IL-4 (clone 11B11, Bio X Cell) for 72 hours at 37C. Following culture, live CD4 T cells were isolated by centrifugation over Histopaque 1083 (Sigma) followed by Dynabeads FlowComp Mouse CD4 kit (Invitrogen). RNA was isolated from WT and STAT4-/- CD4 cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocols and submitted to GENEWIZ for sequencing. Total RNA was sequenced on Illumina HiSeq 2500 (2 x 100 base pair, single-end reads) and aligned using mouse mm10 reference genome. The GI tools software along with DESeq2 software was used for differential expression analysis.

first: Ashlyn

middle: A

last: Buzzelli

first: Ian

last: McWilliams

first: Boyoung

last: Shin

first: Morgan

middle: T

last: Bryars


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues

first: Martin

last: Munoz-Lopez


title: Expression data from liver of male mouse at 10-week-old

city: Mishima

first: Toyoyuki

last: Takada

state: Shizuoka-ken

country: Japan

institute: National Institute of Genetics

summary: To investigate mouse intersubspecific divergence of transcriptional regulation between C57BL/6J (B6) and Japanese wild-derived MSM/Ms strains, we performed transcriptome analysis by microarray on liver from B6 and MSM, and B6-ChrNMSM chromosome substitution strain panel, which carries MSM-derived chromosome or chromosomal segment on the B6 host.

overall_design: Livers were collected from 10-week-old males for RNA extraction and the microarray experiments were performed by using Affymetrix Mouse Genome 430_2. Livers from two different males for each strain were tested independently. Tested samples are from control C57BL/6J (B6) strain, MSM strain, and 28 chromosome substitution strains include mitochondria DNA.

first: Takada

last: Toyoyuki

first: Shiroishi

last: Toshihiko


title: Effect of ANO1 overexpression and/or oncogenic KRAS on gene expression of BxPC3 cells

city: Jilin

first: Meiyan

last: Sun

address: 5 Jilin Ave, Fengman District

institute: Jilin Medical University

summary: RNA seq analysis was performed to assess the transcriptional profiles of BxPC3 cells with different status of ANO1 and KRAS.

overall_design: We perfomed bulk RNA seq analysis of 12 samples including 3 replicates for each of the following 4 groups of cells (1) wild type BxPC3 cells, (2) BxPC3 cells with ANO1 overexpression, (3) BxPC3 cells with oncogenic KRAS, (4) BxPC3 cells with both oncogenic KRAS and overexpression of ANO1.

first: Lei

last: Zhang

first: Hao

last: Wang

first: Jian

last: Guo

first: Huijing

last: Xu

first: Yihua

last: Qian


title: Comprehensive analysis and functional characteristics of differential expression of N6-methyladenosine methylation modification in the whole transcriptome of rheumatoid arthritis

city: Hefei

first: ming

last: Li

state: Anhui

address: No.117 Meishan Road, Shushan District

department: Department of Rheumatology

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: High-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to assess whole-transcriptome m6A modifications in the synovium of patients with RA. The relationship between m6A-modified target genes and RA inflammation and macrophages was determined. The expression of the m6A-modified significant transcript-enriched inflammatory signaling pathway was assessed through animal experiments.Differentially expressed m6A genes were correlated with macrophage activation involved in immune response, vascular endothelium, MAPK signaling pathway, PI3K-Akt signaling pathway, and other inflammatory processes. Furthermore, combined analysis with m6A-seq and RNA-seq revealed 120 genes with significant changes in both m6A modification and mRNA expression.

overall_design: The RA and Healthy control synovial tissue samples  for RNA methylation co-immunoprecipitation high-throughput sequencing (MeRIP-seq)

last: Wan

last: Liu


title: Small non-coding RNA’s profile of sorted plasma extracellular vesicles expressing different cell origin

city: Saint-Petersburg

first: Aleksandr

last: Khudiakov

address: 2, Akkuratova

department: Institute of molecular biology and genetics

country: Russia

institute: Almazov National Medical Research Centre

summary: Extracellular vesicles play a pivotal role in the intercellular communications influencing various physiological and pathological processes. They carry a range of biomolecular cargoes including small non-coding RNAs which could serve as potential diagnostic biomarkers and therapeutic targets. In the current study we applied Next Generation Sequencing to investigate small RNA profiles of erythrocytes (Rbc), platelets (Plt), leukocytes (CD45cells), two plasma fractions and blood cell-derived extra-cellular vesicles (EVs, such as CD41+, CD45+, CD235a+, CD146+) obtained using high-sensitivity fluorescence activated vesicle sorting from plasma of healthy donors. We analyzed the proportions of various small ncRNAs across samples and identified sample specific profiles of microRNA (miRNA) and transport RNA-derived fragments (tRFs). It was found that the cumulative small ncRNAs profiles of EVs originated from platelets, erythrocytes, and leukocytes, which are considered to be dominant among the vesicles circulating in blood, differ from small ncRNAs profiles of plasma fractions, which represent macrovesicles and exosomes in circulation. The proportion of miRNAs in sorted EVs was significantly lower compared to other samples while the proportion of tRFs was higher. Moreover, all sorted EVs carried mostly cell type non-specific miRNAs. Taking together, the results demonstrate that the combination of high-sensitivity fluorescence activated vesicle sorting with small-RNA sequencing technique is a powerful approach to analyze small ncRNAs profiles in cell specific vesicles.

overall_design: Comparative small RNA profiling of sorted plasma extracellular vesicles (CD41+, CD45+, CD235a+, CD146+), plasma fractions and blood cells (erythrocytes, platelets, leukocytes) from healthy donors

first: Olga

last: Kalinina

first: Daniil

last: Panshin

first: Yuri

last: Nikitin

first: Andrey

last: Ivanov

first: Anna

last: Kostareva

first: Alexey

last: Golovkin


title: PCSK9 promotes vein graft lesion development

first: Masanori

last: Aikawa

address: 77 Avenue Louis Pasteur, NRB741

department: Department of Medicine

institute: Brigham and Women's Hospital

summary:
To explore a novel mechanism of macrophage activation and vein graft disease induced by circulating
PCSK9 in an LDLR-independent fashion

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice peritoneal macrophages untreated (control) and treated (PCSK9).

first: Shunsuke

last: Katsuki

first: Prabhash

last: Kumar Jha

first: Adrien

last: Lupieri

first: Toshiaki

last: Nakano

first: Livia

last: Passos

first: Maximillian

last: Rogers

first: Dakota

last: Becker-Greene

first: Thanh

last: Dat Le

first: Julius

last: Decano

first: Lang

last: Ho Lee

first: Gabriel

middle: C

last: Guimaraes

first: Ilyes

last: Abdelhamid

first: Arda

last: Halu

first: Alessandro

last: Muscoloni

first: Carlo

last: Vittorio Cannistraci

first: Hideyuki

last: Higashi

first: Hengmin

first: Amélie

last: Vromman

first: Peter

last: Libby

first: C

middle: K

last: Ozaki

first: Amitabh

last: Sharma

first: Sasha

last: Singh

first: Elena


title: Gene expression profile of kidney tumor samples from BHD patients relative to control kidney samples

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To investigate the role of TFEB/TFE3 in the transcriptional alterations of tumor samples from BHD patients

overall_design: total RNA was extracted from kidney tumor samples and control kidney samples

first: R

last: Di Malta


title: Empagliflozin Ameliorates Aldehyde Dehydrogenase 2 Deficiency-induced Endothelial Dysfunction

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: We conducted RNA sequcing of the homozygous and heterozygous of ALDH2*2 by using human induced pluripotent stem cell-derived endothelial cells (hiPSC-ECs)

overall_design: Examination of genetic effect of ALDH2*2 on the endothelial dysfunction

first: Hongchao

last: Guo


title: Heterogeneity of CML therapy resistant cells

city: Farmington

first: Yuqi

last: Zhao

state: CT

address: 273 Main Street A4

institute: City Of Hope

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A deeper understanding of the biology of therapy resistant cells is important for the development of optimal therapeutic strategies to attain complete cure of leukemia. Here we compared chromatin accessibility of CML patient cells treated with Imatinib vs untreated cells and column enriched deep-quiescent LI (leukemia initiator) cells. ICG-001 treatment of LIs  suggested increased differentiation of LIs.

overall_design: CML patient cells were treated for 8 days with imatinib and therapy-resistant cells were MACS column enriched for CCR7+ deep quiescent LI (leukemia initiator) subset.

first: Nyam-Osor

last: Chimge

first: Michaelk

last: Kahn

first: Xiwei

last: Wu


title: Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

overall_design: Wild type Bacteroides thetaiotaomicron BT5482 Δtdk strain (V3256) was used to compare to the OxyR - deficient strain (V3257).  The strains were obtained from Dr. J. Imlay (Mol Microbiol, 2013. 90(6): 1356-71).

first: Qin

last: Gui


title: Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insect Bemisia tabaci

first: li

last: li

state: c

address: kangxin

institute: university

summary:
Purpose: Compare two cotton cultivars that exhibit either strong resistance (HR) or sensitivity (ZS) to whitefly
Methods:we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stressmice.
Results: We found to adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Li

last: Jia


title: Parathyroid Hormone Receptor-1 Signaling Aggravates Hepatic Fibrosis through Upregulating cAMP Response Element Binding Protein-Like 2

status: Public on Mar 29 2023

city: Shanghai

first: Ting

last: Hong

state: Shanghai

address: 180 Fenglin Road, Xuhui District

department: Department of Endocrinology and Metabolism

institute: Zhongshan Hospital, Fudan University, Shanghai, China

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Banzhilian Formula alleviates psoriasis like lesions via the LCN2/MMP-9 axis based on transcriptome analysis

city: Xi'an

first: Meng

last: Xing

address: No. 2 Xihuamen, Lianhu District

institute: Shanxi Hospital of Traditional Chinese Medicine

summary: Oral Banzhilian Formula (BZLF) is effective in the clinical treatment of psoriasis. However, the effectiveness and mechanism of different drug delivery routes deserve further study. In this study, we externally applied BZLF to the skin lesions in an IMQ-induced psoriasis mice model, and found that BZLF alleviated the psoriasis-like skin lesions, while inhibiting the expression of Ki67 and inflammatory factors (Il17a, Tnf-α, S100a7 and Cxcl1) in the skin lesions. Finally, through transcriptome sequencing combined with bioinformatics and other methods, it was found that the mechanism of action of BZLF against psoriasis is achieved by down-regulating the LCN2/MMP-9 axis. Overall, this study elucidates the effectiveness and mechanism of external application of BZLF in the treatment of psoriasis, and provided a new approach and basis for clinical application.

overall_design: comparative gene expression profiling analysis using data obtained from RNA-seq data for control group, IMQ+NS group and IMQ+BZLF group.

first: Ying

last: Luo


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [scRNA-seq_pancreas_Scipio]

city: Paris

first: Stuart

last: EDELSTEIN

state: Île-de-France

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

country: France

institute: Scipio bioscience

summary: Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.

overall_design: Benchmarking experiments to assess the performances obtained using RevGel-seq (scRNA preparation).

first: Jun

last: Komatsu

first: Stanislas

last: Lipin

first: Ghislaine

last: Guillemain

first: Carine

last: Beaupère

first: Natacha

last: Roblot

first: Alexandra

last: Liboz

first: Bertrand

last: Blondeau

last: Edelstein


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [scRNA-seq_Cardio_Scipio]

first: Hélène

last: Eckert

first: Frédéric

last: Guérin

first: Léa

last: Cathaly

first: Sara

last: Majello

first: Elodie

last: Baldivia

first: Barbara

last: André


title: The arabinose transporter MtLat-1 is involved in hemicellulase induction in Myceliophthora

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: In this study, we investigated the role of L-arabinose transporter MtLat-1 in the induction of hemicellulase genes of M. thermophila. The deletion of MtLat-1 dramatically improved protein secretion and hemicellulase activities on arabinan. Comparative transcriptomic analysis indicated MtLat-1 repressed expression of hemcellulase genes. Furthermore, based on analyses of non-transporting MtLat-1 mutant, we found MtLat-1 in M. thermophila was involved in arabinose transportation, sensing, and tdownstream signalling cascades. Additionally, we also demonstrated Mtlat-1 expression is directly regulated by transcription factor MtAra-1 and MtAra-1 is involved in L-arabinose transporter and metabolism and arabinan hydrolysis.

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to L-arabinose, D-xylose, D-glucose, and arabinan


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [PBMC_perf_10X]

overall_design: Technical assessement of the performances obtained using 10X, on PBMC (scRNA preparation).

first: Antoine

last: Graindorge

first: Dilyana

last: Dimitrova

first: Damien

last: Ulveling


title: Transcriptomic analysis of lpcat1/2 mutant and wild type plants

city: Wuhan

first: Qiang

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: To explore the transcriptional regulations in lpcat1/2 mutant and wild type plants grown on 1/2 MS media (control), or 1/2 MS media containing 20ug/ml lyso-PAF or 20ug/ml lyso-PAF plus 50 µM ONO

overall_design: Total RNA were extracted from wild type and lpcat1/2 mutant root tissue under each condition

first: Jiao

last: Zou


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [scRNA-seq_stopping_Scipio]

first: Stuart

last: EDELSTEIN

first: Nicolas

last: Fernandez

first: Raya

last: Poncin

first: Ulysse

last: Godet

first: Azadeh

last: Saffarien

first: Stanislas

last: Lipin

first: Yannick

last: Fourne


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [PBMC_perf_Scipio]

overall_design: Technical assessement of the performances obtained using RevGel-seq, on PBMC (scRNA preparation).

last: Edelstein


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [NIH-HEK_perf_Scipio]

summary: Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead—cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.

overall_design: Technical assessement of the performances obtained using RevGel-seq, on NIH-HEK mix (scRNA preparation).


title: Expression of Cullin and F-box proteins by microarray in isolated cardiomyocytes and fibroblast

city: Munich

first: Maximilian

last: Fischer

address: Marchioninistr. 15

institute: LMU University

summary:
Microarray expression data from C57/Bl6Nand b1-adrenergic transgenic mice, including heart tissue, isolated cardiomycytes and fibroblast, and lung fibroblasts
Expression data was further used to identify promising targets in cardiomyocytes that are also members of the ubiquitin proteasome system that are upregulated in heart cells

overall_design:
This analysis aimed to evaluate the expression level of member of Cullin-RING ligases in the heart. Cullin-RING complexes (CRLs) constitute the largest group of E3 ligases, which are characterized by two signature components: a cullin (CUL) scaffold protein and the RING (for Really Interesting New Gene) finger protein ROC1. In the prototypic SCF (Skp1•CUL1•F-box protein•ROC1) complex, the CUL1 N-terminus binds to the Skp1•F-box protein substrate-targeting module, whereas the C-terminally located cullin domain anchors ROC1, which recruits E2 conjugating enzyme to catalyze the transfer of Ub to the substrate protein.   SCF contains a substrate recognition subunit known as the F-box protein, characterized by a 40-amino-acid F-box domain (Skaar et al., 2013). F-box proteins are interchangeable components of the SCF type E3 ligases and dictate the ubiquitin ligase's substrate specificity. Of the 69 F-box proteins encoded by the human genome, only a fraction has been studied in the heart. We harvested mice hearts, isolated cardiomyocytes, fibroblasts, and lung fibroblasts to evaluate the expression levels of CRL members We analyzed samples from 5 mice pooled into each sample using the Affymetrix Mouse Expression Set 430. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed. The file Cul Aros array depicts the microarray expression of the Cullin scaffold protein, while the expression data of the various F-box proteins are shown in Fbx Aros array sheet. These two excel sheets depict the expression level in a Log2 scale of the respective samples.
*** Submitter declares the CEL files are no longer available. ***


title: Gene expression profiles of 65 blood samples recovered from 46 COVID-19 convalescent patients and 10 healthy donors were analyzed by RNA-Sequencing.

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

institute: INSERM

summary: Purpose: Following a severe COVID-19 infection, a proportion of individuals develop prolonged symptoms. We investigated the immunological dysfunction that underlies the persistence of symptoms months after the resolution of acute COVID-19. Methods: We analyzed cytokines, cell phenotypes, SARS-CoV-2 spike-specific and neutralizing antibodies, and whole blood gene expression profiles in convalescent severe COVID-19 patients 1, 3, and 6 months following hospital discharge. Results: We observed persistent abnormalities until month 6 marked by i) high serum levels of monocyte/macrophage and endothelial activation markers, chemotaxis, and hematopoietic cytokines, ii) a high frequency of central memory CD4+ and effector CD8+ T cells; iii) a decrease in anti-SARS-CoV-2 spike and neutralizing antibodies, iv) an upregulation of genes related to platelet, neutrophil activation, erythrocytes, myeloid cell differentiation and RUNX1 signaling. We identified a “core gene signature” associated with a history of thrombotic events, with upregulation of a set of genes involved in neutrophil activation, platelet, hematopoiesis, and blood coagulation. Conclusion: The lack of restoration of gene expression to a normal profile after up to six months of follow-up, even in asymptomatic patients who experienced severe COVID-19, signals the need to carefully extend their clinical follow-up and propose preventive measures.

first: Hakim

last: Hocini

first: Fabiola

last: Blengio

first: Cécile

last: Lefebvre

first: Aurélie

last: Wiedemann

first: Pascaline

last: Tisserand

first: Rodolphe

last: Thiébaut

first: Yves

last: Lévy


title: Microglial IL-1RA ameliorates brain injury after ischemic stroke by inhibiting astrocytic CXCL1-mediated neutrophil recruitment and microvessel occlusion

city: Guangzhou

first: Xiaoyan

last: Huang

state: Guangdong

address: 137 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: To invesitgate effect of microglial depletion on acute ischemic stroke

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of tMCAO or sham mice with or without microglial depletion

first: Mingyan

last: Guo

first: Minghui

last: Cao


title: The role of Abl1 and Il-3 in leukemias

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

summary: The role of Abl1 and Il-3 in leukemias

overall_design: 32DAbl1KO cells were culture with or without IL-3.  RNAseq was performed to check the expression differences  between the cells treated with IL-3 and the cells treated without IL-3.  Experiments were biologically duplicated.

first: Tomasz

last: Skorski

first: Jian


title: Parathyroid Hormone Receptor-1 Signaling Aggravates Hepatic Fibrosis through Upregulating cAMP Response Element Binding Protein-Like 2 (mouse)

first: Ting

last: Hong

summary: Background & Aims  Parathyroid hormone receptor-1 (PTH1R) is a class B G protein-coupled receptor central to skeletal development, bone turnover, and calcium homeostasis. However, the role of PTH1R signaling in liver fibrosis is largely unknown. Here, the role of PTH1R signaling in the activation of hepatic stellate cells (HSCs) and hepatic fibrosis was examined.    Approach & Results  PTH1R was highly expressed in activated HSCs and fibrotic liver by using human liver specimens or carbon tetrachloride (CCl4)-treated or methionine and choline-deficient diet (MCD)-fed C57/BL6 mice. The mRNA level of hepatic PTH1R was positively correlated to α-smooth muscle actin (α-SMA) in patients with liver cirrhosis. Mice with HSCs-specific PTH1R deletion were protected from CCl4, MCD, or western diet plus low-dose CCl4-induced liver fibrosis. Conversely, parathyroid hormone (PTH) aggravated liver fibrosis in CCl4-treated mice. Mouse primary HSCs and LX2 cell lines were used for in vitro experiments. Molecular analyses by luciferase reporter assays and chromatin-immunoprecipitation assays in combination with mRNA sequencing in HSCs revealed that cAMP response element-binding protein-like 2 (Crebl2), a novel regulator in HSCs treated by PTH that interacted with Mothers against decapentaplegic homolog 3 (SMAD3) and increased the transcription of transforming growth factor β (TGFβ) in activating HSCs and collagen deposition. In agreement, HSCs-specific Crebl2 deletion ameliorated PTH-induced liver fibrosis in CCl4-treated mice.     Conclusions  In both mouse and human models, we found that PTH1R was highly expressed in activated HSCs and fibrotic liver. PTH1R signaling regulated collagen production in the HSCs via Crebl2/SMAD3/TGFβ regulatory circuits. Blockade of PTH1R signaling in HSCs might help mitigate the development of liver fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice with or without PTH

first: Xuelian

last: Xiong

first: Yaqiong

last: Chen

first: Qiuyu

last: Wang


title: Parathyroid Hormone Receptor-1 Signaling Aggravates Hepatic Fibrosis through Upregulating cAMP Response Element Binding Protein-Like 2 (human)


title: Transcriptome change after miR-206 overexpression

city: Minneapolis

first: Guisheng

last: Song

state: MN

address: MMC36 (PWB1-143), 516 DELAWARE ST SE

department: Medicine

institute: University of Minnesota

summary: We overexpressed microRNA-206 in heptocytes to evaluate its effect on transcriptome.

overall_design: Eight-week old male C57BL/6J mice (Jackson Laboratory, n=3) were hydrodynamically injected with 20 μg pT3-TTR-miR-206-IRES-GFP (TTR promoter drive miR-206 and GFP transcription) and 0.8 μg pCMV/Sleeping Beauty Transposon (SB). Four weeks post injection, primary hepatocytes were isolated via perfusion as previously described.(3) Isolated hepatocytes were subjected to flow cytometry sorting, both of GFP negative (control) and positive hepatocytes (miR-206 overexpressed) were collected for total RNA extraction (Qiagen RNeasy Micro Kit). The library was prepared and sequenced via ultra-low input RNA sequencing in GENEWIZ (New Jersey).

first: Ningning

last: Liu


title: Transcriptome analysis of RNA from cancer cells exposed to chronic hypoxia versus normoxia

city: Ajman

first: Raefa

last: Abou Khouzam

address: AL JURF - 1 Rashid Al-Khadar St - Al Jerf 1

department: Thumbay Research Institute for Precision Medicine

institute: Gulf Medical University

summary:
Transcriptome data from six cancer cell lines passaged twenty times in normoxia (21% oxygen) or hypoxia (1% oxygen)
Transcriptome analysis was conducted to determine the effect of chronic, long passaging, at 1% oxygen (hypoxia) on gene expression and alternative splicing in six cancer cell lines. The cancer cell lines included were two pancreatic (MIA PaCa-2, Capan-1), one lung (H226), one breast (MCF-7), one colon (HT-29), and one ovarian (SKOV-3). They were selected from a panel of 12 cancer cell lines since they showed the highest and lowest sensitivity to hypoxia based on their expression levels of a hypoxia 8-gene signature.

overall_design: For each cell line, four RNA samples (two biological and two technical duplicates) collected from chronic hypoxia and three RNA samples (one technical and two biological duplicates) collected from normoxia were exposed to whole transcriptome analysis using the Human Clariom™ D Assay (Affymetrix, Applied Biosystems™) following manufacturer’s instructions. Sample hybridization to chip was done using the Genechip® Hybridization oven 640 (Affymetrix); washing and staining with the GeneChip Fluidics Station 450 (Affymetrix/Thermo Scientific inc) and scanning using the GeneChip™ Scanner 3000 7G (Affymetrix/Thermo Scientific inc). CHP files were analyzed using Transcriptome Analysis Console (TAC) and differential gene expression was conducted in cells exposed to chronic hypoxia compared to their normoxic controls.

first: Mohak

last: Sharda

first: Shyama

last: Prasad Rao

first: Stephanie

last: Kyerewah- Kersi

first: Nagwa

last: Ahmed Zeinelabdin

first: Ayda

last: shah Mahmood

first: Husam

last: Nawafleh

first: Munazza

last: Samar Khan

first: Goutham

last: Hassan Venkatesh

first: Salem

last: Chouaib


title: Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress

city: Fayettiville

first: Julie

last: ThomaS

state: AR

address: 115 Maple Street

department: CSES

institute: University of arkansas

summary:
The analysis of the mapped QTLs and their genetic dissection in the US grown japonica rice genotypes, Cypress and Lagrue at genomic and transcriptomic levels
The gene expression profiling using Deseq was performed using data collected under control and heat stress For heat stress:a day/night temperature of 30°C (86°F)/28°C (82.4°F) for 10 h (20:00–6:00)  was maintained while the control treatment was set at a day/night temperature of 30°C (86°F)/22.2°C (72°F) until harvest maturity (approximately 18–20% grain moisture content)

overall_design: Comparative gene expression  analysis between Cypress and Lagrue to study the effect of high night temperature during grain filling across two genotypes.

first: Anuj

last: Kumar

last: Thomas

first: Navdeep

last: Gill

first: Yheni

last: Dwiningsih

first: Charles

last: Ruiz

first: Adam

last: Famoso

first: Andy

last: Pereira


title: Bulk RNA-seq analysis in pulmonary endothelial cells between saline and LPS group, WT (Fgfr1loxp/loxp) and endothelial Fgfr1-conditional knock out mice (Fgfr1iΔEC/iΔEC mice).

city: Peking

first: Yue

last: Deng

address: Yinghua street

institute: Peking University

summary: Endothelial cells (ECs) serve as a semipermeable barrier and play a key role in acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). It is well known that fibroblast growth factor receptor 1 (FGFR1) is a requirement for maintaining vascular integrity. However, how endothelial FGFR1 exerts its function remains obscure in ALI/ARDS. Here, we performed RNA-seq analysis to investigate transcriptional changes of ECs between saline and LPS group, WT (Fgfr1loxp/loxp) and endothelial Fgfr1-conditional knock out mice (Fgfr1iΔEC/iΔEC mice).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from saline and LPS group, WT (Fgfr1loxp/loxp) and endothelial Fgfr1-conditional knock out mice (Fgfr1iΔEC/iΔEC mice).

first: Xingming

last: Huang

first: Bi-Sen

last: Ding

first: Chen

last: Wang


title: Concomitant downregulation of neuropeptide precursors in a marine snail with consecutive sexual maturation after a nuclear disaster in Japan

city: Higashi-Hiroshima

first: Fumihiro

last: Morishita

state: Hiroshima

department: Graduate School of Integrated Sciences for Life

institute: Hiroshima University

summary:
Consecutive sexual maturation (CSM), an abnormal reproductive phenomenon of a marine snail, Reishia clavigera, has occurred since 2017 in the vicinity of the Fukushima Daiichi Nuclear Power Plant after the nuclear disaster there.
To determine the molecular basis for CSM, we conducted transcriptome profiling in the ganglia of normal and CSM snails.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the cengtral ganglia in the normal and consecutive sexual maturation of a marine snail.

first: Toshihiro

last: Horiguchi

first: Hiroto

last: Akuta

first: Tatsuya

last: Ueki

first: Takuya

last: Imamura


title: Transcriptome data of bone marrow long-term hematopoietic stem cells (LT-HSCs) from mice with or without 3-month high cholesterol diet (HCD) treatment

city: CHONGQING

first: Chaonan

last: Liu

address: Gaotanyan Street

institute: the Army Medical University

summary: The vulnerability of bone marrow hematopoiesis to perturbations of cholesterol metabolism is well documented, while the underlying cellular and molecular mechanisms remain poorly understood. Here we reveal a distinct cholesterol metabolic signature of hematopoietic stem cells (HSCs) within the hematopoietic compartment.To identify the phenotype switching and function variation in BM LT-HSCs with HCD treatment, we performed RNA-seq of LT-HSCs from the bone marrow of mice with or without3-month HCD treatment.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of BM LT-HSCs (Lin-c-Kit+Sca1+CD34-CD135-) from mice with or without 3-month HCD treatment.

first: Changhong

last: Du

first: Junping


title: LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [twins]

city: Granada

first: Martin

last: Munoz-Lopez

state: GRANADA

address: C/ Ilustración

institute: GENYO

summary: We did not detected de novo endogenous LINE-1 insertions in human twins

overall_design: We searched for de novo LINE-1 insertions by RC-seq in blood from human twins

last: Muñoz-Lopez

first: Jose

last: Garcia-Perez


title: KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma

city: LuZhou

first: Fang

address: No. 25 taiping street

institute: The Affiliated Hospital of Southwest Medical University

summary: KDM2A is a histone demethylase, which primarily catalyzes the demethylation of H3K36me2. Abnormal expression of KDM2A is observed in many types of cancers; however, the molecular events connected to KDM2A expression remain unclear. In this work, to gain further insight into the molecular mechanism underlying the function of KDM2A, we analyzed the expression and function of KDM2A in esophageal squamous cell carcinoma (ESCC) cells.

overall_design: In this study, 20 paired samples from patients that underwent ESCC resection were used to verify the expression of KDM2A by IHC. Subsequently, the KDM2A-specific shRNA was transfected into Kyse150 and TE11 cell lines using a lentivirus system. The growth curving, CCK8,  colony formation and wound healing assays were utilized to access the proliferation and migration capacities. RNA-seq was performed to evaluate the downstream targets of KDM2A.

first: Jian

first: Zhi-ya

last: Zhang

first: Jie

last: Jiang

first: Li

last: Tang

first: Xiao-yan

first: Zhen

first: Xue-lian

last: Yang

first: Xin-lin

last: Yu

first: Chen-chen

first: Feng

last: Chen

first: Shu-juan

last: Ye

first: Haisu

last: Wan


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

first: Stuart

last: EDELSTEIN

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

overall_design: Refer to individual Series


title: Effect of knockdown of CREM on gene expression in CHL-1 cell line

city: Turku

first: Heidi

last: Kaprio

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: To investigate the changes caused by EWSR1::CREM knockdown in CHL-1 cells, we carried out a transcriptome analysis.

overall_design: We performed mRNA sequencing to compare the transcriptomes of ESWR1::CREM and CREM silenced CHL-1 cells with control siRNA treated CHL-1 cells.

first: Vanina

last: Heuser


title: Multi-omics of colon tumor progression organoids reveals putative mediators of colorectal cancer metastasis

city: Gelderland

first: Jelmer

last: Dijkstra

state: Nederland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Science (RIMLS)/Radboud University

summary: The development of metastasis severely reduces the life expectancy of patients with colorectal cancer (CRC). Loss of SMAD4 is a key event in late-stage CRC resulting in the progression to metastatic CRC in 10-30% of the cases. However, the biological processes and underlying molecular mechanisms that it affects are not fully understood. Here, we applied a multi-omics approach to a CRC tumor progression organoid model that faithfully reflects the metastasis-inducing effects of SMAD4 inactivation. We show that loss of SMAD4 results in loss of differentiation and activation of pro-migratory and cell proliferation processes, which is accompanied by the disruption of several key oncogenic pathways, including the TGFB, WNT, and VEGF pathways. In addition, SMAD4 inactivation leads to increased secretion of proteins that are known to be involved in a variety of pro-metastatic processes. Finally, we show that one of the factors that is specifically secreted by metastatic organoids – DKK3 –  reduces the anti-tumor effects of natural killer cells (NKCs). Altogether, our data provides promising new targets concerning the role of SMAD4 perturbation and metastatic disease in CRC.

overall_design: Comparative gene expression analysis by RNA sequencing on colon tumor progression organoids (AKP/AKPS or TPO3/TPO4)

middle: J

first: Hannah

last: Neikes

first: Somayeh

last: Rezaeifard

first: Xuhui

last: Ma

first: Emile

last: Voest

first: Daniele

last: Tauriello

first: Michiel

last: Vermeulen


title: Direct reprogramming of human fibroblasts towards beta-like cells

city: Barcelona

first: Rosa

last: Gasa

address: C/Rosselló 149-153

institute: IDIBAPS

summary: We reprogrammed human foreskin fibroblasts towards beta-like cells via adenovirus-mediated sequential introduction of five transcription factors (Ngn3, Pdx1, Mafa. pax4, Nkx2-2). At day 11 after initial viral infection,  we isolated RNA and performed gene expression profiling analysis using data obtained from RNA-seq of 3 parental fibroblasts and 3 reprogrammed cell samples (corresponding to 3 independent reprogramming experiments)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fibroblasts and reprogrammed beta-like cells.

first: Marta

last: Fontcuberta-Pisunyer


title: Gene expression profile of UOK257 cells silenced for TFEB or TFE3 relative to control UOK257 silenced for luciferase

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: To investigate the role of TFEB and TFE3 in the transcriptional alterations of UOK257 cells

overall_design: total RNA was extracted from UOK257 cells silenced for TFEB or TFE3 or luciferase

first: R

first: C

last: Di Malta


title: EXCESSIVE INFLAMMATION DRIVES POSTOPERATIVE LIVER FAILURE IN HUMANS - mRNA datasets

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: While extensive experimental evidence on rodent liver regeneration (LR) exists, in human LR is poorly understood as underlying liver disease significantly complicates this process. Within our analyses, we found that, in contrast to experimental evidence, patients with dysfunctional LR demonstrated an overall stronger transcriptional inflammatory response, higher ICAM-1 induction, intrahepatic neutrophil accumulation and activation upon induction of LR. This was confirmed using spatial transcriptomics and electron microscopy. While circulating cytokine levels were similar between patient with and without dysfunctional LR, baseline levels of Dual Specificity Phosphatase 4 (DUSP4), affecting responsiveness of liver sinusoidal endothelial cells (LSECs) to cytokines, was significantly reduced in patients developing postoperative dysfunctional. In line, NASH mice showed significantly reduced LSEC DUSP4 levels. This indicates that in humans reduced LSEC DUSP4 levels appear to prime the liver for an excessive inflammatory response which results in dysfunctional LR, identifying LSEC DUSP4 as an attractive new therapeutic target to promote LR.

overall_design: translational research

first: Patrick

last: Starlinger

first: Laura

last: Brunnthaler

first: Chantal

last: McCabe

first: David

last: Pereyra

first: Jonas

last: Santol

first: Jessica

last: Steadman

first: Matthias

last: Hackl

first: Susanna

last: Skalicky

first: Hubert

first: Raphael

last: Gronauer

first: Daniel

last: O´Brien

first: Renate

last: Kain

first: Petra

last: Hirsova

first: Gregory

last: Gores

first: Chen

last: Wang

first: Thomas

last: Gruenberger

first: Rory

last: Smoot

first: Alice

last: Assinger


title: Next Generation Sequencing Analysis of Control and SETDB1-KO H1299 cell Transcriptomes

city: Buffalo

first: Jia

last: Fang

state: New York

address: Elm & Carlton Streets

department: Department of Pharmacology & Therapeutics

institute: Roswell Park Comprehensive Cancer Center

summary: This study compared NGS-derived transcriptome profiling (RNA-seq) of control and SETDB1 knockout H1299 cells to understand SETDB1-mediated transcription regulation in NSCLC cells.

overall_design: mRNA profiles of control knockout (n=3) and SETDB1 knockout (N=3) H1299 cells.

first: Shuhei

last: Ueshima


title: RNA-seq in mouse Th17 cells

city: columbus

first: Ruoning

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

summary:
Purpose: To gain more mechanistic insights into the effects of LDHB deletion on T cells, we performed RNAseq in WT and LDHB cKO Th17 cells which cultured in 5% O2.
Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform
Results: RNA-seq revealed quite small different transcriptome patterns

overall_design: mRNA profiles of Th17 cells were generated by deep sequencing, using Illumina GAIIx.

first: Xuyong

last: Chen


title: Hyperlipidemia elicits an IFN-based CD4+ T cell response

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

institute: Amsterdam UMC, location AMC

summary: Hyperlipidemia is accompanied by increased systemic inflammation. However, how hyperlipidemia affects T cell biology is still unclear. We aimed to detail the effects of hyperlipidemia on the T cell’s transcriptome, metabolome and lipidome. Low-density lipoprotein receptor-deficient (LDLR-/-) mice were subjected to a 0.15% high cholesterol diet (HCD), a normal chow diet (NCD) and T cells were analyzed.  Hyperlipidemia induced an increase in CXCR3 on and IFN in CD4+ T cells, which was accompanied by transcriptomic changes in interleukin-mediated JAK/STAT signaling, interferon-γ signaling and a general pro-inflammatory immune response, suggesting that hyperlipidemia induces a Th1-like response. In these T cells, hyperlipidemia did not affect levels of metabolites involved in glycolysis or fatty acid oxidation, but enhanced amino acids levels. CD4+ T-cells of mice fed a HCD exhibited increased cellular cholesterol accumulation and an increased arachidonic acid (AA) to Docosahexaenoic acid (DHA) ratio, which was associated with T cell activation and IFN signaling. In vitro, T cell exposure to VLDL, but not LDL phenocopied these results. The effect of hyperlipidemia on T cell activation is reversible as transcriptional- and lipid profiles in LDLr-/  mice normalized 6 weeks after switching the HCD to NCD.  In conclusion, hyperlipidemia induces a Th1-like response in CD4+ T cells, which is associated with an AA/DHA ratio in these cells. VLDL, but not LDL is the main lipid component driving hyperlipidemia induced T cell activation.

overall_design: Comparison of gene expression in CD4+ T cells from mice fed a normal cholesterol diet (n=5), a high cholesterol diet (n=6), or that switched from a high cholesterol diet to a normal cholesterol diet (n=6)

first: Bram

middle: W

last: van Os

first: Winnie

middle: G

last: Vos

first: Laura

last: Bosmans

first: Claudia

last: van Tiel

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Sanne

last: Lith

first: Johannes

last: Levels

last: Zaal

first: Celia

middle: R

last: Berkers

first: Chris

last: van de Lest

first: J

last: Helms

first: Christian

last: Weber

first: Dorothee

last: Atzler

first: Menno

last: de Winther

first: Jeroen

last: Baardman

first: E


title: Hyperlipidemia elicits an IFN-based CD4+ T cell response: a key role for VLDL

first: Esther

last: Lutgens

overall_design: Comparison of gene expression in CD4+ T cells exposed to LDL (n=4) or VLDL (n=3) with untreated cells (n=4)


title: Differential mRNA expression analysis of H460 cells and A549 cells after trametinib treatment

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

summary: MAP kinse-ERK kinase inhibitor (MEKi) resistance remains unknown. We determined gene expression profiling in MEKi-resistant cells and MEKi-sensitive cells after MEKi treatment using RNA-seq analysis

overall_design: Transcription profiling of lung cancer cells

first: Juanjuan

last: Feng

first: Zhengke

last: Lian


title: Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

city: Shenzhen

first: Qing

last: Li

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

summary: Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome. It is the paradox comparing with the motif analysis, which usually contains only a few or tens nucleotides, achieved by bioinformatics analysis. To address this issue, we develop an experimental method, termed as massive active enhancer sequencing (MAE-Seq), to designate active enhancer sequences from arbitrary sources of 25bp random DNA libraries. These sequences are constructed in a mini-promoter vector with fluorescent reporter. After transfection, positive cells are sorted out and for sequencing. With the results, we successfully identify hundreds known accurate active enhancer sequences as expected. Besides that, large amounts of unmarked regulatory elements (UREs) that might control gene expression without epigenetic features are also been spotted. In conclusion, MAE-Seq would be useful to refine enhancer sequences and precisely annotate the genome in eukaryotes.

overall_design: Examination of core enhancer sequences in HEK293T cell.

first: Xiusheng

last: Zhu

first: Lei

last: Huang

first: Yubo

last: Zhang


title: Neutrophil activation by IL-4, IL-13 and IFN-g

status: Public on Mar 28 2023

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

institute: University of Tampere

summary:
Interleukin (IL)-4 and IL-13 are related cytokines with well-known roles in type 2 immune response.
However, their effects on neutrophils are less defined and existing research has provided somewhat contradictory results
We measured IL-4-, IL-13- and IFN-g-stimulated gene expression in highly purified human neutrophils.

overall_design:
Human neutrophils purified with Percoll gradient and  thereafter sorted from four healthy donors.
The purified cells were subsequently stimulated with 100 ng/ml of IL-4 , IL-13  or IFN-γ  for 1 hour and the mRNA was extracted and subjected to RNASeq analysis.
The gene expression of cytokine-stimulated cells was compared to unstimulated counterparts.

first: Zsuzsanna

last: Ortutay


title: Novel Transcriptomic Network Dynamics in Response to Divergent Acute Exercise Challenges in Young Adults

city: Birmingham

first: Kaleen

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

institute: University of Alabama at Birmingham

summary: This study measured the transcriptome-wide response in skeletal muscle and circulating extracellular vesicles (EVs) in young adults randomized to a single exposure of TRAD (n=21, 12M/9F, 22±3y) or HITT (n=19, 11M/8F, 22±2y) exercise. Next-generation sequencing captured small (<200nt), long (>200nt), and circular RNA species in muscle and EVs. In parallel, data streams were analyzed to identify transcripts differentially expressed (|log2FC|>1, FDR≤0.05) immediately (h0, EVs only), h3, and h24 postexercise within and between exercise doses. Strongly-trending responsive transcripts (FDR<0.2) underwent singular value decomposition to summarize the data structure into latent variables, LVs) deconvolving inter-regulatory relationships across transcripts; LVs were compared across time and exercise dose.

overall_design: Forty young, healthy adults underwent a single acute exercise bout in either traditional (TRAD) combined training consisting of treadmill running and resistance exercise or high-intensity tactical training (HITT), consisting of high-intensity circuit training and resistance exercise. Biospecimens were collected before (pre, skeletal muscle and blood), immediately post (h0, blood only), and h3 and h24 postexercise (both muscle and blood at both timepoints). RNA was isolated from muscle homogenate and serum-isolated extracellular vesicles (EVs) and processed to undergo next-generation sequencing of long,  smal, and circularl RNA.

first: Zachary

last: Graham

first: Jeremy

middle: S

last: McAdam

first: Samia

last: O'Bryan

first: Devin

last: Drummer

first: Margaret

last: Bell

last: Kelley

first: Manoel

last: Lixandrāo

first: Brandon

last: Peoples

first: Regina

last: Seay

first: Kendall

last: Van Keuren-Jensen

first: Matthew

last: Huentelman

first: Patrick

last: Pirotte

first: Rebecca

last: Reiman

first: Eric

last: Alsop

first: Anna

last: Bonfitto

first: Jerry

last: Antone

first: Bessie

last: Meechoovet

first: Joanna

last: Palade

first: Joshua

last: Talboom

first: Elizabeth

last: Hutchinson

first: Timothy

last: Broderick

first: Marcas

last: Bamman


title: Triple kinase target modulation in an animal model of Alzheimer disease

city: Nanjing

first: Shang

last: Li

state: Jiangsu

address: Tongjia Valley No. 24

institute: China Pharmaceutical University

summary: To investigate the combinative inhibition towards specified kinase targets, we detected gene expression on 3xTg mice after one-month of administration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, 3xTg and 3xTg-10d mice.

first: Xiaobing

last: Wang

first: Lingyi

last: Kong


title: Characterization of MGC 803 cell line

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

summary: Investigation of the mixed origins of the MGC 803 cell line reveals it is a nasopharyngeal HeLa hybrid cell line

overall_design: Characterization of MGC 803 cell line

first: Meime


title: The chromatin remodeler Brg1 directs smooth muscle-derived adventitial progenitor-to-myofibroblast differentiation and in situ vascular fibrosis [CUT&RUN]

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

summary: Smooth muscle-derived Sca1+ adventitial progenitor cells are tissue resident, multipotent stem cells that contribute to progression of vascular remodeling and fibrosis. Upon acute vascular injury, AdvSca1-SM cells differentiate into myofibroblasts and are embedded in perivascular collagen and matrix tissue. While the phenotypic properties of AdvSca1-SM-derived myofibroblasts have been defined, the underlying epigenetic regulators driving the differentiation trajectory of AdvSca1-SM cells to myofibroblasts are unclear. Here we show that the chromatin remodeler Smarca4/Brg1 facilitates AdvSca1-SM myofibroblast differentiation. Brg1 mRNA and protein was upregulated in AdvSca1-SM cells in vivo after acute vascular injury and pharmacological inhibition of the Brg1 bromodomain by the small molecule PFI-3 attenuated perivascular fibrosis and adventitial expansion. TGF-β1 stimulation of AdvSca1-SM cells in vitro reduced expression of stemness-related genes while inducing expression of myofibroblast genes that was associated with enhanced contractility; Brg1 inhibition blocked TGF-β1-induced phenotypic transition. Mechanistically, TGF-β1 promoted redistribution of Brg1 from distal regulatory sequences of stemness-related genes and recruitment of Brg1 to promoters of myofibroblast-related genes. This recruitment of Brg1 to myofibroblast genes was blocked in the presence of PFI-3. These data shed insight into epigenetic regulation of resident vascular progenitor cell differentiation and support that manipulating AdvSca1-SM phenotype will provide important anti-fibrotic clinical benefit.

overall_design: To obtain differential binding analysis of Brg1-DNA interactions in the AdvSca1-SM genome of AdvSca1-SM cells maintained in the following experimental conditions for 72 hours: stem/baseline, 5ng/mL TGF-B, or 5ng/mL TGF-B + 50uM PFI-3.

first: Austin

last: Jolly

first: Sizhao

last: Lu

first: Allison

last: Dubner

first: Keith

last: Strand

first: Marie

middle: F

last: Mutryn

first: Aaron

last: Pilotti-Riley

first: Etienne

last: Danis

first: Rapahel

last: Nemenoff

first: Karen

last: Moulton

first: Mark

last: Majesky


title: Effect of LXR ligands on gene expression in human PDAC cells

city: Houston

first: Chin-Yo

last: Lin

state: Texas

address: 3517 Cullen Blvd, SERC, Third Floor, Room 3018, SERC, Third Floor, Room 3018

institute: University of Houston

summary: Gene expression profiling analysis using data obtained from RNA-seq of 3 different cell lines with 3 LXR ligands.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PDAC cells treated with LXR ligands.

first: Lin

last: Chin-Yo


title: Human neutrophils stimulated with IL-13.

first: Ilkka

last: Junttila

summary: Studying the effect of Th2 cytokine IL13 on on gene expression of human neutrophils by comparing gene expression of neutrophiles isolated from the blood of 3 healthy donors and stimulated with IL-13 (10ng/ml) or left unstimulated.

overall_design: Two-condition experiments, unstimulated vs cytokine-stimulated cells. Biological replicates: neutrofils from 3 healthy donors treated or left untreated.

first: Zsuzsanna

last: Ortutay


title: The chromatin remodeler Brg1 directs smooth muscle-derived adventitial progenitor-to-myofibroblast differentiation and in situ vascular fibrosis.

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

overall_design: Refer to individual Series


title: The chromatin remodeler Brg1 directs smooth muscle-derived adventitial progenitor-to-myofibroblast differentiation and in situ vascular fibrosis [RNA-seq]

overall_design: Global, unbiased differential gene expression analysis of RNA-seq data for AdvSca1-SM cells in the following experimental conditions for 72 hours: stem/baseline, 5ng/mL TGF-B, or 5ng/mL TGF-B + 50uM PFI-3.


title: NHP gene expression after 4 Gy total body irradiation.

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
In the current study, we investigated the gene expression response of blood cells of non-human primates that were total body irradiated with a 4 Gy dose.
We isolated total RNA from peripheral blood at 3 days before irradiation, and then from the same animals on days 3, 5 and 7 days after irradiation. Using Agilent Rhesus microarrays, we identified genes that were significantly differentially expressed across the 7-day time course of this study. We identified common biological functions affected that persisted across the 7-day study.

overall_design: Radiation induced gene expression was measured at 3, 5 and 7 days after total body irradiation. There were 4-7 replicates in this study.

first: Shad

last: Morton

first: Sally

last: Amundson


title: Tmem161a is an important regulator for bone formation and bone strength through P38 MAPK pathway

status: Public on Mar 27 2023

city: Miyazaki

first: TAKUYA

last: NAGAI

state: Miyazaki

address: Kiyotake Kihara 5200

department: Department of Medicine of Sensory and Motor Organs, Faculty of Medicine,

institute: University of MIyazaki

summary:
Bone remoding is an extraordinarily complex process involving a variety of factors, such as genetic, metabolic and environmental impacts. Among them, genetic factor plays a major role, but not all have been identified.
We investigated the role of Transmembrane 161a (Tmem161a) in bone structure and function using wild-type (WT) and Tmem161a depleted (Tmem161aGT/GT) mice.

overall_design: Microarray analysis was used to screen for genes that are related to Tmem161a expression. RNA was isolated from WT and Tmem161a-KO cells (n = 3 each), and cRNA was prepared. cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse. microarray chip, which was then washed, stained, and scanned in an HP ChipScanner (Affymetrix Inc., Santa Clara, USA).

first: Takuya

last: Nagai

first: Narantsog

last: Choijookhuu


title: Human neutrophils stimulated with IFNg.

summary: Studying the effect of Th1 cytokine IFNg on gene expression of human neutrophils by comparing gene expression of neutrophiles isolated from the blood of 3 healthy donors and stimulated with IFNg (10ng/ml) or left unstimulated.


title: Effects of aspirin on placenta-derived MSCs

city: Newark

first: Pranela

last: Rameshwar

address: 185 South Orange Avenue

institute: Rutgers NJ Medical School

summary: Here we report the change in gene expression in placenta-derived MSCs followed exposure to aspirin.

overall_design: RNA sequencing on placenta-derived MSCs before and after exposure to 1mM aspirin to find differentially expressed genes.

first: Lauren

last: Sherman

first: Matthew

last: Romagano

first: Sami

last: Souayah


title: Expression and correlation of circulating miRNAs in healthy obese children

city: Beijing

first: Feifei

last: Ma

address: Road 2 Yabao

institute: Capital Institue of Pediatrics

summary: The miRNA expression profile in the body circulation of obese children differs from normal children.Thirty-six differential expression miRNAs were screened by gene chip, and seven up-regulated miRNAs were verified by TaqMan qPCR This result is attributed to the abnormal metabolism of obese children. hsa-miR-15b-5p and hsa-miR-223-3p could serve as a molecular marker for screening obese children and susceptible population of metabolic syndrome.

overall_design: Thirty children including 15 obese and 15 extremely thin were selected. The miRNA microarray was used to detect the expression of miRNAs in circulating plasma. The reliability of differential miRNA expression was verified using TaqMan qPCR. The correlation between miRNA and obesity was analyzed using multiple linear regression. Target genes for selected miRNAs were analyzed using informatics tools, and a functional network map was constructed.

first: Jianxin

last: Wu


title: Effects of piR_019914 on gene expression in C28/I2 cells

city: Shanghai

first: Yuxuan

last: Gao

state: Shanghai

address: Xinhua Hospital, kongjiang Road, Yangpu District, Shanghai

institute: Shanxi medical University

summary:
In order to study the role of piR_019914 in C28/I2 cells, we established piR_019914_mimics to overexpress piR_019914 in C28/I2 cells
We then performed gene expression profiling analysis using data obtained from RNA-seq of piR_019914 overexpression C28/I2 cells and mimics_NC C28/I2 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for piR_019914 overexpression C28/I2 cells and mimics NC C28/I2 cells.

first: YuXuan


title: Pre-transplant conditioning propagates selective loss of host Helios+/Nrp1+ Treg in aHSCT

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary: Comparative analysis of four murine Treg subsets differentially affected by pre-transplant conditioning and acute gastrointestinal GvHD following allogeneic hematopoietic stem cell transplantation.

overall_design: Four different Treg subsets were FACS sorted and subjected to comparative transcriptome profiling in a pairwise manner, using the following gating stategy: Ly/singlet/Live/CD4+/Foxp3+/Nrp1+/OX40bright Treg cells were sorted from six act-mOVA/Foxp3GFP mice, one sample each, and compared to Ly/singlet/Live/CD4+/Foxp3+/Nrp1-/OX40dim Treg of the same animals, one sample each (animals#1-6), serving as reference. Next, Ly/singlet/Live/CD4+/Foxp3+/Nrp1+/ITGB7+ Treg were sorted from six independent OVA/Foxp3GFP mice (animals#7-12), and compared to Ly/singlet/Live/CD4+//Foxp3+/Nrp1-/ITGB7- Treg of the same animals .

first: Nikolett

last: Lupsa

first: Barbara

last: Érsek

first: Zoltán

last: Pós


title: Treatment of 1,25(OH)2D3 or Antagonist in HCT116 WT and VDRKO cell lines

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

institute: Jyoban Hospital

summary: Purpose: The goals of this study are to compare gene expression between Wild Type and VDR KO in HCT116 cell lines.

overall_design: Examination of triplicate, 2 different treatment in 2 cell types.

first: Miho

last: Iwaki

first: Takahiro

last: Sawada

first: Kazuo

last: Nagasawa

first: Shigeaki

last: Kato


title: Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity

city: Waltham

first: Nathan

last: Harris

state: MA

address: 415 South Street

institute: Brandeis University

summary: Neurons modify their molecular profiles in response to an animal’s experience. How specific experiences are transduced to modulate gene expression and precisely tune neuronal functions are not fully defined. Here, we describe the molecular profile of a thermosensory neuron pair in C. elegans experiencing different temperature stimuli. We find that distinct salient features of the temperature stimulus including its duration, magnitude of change, and absolute value are encoded in the gene expression program in this single neuron, and identify a novel transmembrane protein and a transcription factor whose specific transcriptional dynamics are essential to drive neuronal, behavioral, and developmental plasticity. Expression changes are driven by broadly expressed activity-dependent transcription factors and corresponding cis-regulatory elements that nevertheless direct neuron- and stimulus-specific gene expression programs. Our results indicate that coupling of defined stimulus characteristics to the gene regulatory logic in individual specialized neuron types can customize neuronal properties to drive precise behavioral adaptation.

overall_design: Differential gene expression from C. elegans AFD neurons in worms that have experienced 15 vs 25 degrees celsius. AFD-specific mRNA isolated using Translating Ribosome Affinity Purification (AFD_15 and AFD_25 samples). RNA from whole animal lysates was also sequenced for comparison (whole_15 and whole_25 samples).

first: Piali

last: Sengupta


title: Alteration of m6A epitranscriptome profile in the bleomycin-treated mouse model of scleroderma

first: Liangling

last: Shen

address: 389 Xincun Road

institute: Tongji Hospital, Tongji University

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

summary: The exploration of m6A methylation in scleroderma remains in its infancy. We aimed to reveal the landscape of m6A methylated long noncoding RNAs (lncRNAs) and small RNAs in scleroderma.

overall_design: Two-condition experiment, BLM-treated mouse model of scleroderma group vs. PBS-treated control group. Biological replicates: 4 replicates for each group.

first: Liangliang


title: Gene expression profiling by RNA-seq of control and METTL14-knockdown HT29 human colon cancer cells

first: Yichao

last: Hou

address: 639 Zhi Zao Ju Road

institute: Shanghai Jiao Tong University

summary: In order to define the cohort of genes whose expression is regulated by METTL14 in p53 mutant colorectal cancer, we constructed HT29 cells stably infected with lentivirus carrying control shRNA (shNC) or METTL14 shRNA (shMETTL14). Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: There are four technical replicates in shNC or shMETTL14 group, respectively. Among shMETTL14 group, there existed two equal numbers of biological replicates named shMETTL14-01 an shMETTL14-02.

first: Xintian

last: Zhang

first: Xiangjun

last: Meng


title: RNA-seq and miRNA microarray of control and METTL14-overexpressed HT29 human colon cancer cells


title: Gene expression profiling by miRNA microarray of control and METTL14-overexpressed HT29 human colon cancer cells

summary: In order to define the cohort of miRNAs whose expression is regulated by METTL14 in p53 mutant colorectal cancer, we constructed HT29 cells stably infected with lentivirus carrying control transfectants (vector) or METTL14 overexpression (METTL14). Subsequently, total RNA was isolated and then performed miRNA Microarray.

overall_design: There are three technical replicates in vector or METTL14 group, respectively.


title: Single-cell atlas of human gingival tissues during healing process after ultrasonic scaling and root planing

city: Guangzhou

first: Wejun

last: Zhu

state: Guangdong

address: 56th Lingyuan Road West

department: Periodontology

institute: Sun Yat-sen University

summary:
Objective: To evaluate the composition and function of mural cell populations in human gingival tissues

Results: Two mural cell clusters, RGS5+THY1+ and ACTA2+MYH11+ subpopulations, were identified and confirmed by histological staining and cross-validation with three different single-cell RNA sequencing datasets in the GEO database. RGS5+THY1+ cluster in perivascular areas possessed cellular protrusions and exhibited immunomodulatory and synthetic phenotypes. In contrast, the ACTA2+MYH11+ cluster strictly distributed around vessel walls was characterized by a contractile phenotype. Mural cells closely interacted with endothelial cells through PDGF and NOTCH3 signaling. Mural cell loss was detected in the v_i group and in hopeless periodontal teeth, which might be caused by tumor necrosis factor-alpha induced apoptosis.

overall_design: A cross-sectional study was conducted on seven periodontitis (stage Ⅲ) patients. Gingival tissues were collected two months after scaling and root planing and divided into 3 groups: 1, h_h group (horizontal bone resorption, residual pocket depth ≤3 mm); 2, v_h group (vertical bone resorption >4 mm, residual pocket depth ≤3 mm); 3, v_i group (vertical bone resorption >4 mm, residual pocket depth ≥6 mm). Single-cell RNA sequencing (10X genomics) and subsequent bioinformatics analysis were performed. Protein expression of selected genes was confirmed by histological staining.

first: Wenjun


title: HCT116 human colon cancer cells and METTL14

platform_organism:
Homo sapiens
synthetic construct


title: Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis


title: Analysis of microRNA expression through microarray scan in HCT116 human colon cancer cells  with or without METTL14 overexpression

summary: To reveal the changes of miRNAs levels in HCT116 cells with METTL14 overexpression, we employed miRNA microarray expression profiling in HCT116 human colon cancer cells stably expressing control vector or METTL14.

overall_design: We had two groups: (1) stable-transfected Lv-vector (vectoer) HCT116 cells and (2) stable-transfected Lv-METTL14 (METTL14) HCT116 cells. Each group had 3 biological replicates.


title: RNA-seq and MYC ChIP-seq in A673 Ewing sarcoma cells with RUVBL1 knockout

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: This dataset examined the effect of RUVBL1 knockout in A673 Ewing sarcoma cells. The gene expression profiling (RNA-seq) and the chromatin targeting of MYC (ChIP-seq) are reported.

overall_design: Cas9-expressing A673 cells were transduced with sgCtrl and sgRUVBL1. The total RNA was extracted using the RNeasy Mini Kit (74104, QIAGEN) and submitted for RNA-seq at Novogene (PE150, NovoSeq6000). The MYC antibody (13987S, Cell Signaling Technology) cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000).

first: Chun-Wei

last: Chen

first: Lu

last: Yang

first: Mingli

last: Li


title: 10x Single-cell Gene expression analysis of pMHC-NP-induced Tet+ cells and anti-CD3-induced IL-10-producing cells

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

institute: IDIBAPS

summary: To further explore the transcriptional homogeneity of Tet+ cells with high numbers, we performed scRNAseq of FACS-sorted BDC2.5mi/IAg7 and InsB13-21/IAg7 Tet+ and Tconv cells from pMHCII-NP-treated animals, using the 10x Genomics platform. To study the effect of Bcl6-KO, we also studied transcriptional differences between WT and Bcl6-KO a-CD3-induced IL-10-producing T cells

overall_design: Treat NOD mice with BDC2.5mi/IAg7s or InsB13-21/IAg7-NPs to obtain Tet+ and Tconv T cells and perform scRNAseq with 10x technology and treat NOD or NOD CD4.cre.Bcl6(fl/fl) with a-CD3 antibody to obtain IL-10-producing CD4+ T cells and perform scRNAseq

first: Santamaria

middle: V

last: Pere

first: Solé

last: Patricia

first: Josep

last: Garnica


title: Transcriptional profiline of murine and human T cell populations

summary: T-regulatory-type-1 (TR1) cells comprise a phenotypically heterogenous but prevalent subset of Tregs that arise from unknown precursors in response to ill-defined cues. Here, we perform detailed transcriptional studies of autoantigen-specific TR1-like cell pools arising in response to peptide-major histocompatibility complex class II-coated nanoparticles (pMHCII-NPs) and compare them to other T cell populations to define their unique features.

overall_design: Transcriptional characterization of autoantigen-specific TR1-like cell pools and other T cell populations in mice and human.


title: Human neutrophils stimulated with IL-4.

city: Tampere

first: Ilkka

last: Junttila

address: Arvo Ylpön katu 34

institute: University of Tampere

summary: Studying the effect of Th2 cytokine IL4 on gene expression of human neutrophils by comparing gene expression of neutrophils isolated from the blood of 3 healthy donors and stimulated with IL-4 (1ng/ml) or left unstimulated.

overall_design: Two-condition experiments, unstimulated vs cytokine-stimulated cells. Biological replicates: neutrofils from 3 healthy donors treated or left untreated.

first: Zsuzsanna

last: Ortutay


title: Gene expression profiling by RNA-seq of control and METTL14-knockdown HCT116 human colon cancer cells

summary: In order to define the cohort of genes whose expression is regulated by METTL14 in p53 wild-type colorectal cancer,  we constructed HCT116 cells stably infected with lentivirus carrying control shRNA (sh_NC) or METTL14 shRNA (sh_MET). Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: We had two groups: (1) sh_NC and (2) sh_MET. Each group had 4 biological replicates.


title: CUT-TAG for NB4 cell line with either IgG or LDB1 antibody

status: Public on Mar 26 2023

city: Suzhou

first: Fang

last: Fang

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results for LDB1 in NB4 cell line.

overall_design: 1 NB4 sample for CUT-TAG with IgG antibody and 1 NB4 sample for CUT-TAG with LDB1 antibody

first: Pan

last: Jian

last: Lihui


title: Genome-wide analysis of differentially methylated genes in the fetal pancreas of progenies born from oocytes of maternal hyperglycemia

city: Hangzhou

first: Bin

state: Zhejiang

address: Qingchun East Road 3

department: Assisted Reproduction Unit, Department of Obstetrics and Gynecology

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: MeDIP-seq was performed to identify the epigenetic alterations in the fetal pancreas of progenies born from oocytes of maternal hyperglycemia.

overall_design: Offspring were generated from control and STZ-induced hyperglycemic mothers via female germline epigenetic inheritance. Fetal pancreases of both groups were collected on embryonic day 18.5. Find the genes of differentially methylated regions in the E18.5 fetal pancreases from both groups. 3 pancreases from fetus were pooled as one sample. 2 samples each group were analysed.


title: MicroRNA-185 modulates CYP7A1 mediated bile acid metabolism through posttranscriptionally and posttranslationally regulation of FoxO1

first: Li

last: Wang

address: No.1 Tiantan Xili

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Cholesterol 7alpha-hydroxylase (CYP7A1) is the rate limiting enzyme of bile acid biosynthetic pathway to convert cholesterol to bile acids, which is a major output pathway for cholesterol catabolism. In this study, we aimed to assess the potential regulatory mechanisms of microRNA-185 (miR-185) involved in cholesterol and bile acid homeostasis.
This study provides convincing evidences about the critical role of miR-185 in FoxO1 modulation at both posttranscriptional and posttranslational levels, which account for the effects on CYP7A1 gene and its mediated cholesterol-bile acid metabolism. These results suggest an important role of miR-185 as a novel atherosclerosis-protective target for drug discovery.

overall_design: Eight-week-old male ApoE KO mice fed a high-fat diet (HFD) were injected with lentiviruses encoding antisense miR-185 (miR-185-inh). Microarrays were applied to profile miR-185-regulated genes involved in bile acid metabolism.

first: Jin

last: Zhang

last: Hong

first: Huajun

last: Jiang

first: Fan

first: Xuelei

first: Yu

last: Du


title: Effect of endovascular treatment on gene expression in patients with Budd-Chiari syndrome

city: Wuhan

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

institute: Wuhan Union Hospital

summary: Budd-Chiari syndrome (BCS) results in sinusoidal congestion and hepatocyte apoptosis, which can further progress to liver fibrosis, cirrhosis, and hepatocellular carcinoma. Endovascular (EV) treatment has been the primary therapeutic method and achieved excellent outcomes. However, whether EV treatment could reverse liver cirrhosis in patients with BCS is still unclear. To investigate the effect of endovascular treatment on liver cirrhosis in patients with Budd-Chiari syndrome, we performed gene expression profiling analysis of the liver from patients with or without EV treatment.

overall_design: Liver tissues were obtained from patients with Budd-Chiari syndrome with or without endovascular treatment

first: Chaoyang

first: Pengfei

last: Chen

last: Xiong


title: Retina-Specific Laminin 523 Drives Differentiation of Human Pluripotent Stem Cells to Photoreceptors [bulk_RNAseq]

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

summary: Inherited retinal diseases and aged related macular degeneration are main causes of blindness that involves irreversible photoreceptor loss. Gene therapy approaches do not prevent photoreceptor degeneration during disease progression, and to date protocols for generating photoreceptors from pluripotent stem cells do not exist. Therefore, transplantation of photoreceptors containing retinal organoids is considered a potential option. However, in vitro formation of organoids requires animal-derived materials and they vary considerably in cell composition between batches, which strongly limits their applications in therapy. Here, we show that human recombinant retina-specific laminin isoform LN523, normally present in the extra cellular matrix ECM surrounding photoreceptors, supports differentiation of pluripotent embryonic stem cells to photoreceptor progenitors in vitro. Using a rabbit macular degeneration model, the transplanted and engrafted cells mature in vivo and form synaptic connectivity with the host retina. Furthermore, addition of a rod-derived cone viability factor increased the formation of cone photoreceptors. These results may pave the way for cell therapy treatment of macular degeneration.

overall_design: Human embryonic stem cells H1 were cultured and differentiated in wells with three types of laminin coating: LN-323 alone,  LN-323 + LN-521, and LN-323 + LN-523. CKI-7 and SB431542 was added at Day 2 to inititate differentiation towards neuroectodermal lineage. This medium is replaced by photoreceptor differentiation media (PRDM) on Day 7 for specification towards photoreceptor lineage. The photoreceptor medium consists of 2% B27- without vitamin A supplement, 1% N2 supplement (CTS), 10ng/ml human BDNF (Brain-derived Neurotrophic Factor, PEPROTECH), 10ng/ml human CNTF (Ciliary Neurotrophic Factor, PROSPEC-TANY TECHNOGENE), 0.5uM retinoid acid (Tocris Bioscience) and 10uM DAPT (N-[N-(3,5-Difluorophenacetyl-L-alanyl)]-S-phenylglycine t-Butyl Ester, Selleckchem). All media are changed every other day until D32. RNA was extracted from wells at Day 2, 22 and 32. Note: D0, D20, D30 correspond to D2, D22, D32 in the publication.

first: Hwee-Goon

last: Tay

first: Aida

last: Moreno-Moral

first: Enrico

last: Petretto

first: Karl

last: Tryggvason

first: Swarnaseetha

last: Adusumalli


title: Retina-Specific Laminin 523 Drives Differentiation of Human Pluripotent Stem Cells to Photoreceptors [single cell_RNAseq]

overall_design: Human embryonic stem cells H1, H9 and HS980 were cultured and differentiated in wells coated with LN-523 and LN-521. CKI-7 and SB431542 was added at Day 2 to inititate differentiation towards neuroectodermal lineage. This medium is replaced by photoreceptor differentiation media (PRDM) on Day 7 for specification towards photoreceptor lineage. The photoreceptor medium consists of 2% B27- without vitamin A supplement, 1% N2 supplement (CTS), 10ng/ml human BDNF (Brain-derived Neurotrophic Factor, PEPROTECH), 10ng/ml human CNTF (Ciliary Neurotrophic Factor, PROSPEC-TANY TECHNOGENE), 0.5uM retinoid acid (Tocris Bioscience) and 10uM DAPT (N-[N-(3,5-Difluorophenacetyl-L-alanyl)]-S-phenylglycine t-Butyl Ester, Selleckchem). All media are changed every other day until D32. RNA was extracted and processed to single-cell sequencign from wells at Day 2, 9, 22 and 32 for H1 cells. For reproducibility study, RNA from HS980 and H9 cell lines were extracted and sequenced at  Day 9 and Day 32.

first: Adusumalli

last: Swarnaseetha