title: p38MAPKa stromal reprogramming sensitizes metastatic breast cancer to immunotherapy

city: Saint Louis

first: Douglas

middle: V.

last: Faget

state: MO

address: 660 S. Euclid Ave, Box 8228

institute: Washington University

summary: Femurs bearing breast metastatases (5-pooled animals per sample) were crushed and digested with 2mg/ml Collagenase A.

overall_design: 50k PyMT-BO1-sLPmCherry cells(GFP+ mCherry+) were implanted by intracardiac injection into 6-8-week old albino B6 mice. Treatment started on Day 1 with p38i-compounded chow. After 13 days, femurs were harvested and cells were isolated by digestion and sorted following the above parameters.

middle: V

first: Sheila

last: Stewart


title: Transcriptional profiling of developing rat ovary following intrauterine exposure to known endocrine disruptors

status: Public on Mar 08 2023

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

type: Expression profiling by high throughput sequencing

summary: The main objective of the FREIA project is to identify markers of endocrine disrupting effects in rodents to overcome the lack of sensitive markers of female reproductive toxicity. For that 2 archetypes of endocrine disruption are studied, ketoconazole (KTZ) and diethylstilbestrol (DES) at three different stages (post-natal days 6, 14, and 22) and at three different doses 3, 6 and 12 milligram per kilogram by bodyweight per day for KTZ and 3, 6 and 12 microgram per kilogram for DES.

overall_design: Ovary transcriptional profiles of female rats exposed for 6,14,22 post-natal days to either Diethylstillbestrol or Ketoconazole were generated by BRB-sequencing.

first: Indusha

last: Kugathas

first: Frederic

first: Severine

last: Mazaud-Guittot

first: Terje

last: Svingen


title: Skeletal muscle mitochondrial dysfunction in spinal muscular atrophy

city: Padova

first: Caterina

last: Millino

address: Ugo Bassi 58

department: Biology

country: Italy

institute: University of Padova

summary: The survival motor neuron 1 (SMN1) gene is the causative gene for the spinal muscular atrophy (SMA) disease, the first genetic cause of infant mortality. It affects primarily motor neurons which are the targets of the approved genetic therapies aimed to compensate for the loss of SMN1. However, the limitations of these therapies are now evident since they are not cures, and alternative strategies need to be investigated. Because of the ubiquitous and multifunctional roles of SMN1 in the cell, deeper understanding of the molecular mechanisms underlying intrinsic abnormalities of the different tissues affected by SMA is crucial for the development of new therapeutic approaches. Here we used a muscle specific genetic mouse model for the identification of key cellular processes associated to SMN1 loss, at single myofiber level. We found that mitochondrial dysfunction is a key pathogenetic event in SMA: mitochondria are abnormal with internal degenerated cristae. The ultrastructural changes are coincident with alterations in ROS levels by monoamine oxidase A and Ca2+ homeostasis. Interestingly, the improvements of the myopathic phenotype of the muscle-specific SMA model mice by transplantation of amniotic fluid stem (AFS) cells led to restore mitochondrial function. Our data suggest that a mitochondria-targeting therapy may represent a complementary and broad treatment strategy to further optimize the current treatment.

overall_design: Tibialis anterior mouse muscles were incubated with type I collagenase (Sigma-Aldrich) to dissociate intact myofibers that were separately collected under stereomicroscope. We analyzed the transcription profiles of 27 single isolated myofibers: 8 from 2 control mice 3 months-old (WT), 12 from 3 mice with selective skeletal muscle Smn1 knockout 3 months-old (Smn1deltaSKM), and 7 from 2 mice with selective skeletal muscle Smn1 knockout treated with amniotic fluid stem (AFS) 3 months-old (Smn1deltaSKM+AFS). One-color hybridizations were performed on SurePrint G3 Mouse GE 8x60K Microarrays (Agilent Technologies).

first: Millino

last: Caterina

first: Pacchioni

last: Beniamina

first: Lanfranchi

last: Gerolamo

first: Chemello

last: Francesco


title: Splenic memory CD8 T cell signature of enhanced responsiveness to vaccine boost

city: Rome

first: Francesca

last: Di Rosa

address: viale Regina Elena 291

institute: Italian National Research Council (CNR)

summary: We addressed the question of primed CD8 T cell responsiveness to boost in a Balb/c mouse model of vaccination against gag of HIV-1, namely intramuscular (i.m.) prime with the Chimpanzee adenovector ChAd3-gag and i.m. boost with Modified Virus Ankara MVA-gag. In this setting, boost was more effective at day(d)100 than at d30 post-prime, as evaluated by multi-lymphoid organ assessment of gag-specific CD8 T cell frequency, CD62L-phenotype and in vivo killing activity at d45 post-boost. RNA-sequencing was used to compare memory signature of gag-specific spleen CD8 T cells at d100 post-prime with those at d30.

overall_design: Bulk RNA was sequenced from sorted spleen gag-specific CD8 T cells (average 93% pure Tetr-gag+Pent-gag+CD3+CD8+ cells) at d30 and d100 post-prime, in 4 independent experiments with a total of 7 samples (A_d30; B_d30; C_d30; D_d30; B_d100; C_d100.1; C_d100.2).

first: Ambra

last: Natalini

first: Sonia

last: Simonetti

first: Gabriele

last: Favaretto

first: Lorenzo

last: Lucantonio

first: Giovanna

last: Peruzzi

first: Miguel

last: Muñoz-Ruiz

first: Gavin

last: Kelly

first: Alessandra

middle: M

last: Contino

first: Roberta

last: Sbrocchi

first: Simone

last: Battella

first: Stefania

last: Capone

first: Antonella

last: Folgori

first: Alfredo

last: Nicosia

first: Angela

last: Santoni

first: Adrian

middle: C

last: Hayday


title: RNA sequencing of aortic valves in CTRL, ECKO, SMKO and DKO mice

city: Tsukuba

first: Hiromi

last: Yanagisawa

state: Ibaraki

address: 1-1-1 Tennodai

department: TARA Center

country: Japan

institute: University of Tsukuba

summary: RNA sequencing was performed to compare the transcriptome of aortic valves among 4 mouse models: fibulin-4 (Fbln4; EFEMP2 gene) knockout in endothelial cells (EC) using Tie2Cre (ECKO), Fbln4 knockout in smooth muscle cells (SMC) using SM22Cre (SMKO), EC and SMC Fbln4 double knockout (DKO), and Fbln4loxp/+ and Fbln4+/+ with SM22Cre and/or Tie2Cre used as CTRL. At 2 months old, DKO mice showed significantly thickening aortic valve leaflets than other mouse models. Therefore, this experiment was used to investigate the function of Fbln4 in aortic valve development and Fbln4 role in EC.  RNAseq analysis indicates differences in gene expression in aortic valves of DKO mice compared to other models, that is enriched with EndMT process and fibrosis progression.

overall_design: mRNA expression in whole aortic valves were compared among CTRL, ECKO, SMKO and DKO at 2 months old. Biological triplicate was used for each model.

first: Tram

middle: A

last: Nguyen

first: Kaori

last: Sugiyama

first: Hiroko

last: Matsunaga

first: Haruko

last: Takeyama

first: Yoshito

last: Yamashiro


title: Transcriptome sequencing of RNA isolated from small volumes of blood stabilized in Tempus solution: a technical assessment of different extraction methods and DNase treatment

city: Doha

first: Sara

last: Tomei

address: Gharrafa

country: Qatar

institute: Sidra Medicine

summary: To evaluates the effect of extraction methods and DNase treatment on transcriptomic profiles assessed from small volumes of peripheral blood collected in Tempus stabilizer solution

overall_design: We then performed gene expression profiling analysis using data obtained from mRNA-seq of two different extraction methods and varible sample volume input.

first: Mahesh

middle: K

last: Kalikiri

first: Harshitha

middle: S

last: Manjunath

first: Fazulur

middle: R

last: Vempalli


title: RNA sequencing of CTRL and siFBLN4 HAECs

summary: Fibulin-4 (Fbln4) is an extracellular protein, expressed throughout the aortic wall including endothelial cells (EC), smooth muscle cells (SMC) and fibroblasts. SMC-specific deletion of Fbln4 in mice led to formation of ascending aortic aneurysm with disruption of elastic fibers and Fbln4 is known to play role in elastic fiber formation. However, the function of Fbln4 in EC is unknown. To examine if Fbln4 deletion induces any changes in cellular phenotype of EC, we knocked down FBLN4 in human aortic endothelial cells (HAECs) by FBLN4 siRNA (siFBLN4)  compared with scramble siRNA-treated control cells (CTRL). RNA sequencing was performed to compare the differences in gene expression between CTRL and siFBLN4 cells.

overall_design: mRNA expression was compared between CTRL cells and siFBLN4 cells. Triplicate was used for each treatment.


title: MYCMI-7 - a small MYC-binding compound that inhibits MYC:MAX interaction and tumor growth in a MYC-dependent manner

city: Stockholm

first: Lars-Gunnar

last: Larsson

address: Solnavagen 9

department: Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institute

summary: Deregulated expression of MYC family oncogenes occurs frequently in human cancer and is often associated with aggressive disease and poor prognosis. While MYC is a highly warranted target, it has been considered “undruggable”, and no specific anti-MYC drugs are available in the clinic. We recently identified molecules named MYCMIs that inhibit the interaction between MYC and its essential partner MAX. Here we show that one of these, MYCMI-7, efficiently and selectively inhibits MYC:MAX and MYCN:MAX interactions in cells, binds directly to recombinant MYC and reduces MYC-driven transcription. In addition, MYCMI-7 induces degradation of MYC and MYCN proteins. MYCMI-7 potently induces growth arrest/apoptosis in tumor cells in a MYC/MYCN- dependent manner and downregulates the MYC pathway on a global level as determined by RNA-seq. Sensitivity to MYCMI-7 correlates with MYC expression in a panel of 60 tumor cell lines and MYCMI-7 shows high efficacy towards a collection of patient- derived primary glioblastoma and acute myeloid leukemia (AML) ex vivo cultures. Importantly, a variety of normal cells become G1 arrested without signs of apoptosis upon MYCMI-7 treatment. Finally, in mouse tumor models of MYC-driven AML, breast cancer and MYCN-amplified neuroblastoma, treatment with MYCMI-7 downregulates MYC/MYCN, inhibits tumor growth and prolongs survival through apoptosis with little side effects. In conclusion, MYCMI-7 is a potent and selective MYC inhibitor that is highly relevant for the development into clinically useful drugs for treatment of MYC-driven cancer.

overall_design: RNA-seq of MCF7 breast carcinoma cells treated with either 5 uM MYCMI-7 (n = 2) or DMSO (n = 2) for 24 hrs. MYCMI-7: (2-(5,11-Dimethyl-6H-25-pyrido[4,3-b]carbazol-2-yl)-N,N-diethylethanamine acetate, NSC-359449).

first: Alina

last: Castell

first: Thale

last: Olsen


title: RNA sequencing of eutopic endometrium and of myometrium from women with and without diffuse adenomyosis in the proliferative phase of the menstrual cycle

city: Shanghai

first: Shang

last: Li

address: 845 Lingshan Road

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: This study sought to identify potential mechanisms underlying the pathogenesis and pathophysiology of adenomyosis with a focus on the endometrium and myometrium. Transcriptomic profiles of eutopic endometrium and of myometrium from women with and without diffuse adenomyosis were assessed using RNA sequencing.

overall_design: RNA sequencing comparing eutopic endometrium and myometrium from women with and without diffuse adenomyosis in the proliferative phase of the menstrual cycle

first: Junyu

last: Zhai

first: Sushmita

last: Sen

first: Júlia

last: Vallvé-Juanico

first: Juan

last: Irwin

first: Kim

last: Vo

first: Linda

last: Giudice


title: Single cell RNA sequencing of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes with or without hiPSC-derived endothelial cells

city: Cambridge

first: Jessica

last: Garbern

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

summary: We cultured differentiated hiPSC-derived cardiomyocytes either alone or in co-culture with hiPSC-derived endothelial cells to evaluate potential genes that might facilitate endothelial cell-mediated cardiomyocyte maturation.

overall_design: hiPSC-derived cardiomyocytes were replated on day 10 of differentiation then cultured either alone or co-cultured with hiPSC-derived endothelial cells (ECs) for 14 days prior to sample harvest (until day 24 of cardiomyocyte differentiation; ECs were replated on day 13 of EC differentiated and harvested on dayy 27 of EC differentiation).

first: Zuwan

last: Lin

first: Richard

middle: T

last: Lee

first: Jia

last: Liu


title: RNA-seq for siRpl14+siDux/siRpl11

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Bulk RNA-seq were performed on E14 cells knockdown with siRNA; siRpl14+siDux; siRpl14+siRpl11

overall_design: Transcritional profiles of mouse embryonic stem cells upon factor knockdowns were shown by RNA-seq

first: Y

last: YI

middle: Y

first: H

last: Loh


title: The diurnal demethylation of intronic CpG-rich islands is instrumental in expression of circadian clock-controlled genes [liver]

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

type: Methylation profiling by high throughput sequencing

summary: To identify the methylation status of DNA at two circadian time points (i.e. 8am and 8pm) in liver samples of wild type C57BL6/J mice. The methylated DNA was isolated, prified and immunoprecipated at two time points using 5-methyl cytosine antibody(MeDIP Assay).

overall_design: Examination of circadian methylation profiling in liver samples of wild type mice

first: Manohar

last: Damara

first: Nisha

last: Misra

last: Ye

first: Pierre

last: Chambon


title: The diurnal demethylation of intronic CpG-rich islands is instrumental in expression of circadian clock-controlled genes.

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing  analysis of human Alzheimer’s disease brain samples  reveal neuronal and glial specific cells differential expression

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

summary: Alzheimer’s disease (AD) is the most common dementia worldwide with no current treatment and poorly understood molecular mechanisms. RNA expression studies suggest that AD is determined by diverse molecular events. Single cell technology allows comprehensive investigation of gene expression and cell specific changes in high precision of large number of brain cells. Computational analysis can reveal affected specific cell type marker genes and generate classification of the samples and gene networks. Here, we extensively characterized altered gene expression changes in post mortem brain samples of 2 individuals with AD (the brain samples originating from 3 brain regions, BA41/42,BA 6/8 and anterior hippocampal cortex). Wed detected significant changes in astrocyte marker genes. The samples were taken from patients in Braak stage III-IV. We found significant gene expression changes between the AD compared to the 2 control sequenced  samples. We found significant changes in oligodendrocyte, microglia and astrocyte marker genes and several specific genes that were altered including the neuronal differentiation factor SOX2. Overall, our study thus reinforces a growing body of evidence implicating glia in AD, and highlights the need for greater mechanistic understanding of neuron-glia interactions in AD.

overall_design:
2 AD samples (Braak stage 3, brain regions: BA41/42,BA 6/8 and anterior hippocampal cortex and 2 control brain regions were sequences

***Raw data requires controlled access and has been deposited at ENA (PRJEB45359; ERP129456)***

first: Carlo

last: Frigerio

first: John

last: Hardy

first: Nathan

last: Salomonis

first: Hannah

last: Bird


title: An uncharacterized gene, C7orf26, identified from an autosomal dominant ocular disease functions in mRNA splicing

city: Tokyo

first: Taku

last: Tanaka

address: 2-10-1 Okura, Setagaya

department: Ophthalmology

institute: National Center for Child Health and Development

summary: An uncharacterized gene, C7orf26 was expected to function with the integrator complex in mRNA splicing. To address the involvement of mRNA splicing, we performed microarray analysis of HeLa/C7orf26 siRNA cells and HeLa/non-specific (NS) and identified 700 transcripts that were downregulated by 50% or more in C7orf26 siRNA-treated HeLa cells. Gene set enrichment analysis showed that genes tagged with ‘alternative splicing’ or ‘splice variant’ occupy a large fraction of the downregulated genes.

overall_design: The C7orf26 expression in HeLa cell was knock-downed by siRNA-treated culture for 72H. The function of C7orf26 was investigated by enriched GO analysis of differentially expressed genes in HeLa cells induced by C7orf26 siRNA compared with control siRNA using microarray.

first: Noriyuki

last: Azuma

first: Tadashi

last: Yokoi


title: ATAC-seq for E14 cells knockdown with siRNA or shRNA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq was performed on cells E14 cells knockdown with siRNA or shRNA

overall_design: Chormatin accssibility were evaluated for E14 cells with factors knocked down

last: Li


title: RNA-seq for siRNA 48h

last: Zeng

summary: Bulk RNA-seq were performed on E14 cells knockdown with siRNA

first: Yao

last: Yi


title: miR-483 to 8OH-G miR-483 transversion changes mRNA targetomes in Ecs

status: Public on Mar 07 2023

city: La Jolla

first: Ming

last: He

state: CA

address: 9500 Gilman Dr.

institute: UCSD

summary:
To explore the transcriptional changes in endothelial cells (ECs) caused by the 8OH-G miR-483 transversion, we overexpressed miR-483 or 8OH-G miR-483 in ECs and profiled transcriptomes by RNA-seq
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human ECs transfected with miR-483 or 8OH-G miR-483

last: Shyy


title: Single-cell RNA sequencing reveals maturation trajectory in human pluripotent stem cell-derived cardiomyocytes in engineered tissues

city: Sha Tin

first: Shangli

last: Cheng

address: No. 15 Science Park West Avenue

department: Ming Wai Lau Centre for Reparative Medicine

country: Hong Kong

institute: Karolinska Institutet

summary: Cardiac in vitro models have become increasingly easy and affordable with the optimisation of stem cell-based cardiomyocyte (CM) differentiation. However, the CMs obtained are still far from being as mature as their in vivo counterparts. Here we study the cellular phenotype of human pluripotent stem cell-derived CMs by comparing the single-cell level gene expression profiles among different engineered cardiac tissue configurations: human ventricular cardiac anisotropic sheet, human ventricular cardiac tissue strip, and human ventricular cardiac organoid chamber (hvCOC). As a control, the spontaneously formed 3D cardiac spheroid aggregates (CS) were used. Our results suggest that the level of maturation increases with the level of complexity of the engineered tissues with CS being the least mature and hvCOC the most mature tissue. We show that the contractile components are the first function to mature, followed by electrophysiology and oxidative metabolism. Notably, the cellular structures in the 2D constructs show higher organisation while metabolic maturity preferentially increase in the 3D structures. We conclude that more complex tissue engineering models could offer more physiological and reliable in vitro matured cardiac tissue model for drug screening or disease modelling.

overall_design: Single-cell RNA-seq profiling for three types of engineered cardiac tissue configurations: human ventricular cardiac anisotropic sheet (hvCAS), human ventricular cardiac tissue strip (hvCTS) and human ventricular cardiac organoid chamber (hvCOC). The spontaneously formed 3D cardiac spheroid aggregates (CS) were used as a controls.

first: David

last: Brenière-Letuffe

first: Virpi

last: Ahola

first: Andy

middle: O

last: Wong

first: Jan

last: Keung

first: Bimal

last: Gurung

first: Zongli

last: Zheng

first: Kevin

middle: D

last: Costa

first: Deborah

last: Lieu

first: Wendy

first: Ronald


title: RNA-seq results of podocytes overexpressed lncRNA Dlx6-os1

city: zhengzhou

first: Guo

last: Jia

address: 1 Jianshe Dong Lu, Erqi District,

institute: The First Affiliated Hospital of Zhengzhou University

summary: In order to find out the changes of mRNAs after dlx6-os1 overexpression, we did RNA seq to analyze the mRNAs of podocytes.

overall_design: RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Jia

last: Guo


title: The diurnal demethylation of intronic CpG-rich islands is instrumental in expression of circadian clock-controlled genes [ileum]

first: Tao

last: YE

summary: To identify the methylation status of DNA at two circadian time points (i.e. 8am and 8pm) in ileum samples of wild type C57BL6/J mice. The methylated DNA was isolated, prified and immunoprecipated at two time points using 5-methyl cytosine antibody(MeDIP Assay).

overall_design: Examination of circadian methylation profiling in ileum samples of wild type mice

first: Manohar

last: Damara

first: Nisha

last: Misra

last: Ye

first: Pierre

last: Chambon


title: Integrating transcriptomics and metabolomics to analyze the mechanism of hypertension-induced hippocampal injury

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

summary: Hypertension-induced damage to the hippocampus not only leads to behavioral changes, but also to various brain diseases, but the mechanisms underlying hippocampal lesions are still unclear.

overall_design: The 32-week-old spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats were selected as the study subjects. The behavioral characteristics of rats were evaluated by behavioral experiments and comprehensive transcriptomic and metabolomic analysis was performed. Comprehensive analysis showed that hypertension-induced hippocampal lesions are closely associated with the metabolites and genes.

first: Yanan

last: Li

first: Dadi

last: Xie

first: Luxi

first: Pei

last: Jiang


title: Expression profiling of Solanum chacoense in response to Colorado potato beetle herbivory

city: East Lansing

first: Natalie

last: Kaiser

state: MI

address: 1066 Bogue Street

department: PSM

institute: Michigan State University

summary: We report the transcriptional response to Colorado potato beetle herbivory in leaves of the highly beetle resistant Solanum chacoense diploid line USDA8380-1 (80-) and a susceptible F2 individual (EE501F2_093) derived from a cross between 80-1 and a beetle susceptible line S. chacoense M6. Sampling tissue in a time course during adult Colorado potato beetle feeding provides novel insight to the transcriptomic defense response to this important pest.

overall_design: Examination of gene expression in leaves of two genotypes at three timepoints in response to beetle feeding. Time 0 = Before Colorado potato beetles were placed on plants; T1 = 24 hours after beetle placement; T2 = 48 hours after beetle placement

first: David

last: Douches


title: Identification of Human Pluripotent Stem Cell Derived Astrocytic Progenitors that Correlate with Glioblastoma Subtypes

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

summary: To investigate the heterogeneity of astrocyte progenitor subtypes present during human astrocyte differentiation that share molecular similarities with tumor initiating stem cells in GBM.

overall_design: human ESC derived astrocytic progenitor subtypes at 160 and 220 days after sequential treatment of LIF, BMP4 and FGF1 treatment were dissoiated and used for single cell RNA sequencing

first: Stephanie

last: Van Gulden


title: Gene expression data from aortic tissues of PPE-AAA mice receiving systemic lenvatinib treatment

city: Munich

first: Lars

last: Maegdefessel

address: Ismaninger Strasse 22

country: Germany

institute: Technical University of Munich

summary: Abdominal aortic aneurysm (AAA) is a disease with high morbidity and mortality, especially when ruptured. The rationale of this study was to evaluate the repurposing of lenvatinib, a multi–tyrosine kinase inhibitor, in limiting experimental AAA growth targeting vascular smooth muscle cells (VSMCs) and angiogenesis. We applied systemic lenvatinib treatment to porcine pancreatic elastase(PPE)-induced murine aortic aneurysms and profiled their gene expression through Affymetrix MTA1-0 microarray.

overall_design: Three separate groups (nondilated control aorta, PPE-AAA, PPE-AAA+Lenvatinib systemic treatment; same region of infrarenal aorta in all animals) of mouse aortic tissues were analyzed for differential expression.

first: Albert

last: Busch

first: Greg

last: Winski

first: Valentina

last: Paloschi


title: Monocytes re-enter the bone marrow during fasting and alter the host response to infection

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary:
The aim was to investigate transcriptional differences between circulating Ly6Chi monocytes under feeding and fasting/re-feeding conditions
Ly6Chi monocytes were sorted from blood after contious feeding or after a 24h fast follwed by a four hour re-feeding period

overall_design: Expression profiling by high throughput sequencing

first: Henrike

last: Janssen

first: Filip

last: Swirski

first: Florian

last: Kahles

first: Dan

last: Liu

first: Jeffrey

last: Downey

first: Laura

middle: L

last: Koekkoek

first: Vladimir

last: Roudko

first: Cameron

last: McAlpine

first: Lennard

last: Halle

first: Wolfram

last: Poller

first: Christopher

last: Chan

first: Shun

last: Shun

first: John

middle: E

last: Mindur

first: Máté

middle: G

last: Kiss

first: Sumnima

last: Singh

first: Atsushi

last: Anzai

first: Yoshiko

last: Iwamoto

first: Rainer

middle: H

last: Kohler

first: Kashish

last: Chetal

first: Ruslan

middle: I

last: Sadreyev

first: Ralph

last: Weissleder

first: Seunghee

last: Kim-Schulze

first: Miriam

last: Merad

first: Matthias

last: Nahrendorf


title: Gene expression profile at single cell level of inmmue cells  from the colon and brain

city: Suzhou

first: Qianyu

last: Yang

address: Suzhou

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the inmmune cells  in the intestine and brain.

overall_design: Colon tissue and brain tissue from mice were isolated  analyzed using scRNAseq.

first: Huaxing

last: Dai

first: Ying

last: Chen

first: Chao

last: Wang


title: Portunus trituberculatus larvae

city: Ningbo

first: Chen

last: Jiameng

address: No.169 Qixing South Road, Meishan Street, Beilun District, Ningbo City, Zhejiang Province, China

institute: Ningbo University

summary: Different growth stages of the Portunus trituberculatus larvae

last: Xiayue


title: Transcriptome analysis of Chd8 S62X heterozygote mutant and wild-type mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Autism spectrum disorders (ASD) are ~4-times more common in males than females, and CHD8 (a chromatin remodeler)-related ASD shows a strong male bias (~5:1), although the underlying mechanism remains unclear. Chd8-mutant mice with a C-terminal protein-truncating mutation (N2373X) display male-preponderant behavioral deficits as juveniles and adults, although whether this also applies to other Chd8 mutations remains unknown. Here we report that new Chd8-mutant mice with a stronger N-terminal protein-truncating mutation (S62X) display male-preponderant autistic-like behaviors at juvenile stages, but as adults, both males and females share behavioral deficits. Excitatory synaptic transmission is suppressed and enhanced in male and female juvenile Chd8+/S62X mice, respectively, but similarly enhanced in adults. ASD-like transcriptomic changes occur monophasically in newborn and juvenile (but not adult) males but biphasically in newborn and adult (not juvenile) females. Therefore, a strong CHD8 mutation induces early-onset ASD-like phenotypes in males but late-onset phenotypes in females after juvenile-stage female protection.

overall_design: Whole brain transcriptome analysis of Chd8 S62X heterozygote mutant and wild-type mice

first: Soo-Yeon

last: Lee

first: Hanseul

last: Kweon

first: Hyojin

last: Kang


title: Hematopoietic stem and progenitor cell formation in a BCR-ABL inducible expression embryonic stem cell model

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
Generating hematopoietic stem cells from pluripotent stem cells (PSC) has been a long lasting quest in the field of hematology. Previous studies suggested that the enforced expression of BCR-ABL, the oncogenic driver of chronic myeloid leukemia (CML), in hematopoietic cells derived from mouse embryonic stem cells (ESCs) is sufficient to confer on them in vivo long-term repopulating potential.
To uncover more precisely the events regulated by BCR-ABL expression during the course of ESC differentiation, we engineered a doxycycline inducible system to modulate BCR-ABL expression.

overall_design: LSK cells from adult bone marrow, E14.5 fetal liver and HSCL#A and #C were sorted in triplicates to perform mouse Affymetrix whole transcriptome experiments

first: Jérôme

last: Artus

first: Alina

last: Zenych

first: Isidora

last: Simanic

first: Christophe

last: Desterke

first: Denis

last: Clay

first: Lucas

last: de Souza

first: Coignard

last: Sabrina

first: Annelise

last: Bennaceur-Griscelli

first: Ali

last: Turhan

first: Adlen

last: Foudi


title: Long noncoding RNAs (LncRNA) associated with inflammation and immune response in human

city: Arlington

first: Subhrangsu

last: Mandal

state: TX

address: 700 Planetarium Place

department: Chemistry and Biochemistry

institute: The University of Texas at Arlington

summary: Discovery of lncRNA associated with inflammation

overall_design: Comparative gene expression profiling analysis of RNA-seq data in THP1 derived macrophages stimulated with LPS

first: Avisankar

last: Chini


title: mitochondria-encoded circRNA in Hepatocellular Carcinoma

status: Public on Mar 06 2023

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify mitochondria-encoded circRNA in HCC, we isolated mitochondria and performed RNA sequencing of HCC tissues

overall_design: RNA-seq of Mitochondria. The corresponding adjacent tissues are control samples for analyze.


title: Anti-tumor necrosis factor-alpha monoclonal antibody suppresses colorectal cancer growth in an orthotopic transplant mouse model

city: hiroshima

first: Takeshi

last: Takasago

state: hiroshima

address: kasumi 1-2-3

department: Gastroenterology

institute: Hiroshima university hospital

summary:
In order to investigate the effect of anti-TNFα mAb  on colorectal cancer, we generated a orthotopic transplantation model of colorecatal cancer.
We performed a comprehensive gene expression profiling analysis by extracting total RNA from cecal tumor of mice treated with and without anti-TNFα mAb (MP6-XT22)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cecal tumor of mice that received no treatment and anti-TNFα mAb treatment

first: Ryohei

last: hayashi


title: Expression Profile Analysis of LncRNAs and mRNAs in Endometrium of Women with PCOS undergoing IVF-ET

city: Shijiazhuang

first: Xiuhua

last: Xu

address: 215 Heping Road West

institute: Second Hospital of Hebei Medical University

summary:
To compare the expression levels of long non-coding RNA (lncRNA) and messenger RNA (mRNA) in endometrium between patients with Polycystic Ovary Syndrome （PCOS）and normal ovulation undergoing  in vitro fertilization-embryo transfer (IVF-ET）
LncRNAs and mRNAs of endometrium were identified via RNA sequencing from 3 PCOS and 3 normal ovulation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 PCOS and 3 normal ovulation

first: Aimin

last: Yang


title: Tumor progression is independent of tumor associated macrophages in two lineage-based mouse models of GBM [TAMdepletedVsControl RNAseq]

first: Mollie

last: Chipman

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

summary:
We investigate the transcriptomic changes resulting from TAM depletion in Type 1 and Type 2 GBMs
We perform bulk RNAseq on TAM depleted and Control Type 1 and Type 2 GBM bulk tumor tissue

overall_design: 5 Type 1 Control tumors, 3 Type 1 TAM depleted tumors, 4 Type 2 Control tumors, 4 Type 2 TAM depleted Tumors

first: Luis

middle: F

last: Parada


title: Alcohol-specific transcriptional dynamics of memory reconsolidation

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

summary: To assess gene expression underlying alcohol memory in different regions of the brain, we performed total RNA-sequencing (RNA-seq) on brain tissue (prefrontal cortex or dorsal hippocampus) from C57BL/6 adult mice that had undergone alcohol placement conditioning and either placed back into alcohol context (retrieval, Ret) or briefly handled as a control (no retrieval, NoRet)

overall_design: 2-3 biological replicates, each consisting of prefrontal cortex or dorsal hippocampi from individual mice. Pooled stranded libraries were run on Illumina Hiseq 2000, single-end, 50 bp reads. Data was processed by Bowtie2, Tophat2, featurecounts, and DESeq2 to assess differential gene expression.

first: Koral

last: Goltseker

first: Segev

last: Barak

first: Patricia

last: Garay


title: Tumor progression is independent of tumor associated macrophages in two lineage-based mouse models of GBM

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of transduced human CD4 T cell expressing different IRF4 mutants

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

summary: A heterozygous IRF4 missense variant located within the interferon activation domain of the encoded IRF4 protein (mutIAD) was identified in three patients from a multigenerational family suffering from a novel autosomal dominant disease predominantly presenting as a hypogammaglobulinemia with recurrent infections. In these experiments we aimed to investigate the effect of this IRF4 mutation on the transcriptome of T lymphocytes.

overall_design: RNA-Seq data from naïve CD4+ T cells isolated from 3 healthy donors, activated and transduced with constructs carrying WT IRF4 or IRF4 variants (mutIAD, L368P or R98W).

first: Romane

last: Thouenon

first: Sven

last: Kracker


title: Molecular and spatial profiling of the paraventricular nucleus of the thalamus

city: Bethesda

first: Claire

last: Gao

state: MD

address: 35 Covent Dr, Bldg 35 Rm 2E-614G

department: Unit on the Neurobiology of Affective Memory

institute: NIMH

summary: The paraventricular nucleus of the thalamus (PVT) is known to regulate various cognitive and behavioral processes. However, while functional diversity among PVT circuits has often been linked to cellular differences, the molecular identity and spatial distribution of PVT cell types remains unclear. To address this gap, here we used single nucleus RNA sequencing (snRNA-seq) and identified five molecularly distinct PVT neuronal subtypes. Additionally, multiplex fluorescent in situ hybridization of top marker genes revealed that PVT subtypes are organized by a combination of previously unidentified molecular gradients. Lastly, comparing our dataset with a recently published single-cell sequencing atlas of thalamus yielded novel insight into the PVT’s connectivity with cortex, including unexpected innervation of auditory and visual areas.  This comparison also revealed that our data contains a largely non-overlapping transcriptomic map of multiple midline thalamic nuclei. Collectively, our findings uncover previously unknown features of the molecular diversity and anatomical organization of the PVT and provide a valuable resource for future investigations.

overall_design: Nuclei suspensions were collected from bulk tissue punches of the mouse PVT were collected and processed using snRNAseq.

first: Mario

last: Penzo


title: A central chaperone-like role for 14-3-3 proteins in human cells

city: Toronto

first: Mikko

last: Taipale

state: Ontario

address: 160 college street

department: Molecular Genetics

country: Canada

institute: University of Toronto


title: Tumor progression is independent of tumor associated macrophages in two lineage-based mouse models of GBM [SortedTAM RNAseq]

summary:
We investigate whether TAM gene expression is similar between spontaneous and transplanted mouse models of GBM
We sort Microglia and monocyte derived macrophages (MDM) from subventricular zone (type 1)  and oligodendrocyte progenitor derived (type 2) spontaneous and transplanted mouse GBM tumors and perform bulk RNAseq

overall_design: 3 Spontaneous GBM MDM, 6 spontaneous GBM microglia, 6 transplanted GBM MDM, 6 transplanted GBM microglia, 4 normal brain microglia (control)


title: A central chaperone-like role for 14-3-3 proteins in human cells [iCLIP-seq]

summary: 14-3-3 proteins are highly conserved regulatory proteins that interact with hundreds of structurally diverse clients and act as central hubs of signaling networks. However, how 14-3-3 paralogs differ in specificity and how they regulate client protein function are not known for most clients. Here, we map the interactomes of all human 14-3-3 paralogs and systematically characterize the effect of disrupting these interactions on client localization. The loss of 14-3-3 binding leads to the coalescence of a large fraction of clients into discrete foci in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Congruently, the engraftment of 14-3-3 binding motifs to nonclients can suppress their aggregation or phase separation. Finally, we show that 14-3-3s negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and inhibit its activity as a translational repressor. Our work suggests that 14-3-3s have a more prominent role as chaperone-like molecules than previously thought.

overall_design: iCLIP-seq of EGFP-tagged wild-type SAMD4A or its 14-3-3 binding deficient mutant in HeLa cells . Each experiment was performed in biological duplicate. Control libraries for size-match inputs (SMI) were prepared in parallel

first: Dmitri

last: Segal

first: Stefan

last: Maier

first: Giovanni

middle: J

last: Mastromarco

first: Wesley

middle: W

last: Qian

first: Syed

last: Nabeel-Shah

first: Hyunmin

last: Lee

first: Gaelen

last: Moore

first: Jessica

last: Lacoste

first: Brett

last: Larsen

first: Zhen

last: Lin

first: Abeeshan

last: Selvabaskaran

first: Karen

last: Liu

first: Craig

last: Smibert

first: Zhaolei

last: Zhang

first: Jack

last: Greenblatt

first: Jian

last: Peng

first: Hyun

first: Anne

last: Gingras


title: The blue light receptor CRY1 interacts with FIP37 to promote N6-methyladenosine RNA modification and photomorphogenesis in Arabidopsis

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

summary: Using m6A-seq, we present transcriptome-wide distribution of m6A in wild type, cry1 and cry1 cry2 seedlings with or without blue light treatment. Analysis of m6A distribution reveals CRY1 and CRY1 are involved blue light induced changes of m6A distribution in Arabidopsis

overall_design: This series includes samples for m6A-seq: two biological replicates for dark and blue light treated m6A IP and input samples in wild type, cry1 and cry1 cry2 mutants.

first: Jiaxin

last: Yang

first: Lan

last: Li

first: Xin

first: Xiaoying

last: Zhao


title: DNA G-Quadruplex Recognition In Vitro and in Live Cells by a Structure-Specific Nanobody

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

summary: G-quadruplexes (G4s) are alternative DNA secondary structures of the human genome with key roles in transcription, replication and genome stability. Structure-specific small molecules and antibodies, such as BG4, have facilitated the detection of G4s in cells and chromatin. The availability of an alternative probe to BG4 would help to address some of its potential limitations in mapping G4 structures and would independently confirm and/or extend our earlier findings. Herein, we describe the development of SG4, a camelid single-chain only derived nanobody raised against the human MycG4 promoter structure. SG4 is small, easily expressed and demonstrates low nanomolar affinity for folded G4 structures in vitro. Clues to SG4 binding were obtained experimentally by mutating single amino acids. Moreover, AlphaFold2 protein predictions combined with molecular dynamics/docking simulations generated a de novo binding model of SG4-G4 interactions that identifies key amino acids with significant contributions to G4 binding. Using SG4 in G4 ChIP-seq, we also demonstrate the detection of G4 structures in two cancer cell lines. SG4 thus provides an alternative tool for G4 genome mapping and independently verifies our earlier findings.

overall_design: Two cancer cells lines, U2OS and K562, have been profiled using a nanobody able to bind to DNA G4 secondary structures. For each cell line 3 biological replicates were performed and for each biological replicates 3 technical were prepared along with an input control.

first: Silvia

last: Galli

first: Larry

last: Melidis

first: Dhaval

last: Varshney

first: Jochen

last: Spiegel

first: Sarah

last: Madden

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: A central chaperone-like role for 14-3-3 proteins in human cells [RNA-seq]

first: Mikko

last: Taipale

overall_design: RNA-seq of HeLa cells overexpressing EGFP-tagged wild-type SAMD4A or its 14-3-3 binding deficient mutant. Each experiment was performed in biological duplicate.

first: Dmitri

last: Segal

first: Stefan

last: Maier

first: Giovanni

last: Mastromarco

first: Wesley

last: Qian

first: Syed

last: Nabeel-Shah

first: Hyunmin

last: Lee

first: Gaelen

last: Moore

first: Jessica

last: Lacoste

first: Brett

last: Larsen

first: Zhen

last: Lin

first: Abeeshan

last: Selvabaskaran

first: Karen

last: Liu

first: Craig

last: Smibert

first: Zhaolei

first: Jack

middle: C


title: Functional impact of IRF4 mutations on transcription in patient-derived B-EBV cells [RNA-seq]

first: Emilia

last: Puig Lombardi

summary: An IRF4 de novo mutation affecting the DNA binding domain of encoded IRF4 protein (mutDBD) was identified in a patient presenting with combined immunodeficiency. The patient exhibited profound susceptibility to opportunistic infections notably Pneumocystis jirovecii and humoral immunodeficiency caused by a failure of terminal B cell differentiation. A heterozygous IRF4 missense variant resulting in a phenylalanine-to-leucine replacement within the interferon activation domain of the encoded IRF4 protein (mutIAD) was identified in three patients from a multigenerational family suffering from a novel autosomal dominant disease predominantly presenting as a hypogammaglobulinemia with recurrent infections. In this experiment we aimed to investigate the effect of the two different mutations on IRF4 regulated transcription.

overall_design: RNA-seq data in EBV-B cells of individuals heterozygous for IRF4 mutations and healthy homozygous WT individuals

first: Romane

last: Thouenon

first: Sven

last: Kracker


title: Functional impact of IRF4 mutations on genomic binding in patient-derived B-EBV cells [ChIP-seq]

summary: An IRF4 de novo mutation affecting the DNA binding domain of encoded IRF4 protein (mutDBD) was identified in a patient presenting with combined immunodeficiency. The patient exhibited profound susceptibility to opportunistic infections notably Pneumocystis jirovecii and humoral immunodeficiency caused by a failure of terminal B cell differentiation. A heterozygous IRF4 missense variant resulting in a phenylalanine-to-leucine replacement within the interferon activation domain of the encoded IRF4 protein (mutIAD) was identified in three patients from a multigenerational family suffering from a novel autosomal dominant disease predominantly presenting as a hypogammaglobulinemia with recurrent infections. In this experiment we aimed to investigate the effect of the two different mutations on IRF4 genomic binding.

overall_design: ChIP-seq data in EBV-B cells of individuals heterozygous for IRF4 mutations and healthy homozygous WT individuals


title: Transcriptional control of nucleus accumbens by Retinoid X Receptor Alpha

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: The complex nature of the transcriptional networks underlying addictive behaviors suggests intricate cooperation between diverse gene regulation mechanisms that go beyond canonical activity-dependent pathways. Here we implicate in this process a novel nuclear receptor transcription factor, Retinoid X Receptor Alpha (RXRα), which we identified bioinformatically as associated with addiction-like behaviors. In the nucleus accumbens (NAc) of male and female mice, we show that, while its own expression remains unaltered after cocaine exposure, RXRα controls plasticity- and addiction-relevant transcriptional programs in both dopamine receptor D1- and D2-expressing medium spiny neurons, which in turn modulate intrinsic excitability and synaptic activity of these NAc cell types. Behaviorally, bidirectional viral and pharmacological manipulation of RXRα regulates drug reward sensitivity in both non-operant and operant paradigms. Together, this study demonstrates a key role for NAc RXRα in promoting drug addiction, and paves the way for future studies of rexinoid signaling in psychiatric disease states.

overall_design: Transcriptome of Nucleus Accumbens (NAc) after viral overexpression of RXRa in mouse. The NAc transcriptome following virus administration was assessed in bulk NAc tissue, as well as that of D1 and D2 sorted nuclei.

first: Arthur

last: Godino

first: Marine

last: Salery

first: Romain

last: Durand-de Cuttoli

first: Leanne

middle: M

last: Holt

first: Rita

last: Futamura

first: Caleb

last: Browne

first: Philipp

last: Mews

first: Peter

last: Hamilton

first: Rachael

last: Neve

first: Li

last: Shen

first: Scott

last: Russo

first: Eric

last: Nestler


title: Arabidopsis Shoot versus Root transcriptome

status: Public on Mar 05 2023

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

institute: University of Nottingham

summary: Bulk RNA-Seq datasets were generated for the shoots and roots of Arabidopsis in order to compare expression of nutrient transporters between  tissues

overall_design: Arabidopsis shoot x 4, Arabidopsis root x 4

first: Anthony

last: Bishopp

first: Elina

last: Chrysanthou


title: Functional impact of IRF4 mutations on genomic binding and transcription in patient-derived B-EBV cells

first: Emilia

last: Puig Lombardi

summary:
An IRF4 de novo mutation affecting the DNA binding domain of encoded IRF4 protein (mutDBD) was identified in a patient presenting with combined immunodeficiency. The patient exhibited profound susceptibility to opportunistic infections notably Pneumocystis jirovecii and humoral immunodeficiency caused by a failure of terminal B cell differentiation. A heterozygous IRF4 missense variant resulting in a phenylalanine-to-leucine replacement within the interferon activation domain of the encoded IRF4 protein (mutIAD) was identified in three patients from a multigenerational family suffering from a novel autosomal dominant disease predominantly presenting as a hypogammaglobulinemia with recurrent infections. In these experiments we aimed to investigate the effect of the two different mutations on IRF4 genomic binding and regulated transcription.

This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide localization of Swi6 and H3-Lys9-me2 in wt and mutant starins of S. pombe

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-on-ChIP experiments were performed to quantitate the genome-wide localization of heterochromatin proteins Swi6 and H3-Lys9-me2 in wild type versus polalpha mutant swi7H4, Pol delta mutant, dts2 and cut4 mutant cut4-993. Our results indicate that the localization of Swi6 and H3-Lys7-me2 at heterochromaitn regions, like centromere, telomere and mating-type is abrogated in the swi7H4, dts2 and cut4 mutants.

overall_design: Agilent S. pombe  ChIP-on-chip Microarray, 4X44K (AMADID:015424)

first: Jagmoha

last: Singh

first: Kamlesh

middle: K

last: Bisht


title: JAK inhibition ameliorates bone destructions by simultaneously targeting mature osteoclasts and their precursor stages

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Inflammatory bone destruction was induced by locally injecting lipopolysaccharides into fluorescent reporter mice of mature osteoclasts or their precursors. These mice were treated with a JAK inhibitor, ABT-317, which selectively inhibits the activation of JAK1, and intravital imaging with multiphoton microscopy was conducted. We also investigated the molecular mechanism of the effects of the JAK inhibitor on osteoclasts by exhaustive RNA sequence analysis.

overall_design: To reveal the molecular mechanism that JAK inhibitor prevented the migration of osteoclast precursors to the bone surface, CX3CR1-EGFP+ cells were isolated from calvaria in LPS-induced inflammatory bone destruction model mice which were treated with JAK inhibitor or vehicle, and RNA sequence analysis was performed.

first: Shinya

last: Yari

first: Junichi

last: Kikuta


title: Expression data from abdominal aorta of cutaneous inflammation mice

city: Tsu

first: Takehisa

last: Nakanishi

address: 2-174 Edobashi

institute: Mie university

summary: Vascular disorder such as arteriosclerosis is one of the serious complications of chronic inflammatory skin diseases. We employed spontaneous dermatitis model mice overexpressing human caspase-1 in the epidermal keratinocyte (KCASP1Tg). GeneChip were performed to measure the changes in mRNA levels in the abdominal aorta.

overall_design: The mRNA was extracted from the abdominal aorta of 4-month-old KCASP1Tg and WT mice, and GeneChip analysis was performed. There were several upregulated genes in KCASP1Tg mice.

first: Shohei

last: Iida

first: Junko

last: Maruyama

first: Hayato

last: Urushima

first: Masako

last: Ichishi

first: Yoshiaki

last: Matsushima

first: Kento

last: Mizutani

first: Yuichi

last: Nakayama

first: Kyoko

last: Sugioka

first: Mai

last: Nishimura

first: Ai

last: Umaoka

first: Yoichiro

last: Iwakura

first: Makoto

last: Kondo

first: Koji

last: Habe

last: Tsuruta

first: Osamu

last: Yamamoto

first: Yasutomo

last: Imai

first: Keiichi

last: Yamanaka


title: Transcriptional profiling of DLBCL-like murine pBIC2 tumors (p53F/F; Blimp1F/F; IKK2castopF/stopF; Cg1Cre/+; Eµ-hBCL2tg/+)

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

summary: Germinal center (GC) B cells have been presented as the cell-of-origin of diffuse large B-cell lymphoma (DLBCL), and these cells can be functionally targeted with the use of Cgamma1-cre mice (Cg1cre) in wich the expression of Cre recombinase is induced by transcription of the Ig gamma1 constant region gene segment. Here, we aimed to develop and characterize novel immunocompetent multi-lesion mouse models of DLBCL that, by triggering genetic alterations specifically in GC B cells, recapitulate relatively fast the molecular, cellular and tumor microenvironment of aggressive human DLBCL.

overall_design: RNAseq profiling of FACS-sorted reporter positive splenic B cells from DLBCL murine models (B220+GFP+ lymphoma cells) were compared to normal controls (B220+YFP+ GC B cells) during secondary immune response to sheep-red blood cells (SRBC) immunization (i.e. 10 days after second intraperitoneal immunization with SRBC, following a first immunization 20 days before).

first: Sergio

last: Roa

first: Javier

last: Melchor

first: Marcos

last: Lacarte

first: Sara

last: Grijalba


title: Global expression data from HCT-116 human colorectal cancer (CRC) wild type cells (HCT116/GFP) and CPEB4 over-expressed cells via lenti-virus system (HCT116/CPEB4)

status: Public on Mar 04 2023

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary:
CPEB4 is down-regulated in CRC tissues, a stable cell line was established via lenti-virus system for CPEB4 overexpression.
Microarray experiment by the Affymetrix Human Genome U133 plus 2.0 GeneChips to examine the profiling expression of indicated cells.

overall_design: HCT116-GFP and HCT116-CPEB4 cells were used for the microarray assay.

first: Qifeng

last: Wang


title: MYC regulates chromatin interactions in prostate cancer

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

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

overall_design: Refer to individual Series


title: Translational Landscape in Human Early Neural Fate Determination

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

summary: Gene expression regulation in eukaryotes is a multi-level process, including transcription, mRNA translation, and protein turnover. Many studies have reported the sophisticated transcriptional regulations during neural development, but the global translational dynamics is still ambiguous. Here, we differentiated human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and performed ribosome sequencing and RNA sequencing on both ESCs and NPCs. Data analysis revealed that translational controls engaged in many critical pathways and contributed significantly to neural fate determination regulation. Furthermore, we showed that the sequence characteristics in the untranslated region (UTR) might regulate translation efficiency. Specifically, genes with short 5UTR and intense Kozak sequence are associated with high translation efficiency in human ESCs, while genes with long 3'UTR are related to high translation efficiency in NPCs. In addition, we identified four biasedly-used codons (GAC, GAT, AGA, and AGG) and dozens of short open reading frames during neural progenitor differentiation. Thus, our study reveals the translational landscape during early human neural differentiation and provides insights into the regulation of cell fate determination at the translational level.

overall_design: We differentiated human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and performed ribosome sequencing and RNA sequencing on both ESCs and NPCs.

first: Chenchao

last: Yan

first: Yajing

last: Meng

first: Jian

last: Chen

first: Wei

last: Jiang


title: Spirodela polyrhiza root and frond phosphate starvation RNA-Seq

first: Alexander

last: Ware

summary: Spirodela polyrhiza (9509) was grown under replete conditions for 10d, subject to media without phosphate or control for 24h, and then sequenced.

overall_design: Frond control x4, Frond noPi x4, Root control x4, Root noPi x4

first: Anthony

last: Bishopp

first: Dylan

last: Jones


title: Comprehensive regulatory element interaction landscape in prostate cancer

summary: We used HiChIP technique to assess H3K27ac, AR and CTCF-mediated chromatin interaction in prostate cancer cells.

overall_design:
HiChIP in prostate cancer cells
Please note that processed data generated from both replicates is linked to the corresponding *rep2 sample records

first: Zhao

last: Wei

first: Housheng

last: He


title: Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: Circadian rhythmicity in renal function suggests rhythmic adaptations in renal metabolism. To decipher the role of the circadian clock in renal metabolism, we studied diurnal changes in renal metabolic pathways using integrated transcriptomic, proteomic, and metabolomic analysis performed on control mice and mice with inducible deletion of the circadian clock regulator Bmal1 in the renal tubule (cKOt). With this unique resource, we demonstrated that ~30% RNAs, ~20% proteins and ~20% metabolites are rhythmic in kidneys of control mice. Several key metabolic pathways including NAD+ biosynthesis, fatty acid transport, carnitine shuttle, and b-oxidation displayed impairments in kidneys of cKOt, resulting in a perturbed mitochondrial activity. Carnitine reabsorption from the primary urine was one of the most impacted processes with a ~50% reduction in plasma carnitine levels and a parallel systemic decrease in tissues carnitine content. This suggests that the circadian clock in the renal tubule controls both kidney and systemic physiology.

overall_design:
RNA was extracted from the renal tubules of 60 mice. Of these, 30 were conditional knockouts of Arntl (Bmal1) and 30 were of control genotype. They were housed under 12-hours light/12-hours dark cycles and were sacrificed at six different time points: zeitgeber time ZT 0, ZT 4, ZT 8, ZT 12, ZT 16, ZT 20 (ZT 0 being the time of light on and ZT 12 the time of light off). Five replicates per genotype and time point were included.

Technical note: The FASTQ file for sample 56 ("Renal tubule, cKO genotype, ZT12, rep 5") is incomplete: The last 8201575 of 27714258 reads are missing. The original file was corrupted (truncated) at the sequencing facility due to a technical problem on a server cluster. However, the processed data file of this sample is unaffected and contains the raw read counts from the original, complete FASTQ data.

first: Yohan

last: Bignon

first: Camille

last: Ansermet

first: Sylvain

last: Pradervand

first: Dmitri

last: Firsov


title: Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development [miRNA-Seq]

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

state: PA

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

summary: Mammalian nephron progenitors undergo transcriptional changes over the course of nephrogenesis that sensitize them to signals for differentiation over time. This increases the rate at which they exit their multipotent, self-renewing mesenchymal state and become differentiated epithelial cells, ultimately depleting the progenitor population and leading to the cessation of nephrogenesis. We hypothesized that changes in chromain accessibility and miRNA expression would accompany these transcriptional changes, and that regions of changing chromatin accessibiltiy could reveal chaning regulatory features such as enhancers, including some that affect miRNA expression. To test this, we pooled kidneys from wild-type mouse litters sacrificed at embryonic day 14.5 (E14.5) and post-natal day zero (P0) using positive selection for the surface protein Integrin alpha 8 (Itga8), then sequenced the assay for transposase-accessible chromatin (ATAC-seq) using 50,000 cells, and used the remaining cells for small RNA sequencing (smRNA-seq). smRNA-seq libraries were generated using the QIAseq miRNA library preparation kit (Qiagen 331502), and all sequencing was performed using an Illumina NextSeq500 by the Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh.

overall_design: Sequencing libraries generated from nephron progenitor cells isolated and pooled from the same litter of embryos/pups. Isolation performed at E14.5 or P0, and three biological replicates were produced per condition (6 samples total)

last: Bodnar

first: Debora

last: Malta Cerqueira

first: Yu

last: Phua

first: Andreas

last: Pfenning

first: Kristy

last: Boggs

first: Jacqueline

last: Ho

first: Dennis

last: Kostka


title: Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development [ATAC-Seq]

summary: Mammalian nephron progenitors undergo transcriptional changes over the course of nephrogenesis that sensitize them to signals for differentiation over time. This increases the rate at which they exit their multipotent, self-renewing mesenchymal state and become differentiated epithelial cells, ultimately depleting the progenitor population and leading to the cessation of nephrogenesis. We hypothesized that changes in chromain accessibility and miRNA expression would accompany these transcriptional changes, and that regions of changing chromatin accessibiltiy could reveal chaning regulatory features such as enhancers, including some that affect miRNA expression. To test this, we pooled kidneys from wild-type mouse litters sacrificed at embryonic day 14.5 (E14.5) and post-natal day zero (P0) using positive selection for the surface protein Integrin alpha 8 (Itga8), then sequenced the assay for transposase-accessible chromatin (ATAC-seq) using 50,000 cells, and used the remaining cells for small RNA sequencing (smRNA-seq). ATAC-seq libraries were generated using the Nextera DNA Flex Library Prep Kit (Illumina FC-121-1030) with modifications according to a previously published method (Buenrostro et al., 2013), and all sequencing was performed using an Illumina NextSeq500 by the Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh.

overall_design: Sequencing libraries generated using 50,000 nephron progenitor cells isolated and pooled from the same litter of embryos/pups. Isolation performed at E14.5 or P0, and three biological replicates produced per condition (6 samples total).


title: Novel genetically engineered H3.3G34R model reveals cooperation with ATRX loss in upregulation of PRC2 targets, NOTCH activation, promotion of neuronal lineage

city: New York

first: Oren

last: Becher

address: 1468 Madison Ave 4th Fl,

department: Pediatric Hematology-Oncology

institute: Mount Sinai

summary: Pediatric high-grade gliomas (pHGGs) are an aggressive pediatric CNS tumor, often characterized by mutations in H3F3A, the gene that encodes Histone H3.3 (H3.3). Substitution of the Glycine at position 34 of H3.3 with either Arginine or Valine (H3.3G34R/V), was recently described and characterized in a large cohort of pHGG samples as occurring in 5-20% of pHGGs. We developed a genetically engineered mouse model (GEMM) that incorporates PDGF-A activation, TP53 loss and the H3.3G34R mutation both in the presence and loss of Alpha thalassemia/mental retardation syndrome X-linked (ATRX), which is commonly mutated in H3.3G34 mutant pHGGs. Nestin Tv-a; p53 fl/fl and Nestin Tv-a; p53 fl/fl; ATRX fl/fl mice were injected with DF-1 cells transfected with RCAS-Cre, RCAS-PDGFA, and either RCAS-H3.3WT-GFP or RCAS-H3.3G34R-GFP. By 210 days old, a majority of mice develop symptoms of tumor growth (erratic behavior, domed head, ataxia) or have 20% weight loss and are euthanized. Our goal is to develop a biologically relevant animal model of pHGG in order to probe the downstream effects of the H3.3G34R mutation in the context of vital co-occurring mutations.

overall_design: Examination of gene expression differences in mouse frontal Cortex of H3.3G34R expression and ATRX loss

first: Aalaa

middle: A

last: Abdallah


title: Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development


title: RNA-seq established gene expression data to determine the effects of various stresses on Bacillus subtilis str.168

status: Public on Mar 03 2023

city: Newcastle upon Tyne

first: David

last: Markham

address: Devonshire Building

department: ICOS

institute: Newcastle University

summary: To explore the effects of different stress conditions on Bacillus subtilis str.168, a selection of conditions were applied to the organism and RNA-seq data gathered. A matrix of gene counts was produced as a basis for further analysis into the transcription profiles of Bacillus subtilis str.168.

overall_design:
Bacillus subtilis str.168 was subjected to the following stress conditions: Diamide, Ethanol, High Temperature, Low Temperature, Glucose to Malate Nutrient Shift, Malate to Glucose Nutrient Shift, Anaerobic Growth, Competence, Stationary Growth. For each condition, a control without the stress was conducted and each experiment has three replicates.
This work was funded by the EPSRC, EP/N031962/1. Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies

first: Wendy

last: Smith

first: Yiming

last: Huang

first: Lucy

last: Eland

first: Anil

last: Wipat


title: Acetylation of TEAD2 is essential for YAP-TEAD transcriptional complex formation

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

summary: To investigate the effect of TEAD2 acetylation in transcriptional regulation through profiling three groups of cells with different TEAD2 acetylaiton state.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cells transfected with different acetylation state TEAD2

first: Lei

last: Zhang

first: Bo

last: Liu

first: Youzhi

last: Tang

first: Miao

last: Yu

first: Jiaqi

last: Jin

first: Siyuan

last: Yang

first: Zhenbin

last: Wang

first: Hongquan


title: Transcriptome analysis of wild-type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development

city: Beijing

first: Weimin

last: Shen

address: Tsinghuayuan park

institute: School of life science, Tsinghua University

summary: To study the function of zebrafish nuclear pores during early embryogenesis, we generated maternal zygotic double mutant of nup85;nup133 (MZnup85;nup133) using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal-to-zygotic transition.

overall_design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology

first: Anming

last: Meng


title: LINC01876: A human-specific L1-derived lncRNA

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

institute: Lund University

summary: Functional characterization of LINC01876 in human fbNPCs and neural organoids using CRISPRi.

overall_design: To characterize the effect of LINC01876, we set up CRISPR inhibition of LINC01876 in human fbNPCs. Our results show that this lncRNA regulates the expression of genes related to development. To functionally study the developmental relevance of LINC01876, we grew neural organoids with CRISPR-mediated LINC01876 inhibition and performed 10x single nuclei RNAseq.

first: Raquel

last: Garza


title: Gene expression of small peritoneal macrophages (SPM)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: Transcriptome of SPM (small peritoneal macrophages) from mice infected with LPS and treated with LCC-12

overall_design: Experiments were performed on 5-week-old male SWISS mice. Male littermates were randomly assigned to experimental groups. The experimental endotoxemic model was induced by intraperitoneal (IP) injection of LPS (20 mg/kg) )(Escherichia coli O55:B5, Sigma-Aldrich, L2880). All the animals were resuscitated with 30 mL/kg body weight of saline administered subcutaneously 6 h post LPS administration. Mice were intra-peritoneally injected with LCC-12 (0.3 mg/kg  6 h after LPS challenge). Mice were sacrificed 22 h post-LPS challenge.

first: Stéphanie

last: Solier

first: Sebastian

last: Muller

first: Tatiana

last: Caneque

first: Antoine

last: Versini

first: Pierre

last: Gestraud

first: François

last: Trotten

first: Sarah

last: Watson

first: Raphaël

last: Rodriguez


title: Gene expression analysis of activated monocyte-derived macrophages (aMDM) in CD44 knock out conditions

summary: Analysis of the transcriptome of human monocyte-derived macrophages activated with IFN-gamma and LPS,  in CD44 knock out conditions

overall_design: Peripheral blood samples were collected from healthy donors and monocytes were sorted. Human primary monocytes were transfected with CAS9/CD44 sgRNA mix, and the following day, GM-CSF was added to the medium. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.


title: Transcriptional profiling of human prefrontal cortex using single cell/nuclei and bulk RNAseq

summary: This study aims to profile transposable element expression in human adult cortex

overall_design: We performed 10x single cell/nuclei RNAseq of human cortex to characterize transcriptional changes of gene and transposable elements in different cell types of the adult human prefrontal cortex. We complimented our analysis using bulk RNAseq using short and long read sequencing technologies


title: Impact of aging on intestinal epithelial cells and reversible aspects by metformin or rapamycin treatment

city: Bronx

first: Jiahn

last: Choi

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Aging is a risk factor that initiates pathogenesis in the intestinal mucosa. We used single cell RNA sequencing to dissect the aging process and how effectively geroprotectors delays the process.

overall_design: Intestinal epithelial cells from CB6F1 male mice were isolated by FACS (Epcam+, CD45 neg) at either 5-month-old (Young), or 24-month-old (Old). For treatment group, metformin or rapamycin treatment for old mice began at 21-month-old and sacrificed at 24-month-old.

first: Xusheng

last: Zhang

first: Leonard

last: Augenlicht


title: Transcriptomic regulation of acidic biofilms by Candida albicans Sfl1

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

summary: Transcriptional profiling of Candida albicans cells grown under planktonic and biofilm-inducing conditions, comparing SN76 and sfl1Δ/sfl1Δ strains. Goal was to study the effect of SFL1 deletion on the transcriptomic profile of C. albicans planktonic and biofilm cells under acidic conditions, in order to reveal the function of the Sfl1 transcription factor in C. albicans biofilm development.

overall_design: Candida albicans sfl1Δ and SN76 strains were cultivated in RPMI at pH 4 for 24 h under planktonic and biofilm-inducing conditions, and then the RNA was extracted from the cells and hybridised in a species-specific DNA microarray for C. albicans (sfl1Δ/sfl1Δvs. SN76)

first: Bruna

last: Gonçalves

last: Barbosa

middle: R

first: Mariana

last: Henriques

first: Sónia

last: Silva


title: scRNA-Seq analysis of Trim28-deleted NPp53 mouse prostate tissue

city: Washington

first: Maho

last: Shibata

state: DC

address: 800 22nd Street, NW SEH 8430

institute: The George Washington University

summary: The Tripartite motif-containing 28 (TRIM28) transcription factor is upregulated in high-grade prostate cancers and was recently proposed as a therapeutic target for castration-resistant prostate cancers. To study the role of TRIM28 in prostate cancer progression in vivo, we used a genetically engineered mouse model, combining prostate-specific Trim28 inactivation with inactivation of Trp53 and Pten. We analyzed the prostates using single cell RNA-Seq.

overall_design: scRNA-Seq expression profiles from NPp53 (Pten;Tp53 deleted) and NPp53T (Pten;Tp53; Trim28 deleted) mouse prostates with EYFP for lineage tracing

first: Anelia

last: Horvath


title: Histone profiling of monocyte-derived macrophages (MDM)

first: Nicolas

last: Servant

country: France

summary: ChIP-seq of naMDM, aMDM and aMDM+LCC-12

overall_design: Peripheral blood samples were collected from healthy donors. Monocytes were sorted, then  exposed to granulocyte-macrophage colony-stimulating factor to generate their differentiation. After 5 days of differentiation, macrophages were activated or not with IFN-gamma and LPS during 24 hours. Moreover, after 5 days of differentiation, macrophages were treated or not with LCC-12 during 24 hours.

first: Stéphanie

last: Solier

last: Muller


title: Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

summary: A large swath of the human proteome is dedicated to RNA homeostasis, but most RNA-binding proteins lack chemical probes1,2. Here, phenotypic screening led to the discovery of electrophilic small molecules that swiftly (within 4 h) and stereospecifically decrease transcripts encoding the androgen receptor (AR) and its major V7 splice variant in human prostate cancer cells.  We show by chemical proteomics that these compounds covalently engage cysteine-145 on the RNA-binding protein NONO. Transcriptomics and proteomics profiling revealed that covalent NONO ligands suppress a discrete set of transcripts and proteins, including multiple oncogenic transcription factors, and impair the proliferation of cancer cells. These effects were not observed following genetic disruption of NONO, which instead blocked ligand activity. The covalent ligands promote accumulation of NONO in nuclear foci and at the first 5 splice site of immature transcripts, pointing to a trapping mechanism that may prevent compensatory action by the related protein PSPC1, which was found to increase in cancer cells following genetic or chemical perturbation of NONO. These findings, taken together, designate NONO as a druggable RNA-binding protein that can be co-opted by covalent small molecules to suppress pro-tumorigenic transcriptional networks.

overall_design: Examination of RNA-seq and eCLIP-seq in 22Rv1 human prostate cancer cell line with 3 ligand treatmetns: SKBG-1(R), SKBG-1(S), DMSO under the context of WT and NONO-KO

first: Stefan

last: Kathman

first: Hsuan-lin

first: Seong

last: Koo

first: Garrett

last: Lindsey

first: Steven

last: Blue

first: Haoxin

last: Li

first: Steffen

last: Jaensch

first: Jarrett

last: Remsberg

first: Kay

last: Ahn

first: Gene

last: Yeo

first: Brahma

last: Ghosh

first: Benjamin

last: Cravatt


title: RNA-seq analysis of CREB3L2 dimers in Hippocampal Neurons

first: Claudio

last: Gouveia Roque

address: 650 West 168th Street

department: The Taub Institute for Research on Alzheimer's disease and the Aging Brain

institute: Columbia University

summary: To investigate differential gene expression profiles mediated by CREB3L2 transcription factor dimers in order to assess their differential contribution to Alzheimer's disease pathogenesis.

overall_design: Rat primary hippocampal neurons were infected with different CREB3L2 dimers using lentiviruses. Specific dimer combinations were promoted using cheimically induced proximty. Total RNA extraction was performed after four days of incubation of this chemogenetic system. RNA-seq was employed to examine gene expression changes.

first: Ulrich

last: Hengst

first: Cláudio


title: Next Generation Sequencing Quantitative Analysis of Wild Type and TMEM9 KD Transcriptomes

city: Houston

first: Shengzhe

last: Zhang

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

summary:
Purpose: The goals of this study are to check signaling pathway change upon TMEM9 KD using NGS-derived retinal transcriptome profiling (RNA-seq).
Methods: Retinal mRNA profiles of MDA-MB-453 WT and TMEM9 KD were generated by deep sequencing, using Illumina. The sequence reads that passed quality filters were analyzed.
Results: Using GSEA analysis, we found mTOR signaling pathway was suppressed after TMEM9 KD.
Conclusions: Our study revealed the signaling pathway change upon TMEM9 KD in BRCA cells.

overall_design: Retinal mRNA profiles of MDA-MB-453 cells


title: Gene expression in lungs from SARS-CoV-2 mice treated with biguanides [RNAseq_murine]

first: Nicolas

last: Servant

summary: Transcriptome of lung cells from mice infected with SARS-Cov-2 and treated with biguaniddes

overall_design: Eight week-old male K18-human ACE2 expressing C57BL/6 mice were intranasally infected with 50 µl of DMEM containing 5x102 TCID50 of hCoV-19_IPL_France strain of SARS-CoV-2 (NCBI MW575140). LCC-12 was inoculated intranasally (0.5 mg/ml, 50 µL) 6 h post-infection, and once a day until day 2. Mice were sacrificed at day 4 post-infection.

first: Stéphanie

last: SOLIER

first: Sebastian

last: MULLER

first: Tatiana

last: CANEQUE

first: Antoine

last: VERSINI

first: Delphine

last: GUILLEMOT

first: Pierre

last: GESTRAUD

first: François

last: TROTTEIN

last: SERVANT

first: Sarah

last: WATSON

first: Raphaël

last: RODRIGUEZ


title: Chromatin States in Murine Spermatogonia

city: Pullman

first: Michael

last: Griswold

state: WA

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

summary: We report ATAC-seq analysis throughout spermatogonial development.  We have assayed two biological replicates at 0, 18, 48, and 120 hours post WIN 18,446/RA treatment.

overall_design: Chromatin accessibility assessment of several spermatogonial subpopulations in the neonatal mouse testis.

first: Rachel

last: Gewiss

first: Christine

last: Schleif


title: Gene expression analysis in inflammatory macrophages treated with biguanides [batch2]

summary: Analysis of the transcriptome of human monocyte-derived macrophages activated with IFN-gamma and LPS and treated with biguanides

overall_design: Peripheral blood samples were collected from 5 healthy donors. Monocytes were sorted, then exposed to granulocyte-macrophage colony-stimulating factor to generate their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma, LPS and biguanides during 24 hours.

last: Solier

last: Muller

last: Caneque

last: Versini

last: Guillemot

last: Gestraud

first: Elodie

last: Girard

last: Watson

last: Rodriguez


title: Gene expression analysis in inflammatory macrophages [batch1]

last: Servant

summary: Analysis of the transcriptome of human monocyte-derived macrophages activated with IFN-gamma and LPS

overall_design: Peripheral blood samples were collected from 5 healthy donors. Monocytes were sorted, then exposed to granulocyte-macrophage colony-stimulating factor to generate their differentiation. After 5 days of differentiation, macrophages were activated or not with IFN-gamma and LPS during 24 hours.


title: Integrated epigenomic analysis identifies structural alterations associated with oncogenic gene expression in liposarcoma

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

summary: Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults. The two most frequent subtypes well differentiated (WD) and dedifferentiated (DD) LPS are often marked with the giant chromosome and the amplifications of chromosome 12q13-15. However, it remains unknown how this genomic aberrancy contributes to the dysregulation of the oncogenes. Here, we reported a comprehensive molecular characterization of both tumor and normal tissues from the same batch of LPS patients, including Hi-C, H3K27ac ChIP-seq, RNA-seq and WGS datasets. We identified a library of tumor-specific enhancers that may play a critical role in oncogenesis. We also demonstrated the enhancer co-amplification and hijacking events involved with proto-oncogenes such as MDM2, CDK4 and HMGA2, which have not been previously reported and as a novel mechanism to upregulate these genes. By combining Hi-C, optical mapping, Nanopore long reads and WGS data, we partially resolved complex structure variations (SVs) and reconstructed the local genome and the giant chromosome. We further validated the presence of multiple copies of  MDM2 and CDK4 are located on the giant chromosome by fluorescent in situ hybridization (FISH). Consequently, this study provides a comprehensive resource for further research in LPS.

overall_design:
We started with 5 pairs of WD-LPS, 14 pairs of DD-LPS patient samples, and 1 DD-LPS cell line. Each pair of patient samples contains one tumor tissue and one matched peritumoral tissue as control. To profile the transcribed regions and to reveal the differential transcriptomes between tumors and peritumoral tissues, we performed mRNA sequencing (mRNA-seq) in all patient samples and cell lines. In 4 pairs of DD-LPS patient samples (P241, P298, P69 and P209) and 1 DD-LPS cell line (Lipo863B), we performed 1) chromatin immunoprecipitation followed by DNA-seq (ChIP-seq) for histone modifications H3 lysine 27 acetylation (H3K27ac), to chart the open chromatin regions and DD-LPS-specific regulatory elements, such as enhancers; 2) Hi-C experiments to study high-order chromatin structure and link distal enhancers to their target genes; 3) whole genome sequencing (WGS) to profile CNVs and dissect genome rearrangements. To better reveal the sequence details of genome rearrangements, we performed Nanopore long-read sequencing and BioNano optical mapping in Lipo863B cells to help assemble the rearranged regions. In total, we generated 71 genomic datasets, including 62 for the patient tissue samples and 9 for the cell line Lipo863B.
Raw data not provided for patient samples due to patient privacy concerns.

first: Tingting

last: Liu

first: Juan

last: Wang

first: Hongbo

last: Yang

first: Qiushi

last: Jin

first: Yihao

last: Fu

first: Mark

last: Youngblood

first: Xinyan

last: Lu

first: Lucia

last: Casadei

first: Raphael

last: Pollock


title: CD38 causes autophagic flux inhibition and cardiac dysfunction through a transcriptional inhibition pathway under hypoxia/ischemia conditions

city: ChongQing

first: Xingyue

last: Zhang

institute: Southwest Hospitial

summary: To comprehensively identify CD38 binding sites on Plekhm1.

overall_design: Examination of CD38 binding sites on Plekhm in the hypoxia/ischemia-induced C57BL/6J neonatal primary cardiomyocytes or the control C57BL/6J neonatal primary cardiomyocytes.


title: Genome-wide DNA-binding program of CREB3L2-ATF4 heterodimers

first: Claudio

last: Gouveia Roque

summary: We report the development of ChIPmera, a method that resolves the DNA-binding program of dimeric transcription factors in vivo.

overall_design: ChIPmera exploits chemically induced proximity to induce the interaction of specific transcription factor pairs. Each monomer is engineered with two unique features: a specific dimerization domain (FRB or FKBP, C-terminally fused), and an N-terminal epitope tag (HA or V5). They can then be brought together in cells using a bivalent ligand that recognizes both the FRB and the FKBP domains with high affinity. Dimer-specific DNA-binding programs are elucidated from parallel HA and V5 ChIP-seq analyses. Here, CREB3L2-CREB3L2 homodimers and ATF4-ATF4 homodimers were examined alongside CREB3L2-ATF4 heterodimers. ChIPmera background signals were established using a chemically induced Renilla luciferase homodimer. CREB3L2 and ATF4 are transcription factors of the bZIP family.

first: Ulrich

last: Hengst

first: Cláudio


title: Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states

status: Public on Mar 02 2023

city: Haifa

first: Julia

last: Panov

address: Aba Hushi Blvd 199  Mount Carmel

country: Israel

institute: Tauber Bioinformatics Research Center

summary: Harsh environments enforce the expression of behavioural, morphological, physiological, and reproductive rejoinders, including torpor. Here we study the morphological, cellular, and molecular alterations in torpor architype in the colonial urochordate Botrylloides aff. leachii by employing whole organism Transmission electron (TEM) and light microscope observations, RNA sequencing, real-time polymerase chain reaction (qPCR) quantification of selected genes, and immunoloc- alization of WNT, SMAD and SOX2 gene expressions. On the morphological level, torpor starts with gradual regression of all zooids and buds which leaves the colony surviving as condensed vasculature remnants that may be ‘aroused’ to regenerate fully functional colonies upon changes in the environment. Simultaneously, we observed altered distributions of hemolymph cell types. Phagocytes doubled in number, while the number of morula cells declined by half. In addition, two new circulating cell types were observed, multi-nucleated and bacteria-bearing cells. RNA sequencing technology revealed marked differences in gene expression between different organism compartments and states: active zooids and ampullae, and between mid-torpor and naive colonies, or naive and torpid colonies. Gene Ontology term enrichment analyses further showed disparate biological processes. In torpid colonies, we observed overall 233 up regulated genes. These genes included NR4A2, EGR1, MUC5AC, HMCN2 and. Also, 27 transcription factors were upregulated in torpid colonies including ELK1, HDAC3, RBMX, MAZ, STAT1, STAT4 and STAT6. Interestingly, genes involved in developmental processes such as SPIRE1, RHOA, SOX11, WNT5A and SNX18 were also upregulated in torpid colonies. We further validated the dysregulation of 22 genes during torpor by utilizing qPCR. Immunohistochemistry of representative genes from three signaling pathways revealed high expression of these genes in circulated cells along torpor. WNT agonist administration resulted in early arousal from torpor in 80% of the torpid colonies while in active colonies WNT agonist triggered the torpor state. Abovementioned results thus connote unique transcriptome landscapes associated with Botrylloides leachii torpor.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from colonies in the three different physiological states (active, mid torpor, fully torpid colonies).

first: Yosef

last: Hyams

first: Amelia

last: Rosner

first: Leonid

last: Brodsky

first: Yuval

last: Rinkevich

first: Baruch


title: Discovery of a druggable copper-signaling pathway that drives inflammation

first: Nicolas

last: Servant

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells

city: Guangzhou

first: Yu

last: Lin

state: China

address: No. 1838, Guangzhou Dadao North, Baiyun District, Guangzhou

institute: Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital

summary:
Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated.
Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts.
Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding.The Kyoto Encyclopedia of Genes and Genomes（KEGG）pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway.
Conclusions: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.

overall_design: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to investigate the m5C modification level and distribution characteristics of mRNA in HCT15 cells and shNSUN2 HCT15 cells.

first: Zhifang

last: Zhao

first: Wenqiang

last: Nie

first: Manting

last: Huang

first: Jiazhong

last: Cai

first: Yadong

last: Wang

first: Hesong

first: Yang

last: Bai


title: Nrf2-regulated L-2-hydroxyglutarate sensitizes erythroid cells to ferroptosis in sickle cell disease [ChIP]

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

summary: SCD had hemolysis with elevated levels of heme and iron, which induced ferroptosis. Here, we found Nrf2 knockout in SCD mice accumulated the levels of the metabolite L-2-hydroxyglutarate (L2HG), which impaired ferroptosis stress response to exacerbate SCD symptom. Mechanistically, L2HG was found to regulate the expression of genes involved in the iron and heme metabolism via histone epigenetic hypermethylation. Our findings indicate an important role of Nrf2/L2HG in SCD for ferroptosis response.

overall_design: Comparison the genome-wide distribution of NRF2 in day-12 cultured sickle patient erythoid progeniotrs after L2HG treatment.

first: Caixia

last: Xi

first: Junfeng

last: Pang


title: Physiological responses and molecular regulatory mechanisms during leaf colour change in Acer rubrum L.

first: Baoli

address: No.7 Beinong Road, Shigezhuang Street

institute: College of Landscape Architecture, Beijing Agricultural College

summary: In order to investigate the physiological and biochemical characteristics and molecular mechanisms during the leaf colour change of Acer rubrum L, this study used Acer rubrum L. 'Autumn Blaze' cuttings as material and analysed the transcriptome and miRNAs of Acer rubrum L leaves under different light and temperature treatments. The transcriptome and miRNAs of Acer rubrum L leaves were analysed under different light and temperature treatments, and miRNA-mRNA association analysis was performed for the differentially expressed mRNAs and miRNAs.

overall_design:
We then performed gene expression profiling using data from fifteen sets of material from the CC, CL, Control, LC, and LL periods obtained by RNA-seq.
We treated Acer rubrum L. 'Autumn Blaze' cuttings with different light and temperature treatments: CC. 100 % full light, 30°C/20°C day/night; LC. 100 % full light, 15°C/5°C day/night; CL. 40 % low light, 30°C/20°C day/night; LL. 40 % low light, 15°C/5°C day/night. 30 °C/20 °C day/night; LL. 40 % low light, 15 °C/5 °C day/night. Leaf samples from day 0 and day 14 were then taken for transcriptome and miRNA sequencing for gene expression profiling, respectively.（CC,LC,CL,LL,control）

first: Baolil

first: Jinteng

last: Cui


title: The Cardiac Endothelial Cell cGAS-STING Pathway Promotes Doxorubicin-Induced Cardiotoxicity via CD38-Mediated NAD Decline and Mitochondrial Dysfunction [mouse]

city: Shanghai

first: Wei

last: Luo

address: Fenglin Road No.180

institute: Fudan University

summary: Doxorubicin is an effective chemotherapy drug for treating various types of cancer. However, lethal cardiotoxicity severely limits its clinical use. Recent evidence has indicated that aberrant activation of the cytosolic DNA-sensing cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway plays a critical role in cardiovascular destruction. Here, we investigate the involvement of this mechanism in doxorubicin-induced cardiotoxicity (DIC).

overall_design: Mice were treated with low-dose doxorubicin to induce chronic DIC. The role of the cGAS-STING pathway in DIC was evaluated in cGAS-deficiency (cGAS-/-), Sting-deficiency (Sting-/-), and interferon regulatory factor 3 (Irf3)-deficiency (Irf3-/-) mice. Endothelial cell (EC)-specific conditional Sting-deficiency (Stingflox/flox/Cdh5-CreERT) mice were used to assess the importance of this pathway in ECs during DIC. We also examined the direct effects of the cGAS-STING pathway on nicotinamide adenine dinucleotide (NAD) homeostasis in vitro and in vivo.

first: Xiaoyi

last: Zou

first: Yidan

first: Zheng

last: Dong

first: Xinyu

last: Weng

first: Zhiqiang

last: Pei

first: Shuai

last: Song

first: Yongchao

first: Zilun

last: Wei

first: Rifeng

last: Gao

first: Beijian

last: Zhang

first: Liwei

last: Liu

first: Peiyuan

first: Jin

first: Xiang

first: Tingwen

first: Xiaolei

last: Sun

first: Hang

last: Chen

first: Kai

last: Hu

first: Shisuo

last: Du

first: Aijun

first: Junbo

last: Ge


title: The Cardiac Endothelial Cell cGAS-STING Pathway Promotes Doxorubicin-Induced Cardiotoxicity via CD38-Mediated NAD Decline and Mitochondrial Dysfunction

first: Wei


title: The Cardiac Endothelial Cell cGAS-STING Pathway Promotes Doxorubicin-Induced Cardiotoxicity via CD38-Mediated NAD Decline and Mitochondrial Dysfunction [human]

first: Xiaoyi

first: Yidan

last: Wang

first: Zheng

first: Xinyu

first: Zhiqiang

first: Shuai

last: Zhao

last: Bai

first: Yang


title: Comparative analysis of transcriptomic changes induced by zearalenone and bisphenol A in human ovarian cancer cells

city: Debrecen

first: Melinda

last: Szilágyi-Bónizs

address: Egyetem tér 1

department: Human Genetics

country: Hungary

institute: University of Debrecen

summary: Xenoestrogens are natural or synthetic compounds that mimic the effect of endogenous estrogens and might cause cancer. We aimed to compare the global transcriptomic response to zearalenone (ZEA; mycotoxin) and bisphenol A (BPA; plastic additive) with the effect of physiological estradiol (E2) in the PEO1 human ovarian cell line by mRNA and microRNA sequencing. Estrogen exposure induced remarkable transcriptomic changes: 308, 288 and 63 genes were upregulated (log2FC > 1); 292, 260 and 45 genes were downregulated (log2FC < -1) in response to E2 (10 nM), ZEA (10 nM) and BPA (100 nM), respectively. Furthermore, the expression of 13, 11 and 10 miRNAs changed significantly (log2FC > 1, or log2FC < -1) after exposure to E2, ZEA and BPA, respectively. Functional enrichment analysis of the significantly differentially expressed genes and miRNAs revealed several pathways related to the regulation of cell proliferation and migration. The effect of E2 and ZEA was highly comparable: 407 genes were coregulated by these molecules. We could identify 83 genes that were regulated by all three treatments that might have a significant role in the estrogen response of ovarian cells. Furthermore, the downregulation of several miRNAs (miR-501-5p, let-7a-2-3p, miR-26a-2-3p, miR-197-5p and miR-582-3p) was confirmed by qPCR, which might support the proliferative effect of estrogens in ovarian cells.

overall_design: The PEO1 human epithelial ovarian cell line was treated with 10 nM estradiol, 10 nM zearalenone and 100 nM bisphenol A. A non-treated control was also included as a negative control that was faced to the same culturing conditions except estrogen treatment. Total RNA was isolated 8 h-s after the treatment. Global transcriptomic profile was studied by RNA-sequencing applying the Illumina NextSeq500 platform including both mRNA and microRNA sequencing. In the case of all the samples 3 replicates were included. In order to identify up-, or down-regulated genes and microRNAs the treated samples were compared to the non-treated control samples.