title: Gene expression profile at single cell level of human pulmonary arteries (PA) of healthy and Pulmonary hypertension affected lungs and murine PA exposed to normoxia and hypoxia

status: Public on Nov 11 2022

city: Graz

first: Francesco

last: Valzano

address: Neue Stiftingtalstraße 6, 8010 Graz

institute: Ludwig Boltzmann Institute for lung vascular research

summary: A central feature of progressive vascular remodeling is altered smooth muscle cell (SMC) homeostasis; however, the understanding of how different cell populations contribute to this process is limited. Here, we utilized single cell RNA sequencing to provide insight into cellular composition changes within isolated pulmonary arteries (PA) from pulmonary arterial hypertension (PAH) and donor lungs. Our results revealed that remodeling skewed the balanced communication network between immune and structural cells, in particular SMC. Comparative analysis with murine PA showed that human PA harbor heterogeneous SMC populations with an abundant intermediary cluster displaying a gradient transition between SMC and adventitial fibroblasts. Transcriptionally distinct SMC populations were enriched in specific biological processes and could be distinguished into four major clusters: oxygen sensing (enriched in pericytes), contractile, synthetic and fibroblast-like. End-stage remodeling was associated with phenotypic shift of pre-existing SMC populations and accumulation of synthetic SMC in neointima. Distinctly regulated genes in clusters built non-redundant regulatory hubs encompassing stress response and differentiation regulators. The current study provides a blueprint of cellular and molecular changes on a single cell level that are defining pathological vascular remodeling process.

overall_design: Using droplet-based single cell RNA sequencing we analyzed 3 pulmonary arteries (PA) from lungs affected with pulmonary arterial hypertension (PAH) against PA from 3 healthy controls. Clustering, dimensionality reduction, trajectory inference and pseudotime, as well as transcription factor analyses were performed and select marker gene were examined for specific segregation of PA media layer using immunofluorescence in both the conditions. Validation of human findings was also performed in a mouse animal model of pulmonary hypertension (PH)

first: Slaven

last: Crnkovic

first: Elisabeth

last: Fließer

first: Jürgen

last: Gindlhuber

first: Helene

last: Thekkekara Puthenparampil

first: Maria

last: Basil

first: Mike

last: Morley

first: Jeremy

last: Katzen

last: Gschwandtner

first: Walter

last: Klepetko

first: Edward

last: Cantu

first: Heimo

last: Wolinski

first: Horst

last: Olschewski

first: Jörg

last: Lindenmann

first: You-Yang

last: Zhao

last: Morrisey

first: Leigh

last: Marsh

first: Grazyna

last: Kwapiszewska


title: In Vitro Modeling of CD8 T Cell Exhaustion [RNA-seq]

status: Public on Dec 01 2022

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: RNA-seq was used to study the gene expression of Invitro CD8 T cell exhaustion cells

overall_design: Invitro generated CD8 Tcell subsets were assayed by RNAseq in replicates

first: Jennifer

last: Wu

middle: J

last: Wherry


title: Single-cell RNA Sequencing of rats in early diabetic retinopathy

status: Public on Nov 25 2022

city: Guangzhou

first: Min

last: Fu

address: No. 253, Industrial Avenue Middle, Haizhu District

country: China

institute: The Second Clinical School, Southern Medical University

summary: In diabetic retinopathy (DR), a blinding disease, retinal microglia-induced inflammatory responses precede microangiopathy. However, the binary concept of microglial M1/M2 polarization paradigms during inflammatory activation has been debated. In this study, we confirmed microglia had the most significant changes in early DR using single-cell RNA sequencing. Besides, at cellular level three new microglial subtypes were defined, including two M1 types (Egr2+ M1 and Egr2- M1) and one M2 type. We also revealed the anatomical locations, different activation orders, mutual activation regulation mechanisms and dynamic changes in polarization phenotypes between these subtypes. Furthermore, we constructed an inflammatory network involving microglia, blood-derived macrophages and other retinal nonneuronal cells. The targeted study of new disease-specific microglial subtypes can shorten the time for drug screening and clinical application, which provided insight for the early control and reversal of DR.

overall_design: A total of five retinal specimens were collected from donor SD rats, including two at 0 weeks (control group) and one each after 2 weeks, 4 weeks, and 8 weeks of DR (experimental group). The SD rats were acclimatized for 1 week on a standard diet. After acclimatization, diabetes was induced in the experimental rats with STZ after overnight fasting (Sigma, St. Louis, MO, USA; 45 mg/kg, IP). The STZ was freshly dissolved in citrate buffer (0.1 M, pH 4.5) and maintained on ice before use. Two randomly selected rats, referred to as the control rats, were injected intraperitoneally with 10 mL of 0.1 M citrate phosphate buffer (pH 6.3) per kg of body weight after 12 hours of fasting. The remaining rats, referred to as the experimental rats, were intraperitoneally administered 45 mg of STZ per kg of body weight in a single injection. Induction of diabetes was confirmed by the fasting blood glucose concentration on the third day after administration of STZ. Rats with blood glucose levels above 200 mg/dL were considered to have diabetes and were used for the experiment. After successful induction, they were fed with high fat and high sugar for 2, 4 and 8 weeks respectively.

first: Yan

last: Wang

first: Guoguo

last: Yi

first: Mingzhe

last: Cao


title: LNCAP in-vitro treatment with androgen receptor targeting drugs

status: Public on Sep 07 2022

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: Gene expression in LNCaP cells after treatment with the androgen receptor targeting drugs bicalutamide (BIC), enzalutamide (ENZ) and apalutamide (ARN) in the presence or absence of dihydrotestosterone (DHT).

overall_design: 16 samples, biological duplicates of LNCaP cells treated with bicalutamide (BIC), enzalutamide (ENZ) or apalutamide (ARN) in the presence or absence of dihydrotestosterone (DHT), respectively.

first: Stephen

last: McPherson

first: Nenad

last: Bartonicek

first: Melanie

last: Lehman

first: Anja

last: Rockstroh

middle: C


title: Cell cycle arrest of neural progenitors causes impaired dopaminergic neuronal differentiation in GBA associated Parkinson’s disease midbrain organoids [2]

status: Public on Jul 24 2022

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary: The mechanisms underlying Parkinson's disease (PD) etiology are only partially understood despite intensive research conducted in the field. Recent evidence suggests that early neurodevelopmental defects might play a role in cellular susceptibility to neurodegeneration. To study the early developmental contribution of GBA mutations in PD we used patient-derived iPSCs carrying a heterozygous N370S mutation in the GBA gene. Patient-specific midbrain organoids displayed GBA-PD relevant phenotypes such as reduction of GCase activity, autophagy impairment and mitochondrial dysfunction. Genome-scale metabolic (GEM) modeling predicted changes in lipid metabolism which were validated with lipidomics analysis, showing significant differences in the lipidome of GBA-PD. In addition, patient-specific midbrain organoids exhibited an increase in the neural progenitor population showing signs of cellular senescence. This was accompanied by a decrease in the number and complexity of dopaminergic neurons. These results provide insights into how GBA mutations may lead to neurodevelopmental defects thereby predisposing to PD pathology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from GBA-PD patient-derived organoids and control organoids

first: Isabel

last: Rosety

first: Alise

last: Zagare

first: Claudia

last: Saraiva

first: Sarah

last: Nickels

first: Paul

last: Antony

first: Catarina

last: Almeida

first: Rashi

last: Halder

first: Sergiy

last: Velychko

first: Thomas

last: Rauen

first: Hans

last: R Scholer

first: Silvia

last: Bolognin

last: Sauter

first: Javier

last: Jarazo

first: Rejko

last: Krueger

first: Jens

last: C Schwamborn


title: Single-cell RNA sequencing of pancreatic islets from obese mice with different diabetes risk reveals diabetes-susceptible β cell clusters

status: Public on Jul 07 2022

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung

summary: Single-cell RNA sequencing of pancreatic islets from 18-week-old male New Zealand Obese (NZO/HIBomDife) and B6.V-Lepob/ob (OB) mice were fed a standard diet or a carbohydrate-enriched diet for 2 additional days (+CH / -CH).

overall_design: 4 single-cell RNA sequencing experiments of pancreatic islets of 3 pooled mice per condition were performed using the Chromium Single Cell 3ʹ Reagent Kit v3 (10X Genomics, PN-1000075, Pleasanton, USA), to generate single cell expression profiles of OB and NZO mice with and without a diabetonic treatment.

first: Mandy

last: Stadion

first: Michael

last: Sterr

first: Annette

last: Schürmann


title: Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology

status: Public on Jul 20 2022

city: Oslo

first: Lasse

last: Pihlstrøm

address: Sognsvannsveien 20

department: Department of Neurology

country: Norway

institute: Oslo University Hospital

summary: The goal of the study was to investigate if DNA methylation is associated with Lewy body pathology in human brain tissue. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in postmortem human frontal cortex samples from European donors in the Netherlands Brain Bank. Following quality checks, sample filtering and normalization, association between CpG methylation and Braak alpha-synuclein stage was assessed using linear models.

overall_design: Bisulphite converted DNA from 492 samples including 453 unique donors and 39 technical replicates were hybridised to the Illumina Infinium MethylationEPIC Beadchip v. 1.0

first: Wilma

last: van de Berg


title: Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Lung Adenocarcinoma by MeRIP Sequencing

status: Public on Jun 27 2022

city: Shenzhen

first: Wenli

last: Mao

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

summary: To investigate the role of m6A modification,MeRIP-seq was used to identify differential m6A modifications in lung adenocarcinoma .

overall_design: m6A analysis of  three pairs of LUAD samples and tumor-adjacent normal tissues


title: Loss of FERM domain-containing protein 3 (FRMD3) is associated with severity of chronic kidney disease

status: Public on Oct 24 2022

city: Dublin

first: Eoin

last: Brennan

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

summary:
Purpose: Transcriptiome profiling of chronic kidney disease

Methods: Transcriptome profiling was performed in human renal biopsy tissue and correlated with parameters of kidney function, including estimated glomerular filtration rate (eGFR), degree of renal tubulointerstitial fibrosis (%TIF), as well as CKD progression over a median follow-up period of 60 months.

Results: Transcriptome analysis performed in two independent cohorts of patients with CKD (n=24 and n=17, respectively) identified a cluster of genes (n=93) significantly correlated (FDR P<0.05) with eGFR and %TIF, and associated with CKD progression, with enrichment for pathways associated with inflammation and immune-cell mediated infiltration. Expression of FRMD3, a previously reported candidate gene from human genetics studies in CKD, was negatively correlated with indices of CKD severity and progression. Knockdown of FRMD3 in human kidney epithelial cells enhanced fibrotic responses to the cytokine transforming growth factor-beta (TGF-β1). Analysis of FRMD3 binding partners indicated enrichment of proteins implicated in mitochondrial function and remodeling of epithelial adherens junctions. Lentivirus-mediated knockdown of FRMD3 in renal tubule epithelial cells yielded a significant reduction (>35%) in NAD(P)H-dependent oxidoreductase activity, and a corresponding increase in caspase activity (50%).

Conclusions: Using global transcriptome profiling we define a cluster of transcripts associated with severity of CKD and identify loss of FRMD3 expression as a potential molecular driver. Loss of FRMD3 expression may contribute to mitochondrial function and TIF.

overall_design: We examined the transcriptional profile of human kidney biopsies, aiming to provide insight into the mechanisms of progressive CKD. This approach led to the identification of FERM domain protein 3, (FRMD3) as a molecular driver of disease.

first: R

last: Doyle

first: C

last: McEvoy

first: O

last: Gough

first: S

last: McAnallen

first: M

last: Hughes

last: Xin

first: B

last: Crifo

first: E

last: Dillon

first: D

last: Crean

first: A

last: Konvalinka

last: Murphy

first: W

last: Jhang

first: Z

last: Yi

first: K

last: Susztak

last: Kretzler

first: Y

last: O'Meara

last: Dorman

first: F

last: Martin

first: P

last: Conlon

last: Sadlier

last: Godson


title: The effect of fructose vs glucose supplementation on stable AKR1B1 knockdown in A549 lung cancer cells

status: Public on Oct 03 2022

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary:
To investigate the cytotoxic effect of AKR1B1 depletion, we induced stable AKR1B1 knockdown via shRNA under different growth conditions (glucose vs fructose)
We then performed gene expression profiling analysis using data obtained from RNA-seq of control (non-targeting shRNA) or shAKR1B1 A549 cells 5 days after shRNA delivery.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 control or shAKR1B1 cells, maintained in media containing either 5mM glucose or fructose.

first: Irfan

middle: A

last: Asangani

first: Mohammed

last: Alhusayan

first: Vignesh

last: Ramesh


title: Epigenetic priming enhances anti-tumor immunity in resistant ovarian cancer [methylation array]

status: Public on Jun 20 2022

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Here we describe the clinical and biological activity of guadecitabine, a second generation HMA, given in a low dose as a priming strategy before pembrolizumab, a humanized anti-PD1 antibody in a clinical trial for patients with recurrent, platinum resistant ovarian cancer. The methylomic and transcriptomic effects of the combination demonstrate readily activation of the anti-tumor immunity. High dimensional immune profiling of periferal mononuclear cells (PBMCs) and tumor biopsies obtained before and after treatment show distinct immune profiles and tissue architectural features associated with clinical benefit. Our study provides an in-depth view of the immune milieu of platinum resistant ovarian cancer and of the effects of the combination of HMAs and pembrolizumab on the interactions between immune cell populations and tumor cells.

overall_design: This was a non-randomized open-label two stage phase II trial testing guadecitabine and pembrolizumab in recurrent platinum-resistant OC. Patients all had epithelial ovarian, fallopian tube or primary peritoneal cancer that had recurred or progressed <6 months after their last dose of platinum-based chemotherapy. Guadecitabine (G) 30 mg/m2 was administered by subcutaneous (sc) injection on days 1 - 4 of a 21-day cycle. On day 5 pembrolizumab 200 mg was administered intravenously (iv). Each cycle was 21 days. The drug combination was given until progression of disease or unacceptable toxicity. Imaging-guided tumor biopsies, ascites, or blood for determining cytokine response and collection of PBMCs were obtained from consenting patients at specific timepoints. Three 18-gauge tumor cores were obtained on C1D1 (day 1 of cycle 1) and C2D8 (day 8 of cycle 2) and the material was immediately snap frozen (~25-50mg/specimen).  C1D1 and C2D8 tumor samples were obtained from 11 patients (total of 22 samples). When available, ascites or pleural fluid was centrifuged and fluid and cell pellets were separated prior to cryo-preservation.

first: Pin

last: Xie

first: Siqi

last: Chen

first: Mathew

last: Cowan

first: Horacio

last: Cardenas

first: Russell

last: Keathley

first: Hao

last: Huang

first: Eduard

last: Tanner

first: Ramana

last: Davuluri

first: Masha

last: Kocherginsky

first: Bin

last: Zhang


title: Epigenetic priming enhances anti-tumor immunity in resistant ovarian cancer

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

overall_design: Refer to individual Series


title: Epigenetic priming enhances anti-tumor immunity in resistant ovarian cancer [RNA-Seq]


title: Single-nucleus transcriptomic analysis in the prefrontal cortex of postmortem human brain

status: Public on Jun 17 2022

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: These data describe single-nucleus RNA sequencing in postmortem human brain.

overall_design: Single-nucleus RNA sequencing was performed in postmortem orbitofrontal cortex tissue from two psychiatrically healthy donors.

first: Anna

middle: S

last: Fröhlich

first: Nathalie

last: Gerstner

first: Simone

last: Roeh

first: Janine

last: Knauer-Arloth


title: Chromatin reader Dido3 regulates the genetic network of B cell differentiation

status: Public on Sep 29 2022

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The development of hematopoietic lineages is based on a complex balance of transcription factors whose expression depends on the epigenetic signatures that characterize each differentiation step. The B cell lineage arises from hematopoietic stem cells through the stepwise silencing of stemness genes and balanced expression of mutually regulated transcription factors, as well as DNA rearrangement. Here we report the impact on B cell differentiation of lack of Dido3, a reader of the chromatin status, in the hematopoietic compartment. We found a reduced DNA accessibility in hematopoietic precursors, leading to severe deficiency in the generation of successive B cell differentiation stages. The expression of essential transcription factors and differentiation markers is affected, as is the somatic recombination process.

overall_design: List of chromatin accessibility regions and mRNA profiles of DIDO3 wild type and mutants in mouse hematopoietic precursors

first: Fernando

last: Gutiérrez del Burgo

first: Carlos

last: Martinez-A

first: Ricardo

last: Villares


title: The murine liver x receptor is selectively modulated by different ligands to differentially alter tumor-associated myeloid cells [scRNA-seq]

status: Public on Jun 01 2022

city: Urbana

first: Erik

last: Nelson

state: Illinois

address: 407 S Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana Champaign

summary: Dysregulation of cholesterol metabolism and homeostasis is associated with the pathology of many diseases such as cardiovascular disease and cancer. Two major upstream regulators of cholesterol homeostasis are the SREBP2 pathway and the actions of the liver X receptors (LXRs), with the liver thought to handle the majority of cholesterol homeostasis at the organismal level. Endogenous cholesterol metabolites such as 27-hydroxycholesterol (27HC), which serve to activate the nuclear receptor LXR, result in increased expression of genes associated with cholesterol catabolism and efflux. LXR and various LXR ligands such as 27HC have been described to influence several extra-hepatic biological systems. However, disparate reports of LXR function have emerged, especially with respect to immunology and cancer biology. This would suggest that similar to steroid nuclear receptors, the LXR may be selectively modulated by ligands. Here, we use bulk RNA-sequencing of bone marrow-derived macrophages and single-cell RNA-sequencing of immune cells from murine lungs bearing metastatic mammary cancer, to prove that LXR satisfies the two principles of selective nuclear receptor modulation: (1) different LXR ligands result in overlapping but distinct gene expression profiles within the same cell type, and (2) the same LXR ligands differentially regulate gene expression in a highly context-specific manner, depending on cell or tissue type. The concept that the LXR can be selectively modulated provides the foundation for the development of ligands that are tailored to promote those activities that are desirable (pro-immune), but at the same time minimizing harmful side effects (such as elevated triglyceride levels).

overall_design: Examine the effect of different LXR ligands/CYP27A1 inhibitor on metastatic breast tumor microenvironment. Treatments are in triplicates.

first: Liqian

last: Ma

first: Hashni

middle: E

last: Gamage

first: Srishti

last: Tiwari

first: Chaeyeon

last: Han

first: Madeline

last: Henn

first: Natalia

last: Krawczynska

first: Payam

last: Dibaeinia

first: Graeme

last: Koelwyn

first: Chris

last: Wright

first: Fangxiu

last: Xu

first: Kathryn

last: Moore

first: Saurabh

last: Sinha

middle: R


title: The murine liver x receptor is selectively modulated by different ligands to differentially alter tumor-associated myeloid cells [bulk RNA-seq]

overall_design: Examine the effect of distinct LXR/ER ligands on BMDMs. For each treatment, 5-6 replicates included.


title: The expression of circular RNAs in tumor tissues from three non-cirrhotic hepatocellular carcinoma patients and three cirrhotic hepatocellular carcinoma patients

status: Public on May 10 2022

city: Chengdu

first: Liangliang

state: Sichuan

address: Number 37 Guoxue Lane

institute: West China Hospital of Sichuan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Six frozen hepatocellular carcinoma (HCC) samples (three without cirrhotic and three with cirrhotic background) were selected to analyze the circRNA expression profile through circRNA-seq. A total of 20334 circRNAs were identified in these tumor tissues, which were widely distributed in all chromosomes. Differential analysis revealed that 393 were significantly dysregulated in non-cirrhotic HCC when compared with cirrhotic HCC tissues (log2(fold change) > 1 and p < 0.05). Our study undoubtedly provide a new insight in investigating the initiation of HCC.

overall_design: circRNA-seq was employed to identify the dysregulated circRNAs between non-cirrhotic and cirrhotic HCC tissues

first: HY

last: Li

first: LL

first: L

first: T

last: Yan

last: Xie

first: ZJ

last: Zhu


title: Cell cycle arrest of neural progenitors causes impaired dopaminergic neuronal differentiation in GBA associated Parkinson’s disease midbrain organoids

first: Enrico

last: Glaab


title: Differential gene expression in seedlings of pi4kb1b2-Study of pi4kb1b2 mutant

status: Public on May 04 2022

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

summary: ngs2020_14_pi4kb1b2-differential gene expression in seedlings of pi4kb1b2-Differential gene expression in roots and leaves of seedlings, pi4kb1b2 mutant vs WT-Comparison of gene expression profile between roots and leaves of A.thaliana Col-0 as WT and pi4kb1b2 mutant, 7 days old (developmental stage 1.02), cultivated on MS/2 media supplemented with 0.8% agar and 1% sucrose, 22°C, 16h/8h light)

overall_design: 12 samples with 3 biological replicats. gene knock out,genotype comparaison,normal vs transgenic comparaison,organ comparison

first: José

last: Caius

first: Eric

last: Ruelland

first: Etienne

last: Delannoy

first: Ludivine

last: Taconnat-Soubigou


title: The immune cell atlas of human neuroblastoma

status: Public on May 05 2022

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: Our current knowledge of the different immune cells in neuroblastoma is based on in vitro and in vivo studies mainly focusing on a single cell type. Importantly, different studies have conveyed conflicting results. Moreover, a comprehensive immune cell overview at the single-cell level is still missing and understanding the complete immune cell composition of neuroblastoma will be crucial for the development of novel immunotherapeutics against the disease. In this study, we performed single-cell RNA-sequencing on nineteen human neuroblastoma samples coupled with multiplex immunohistochemistry and survival analysis using additional datasets to provide a comprehensive cellular and molecular immune cell landscape of human neuroblastoma. Further, we contrasted our data with single-cell RNA-sequencing data from normal fetal adrenal gland to characterize cell-state changes from normal tissue to cancerous neuroblastoma. Our analysis revealed 27 immune cell subtypes including distinct subpopulations of myeloid, NK, B and T cells not identified in neuroblastoma before. Several immune cell subtypes demonstrated a survival benefit such as inflammatory monocytes, tumor associated macrophages, various T cell populations, and Active NK cells. Furthermore, in contrast to adult cancers and previous neuroblastoma studies, we demonstrated an increase in inflammatory monocyte cell-state when contrasting normal and tumor tissue, while we do not observe differences in cytotoxicity and exhaustion score for cytotoxic T cells, nor in Treg activity. Finally, we performed a systemic receptor-ligand interaction analysis between tumor, stroma and immune cells, where we showed the neuroblastoma tumor microenvironment is highly complex and strongly correlated to survival. In addition, we highlighted several interactions that we suggest to be tested in future studies as a therapeutic option in human neuroblastoma. Taken together, our study significantly adds to the in depth understanding of the immune cell landscape, the complexity of the tumor microenvironment and it provides a resource for the development of novel immunotherapeutics for neuroblastoma.

overall_design:
Neuroblastoma were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.
*** RNA-Seq raw data to be made available through dbGaP (controlled access) due to patient privacy concerns: https://www.ncbi.nlm.nih.gov/gap/?term=phsxxxxx

first: Ninib

last: Baryawno


title: Changes in cellular gene expression during prototype foamy virus infection

status: Public on Apr 08 2022

city: Tianjin

first: Junshi

last: Zhang

address: No. 94, Weijin Road

institute: Nankai University

summary: Changes in cellular gene expression levels in the presence of prototype foamy virus (PFV) infection were analyzed using a transcriptomic sequencing system. The results showed that the greatest changes in cellular gene expression levels were observed after 24h of infection compared to 6h and 12h of PFV infection. These results provide a reference for our study of PFV and host interactions.

overall_design:
To screen cellular factors involved in PFV replication, we performed transcriptome sequencing on the cellular RNA of PFV-infected HT1080 cells at 6, 12, and 24 h.
** Submitter declares that the raw data are no longer available. ***

first: J

first: M

last: Qiu

first: W

last: Qiao

last: Tan


title: Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma

status: Public on May 06 2022


title: Genes affected by auxin and decapitation in moss gametophores

status: Public on Jun 21 2022

summary:
The goal of this study is to identify genes whose expression is affected by decapitation and auxin in moss gametophores

Project ngs2017_09_moss1-auxin in CATdb
What genes are misregulated in response to decapitation or auxin response?

overall_design: 21 samples in total, 7 conditions, 3 biological replicates per condition. CUT_T0 samples are controls for CUT_XX samples, MOCK_30Min are controls for IAA_30Min samples.

first: Yoan

last: Coudert

first: Stephanie

last: Huguet


title: Transcriptomics signature of human heart vascular pericytes

status: Public on Mar 29 2022

city: Bristol

first: Elisa

last: Avolio

address: Upper Maudlin Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

summary: Pericytes (PC) are abundant yet remain the most enigmatic and ill-defined cell population in the heart. Here, we investigated whether PC can be reprogrammed to aid neovascularisation of the heart post-myocardial infarction. We discovered that culture of human cardiac PC for 10 days in the presence of an inhibitor of ERK1/2 signalling (PD0325901, specific MEK1/2 inhibitor) induces the PC switch towards a vascular smooth muscle cells (VSMC)-like phenotype. Differentiated PC became more proangiogenic, more responsive to vasoactive agents, and insensitive to chemoattractants. RNA-Sequencing revealed transcripts marking the PD0325901-induced transition into proangiogenic, stationary VSMC-like cells.

overall_design: We analysed 3 primary cultures of human cardiac PC (extracted from 3 adult patients). PC were cultured for 10 days with the MEKi PD0325901 (250 nM, exchanging medium every 2 days) to induce the PC differentiation into VSMC-like cells. Control PC were cultured in parallel using the drug vehicle (DMSO). After 10 days, the total RNA was collected for RNA-Seq. Cells are named CP24, CP25, CP27. We also included two samples of human coronary artery smooth muscle cells (CASMC) as reference control for the differentiated PC.

first: Paolo

last: Madeddu

first: Andrea

last: Caporali

first: Massimo

last: Caputo


title: Transcriptome analysis to investigate COPD exacerbations to influenza infection

status: Public on Apr 01 2022

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

summary: Lung infection by influenza A viruses is a common cause of disease exacerbations in patients with chronic obstructive pulmonary disease (COPD), however, this process is difficult to study in human patients. Here we used a microfluidic human lung airway-on-a-chip (Airway Chip) lined by primary human bronchial epithelium interfaced with primary human pulmonary microvascular endothelium to model this process in vitro. Airway Chips containing bronchial epithelial cells from COPD patients successfully replicated the increased sensitivity to the lung airway to infection by both influenza H1N1 and H3N2 viruses compared to chips lined by epithelium from healthy donors, including enhanced viral loads and increased production of inflammatory cytokines. Transcriptomics analysis of the healthy and COPD epithelium following infection with influenza H1N1 virus on-chip resulted in identification of several novel markers of COPD

overall_design: Primary human lung bronchial-airway epithelial basal cells and primary diseased human lung bronchial-airway epithelial basal cells were used to generate human airway air-liquid (ALI) culture. Then these cells were infected wth influenza A virus, with MOCK infection and PolyIC as controls. Samples were harvested 4 h and 18 post infection for RNA-seq analysis.

first: Bai

last: Haiqing

first: Rodas

last: Melissa

first: Ingber

last: Donlad


title: Bioengineered models of Parkinson’s Disease using Patient-derived Dopaminergic Neurons exhibit distinct Biological Profiles in a 3D Microenvironment

status: Public on Mar 16 2022

city: Medford

first: Nicholas

middle: James

last: Fiore

address: 200 College Ave

department: Biomedical Engineering

institute: Tufts University

summary:
Background: Three-dimensional (3D) in vitro culture systems using human induced pluripotent stem cells (hiPSCs) represent impactful platforms to model neurodegenerative disease biology in physiologically relevant microenvironments. Though many successful biomaterials-based 3D model systems have been established for other neurogenerative diseases, such as Alzheimer’s Disease, relatively few exist for Parkinson’s Disease (PD) research.
Methods: We employed tissue engineering approaches to construct a 3D silk scaffold-based platform for the culture of hiPSC-dopaminergic (DA) neurons derived from healthy individuals and PD patients harboring LRRK2 G2019S or GBA N370S mutations. We then compared results from protein, gene expression and metabolic analyses obtained from two-dimensional (2D) and 3D culture systems.
Results: The 3D platform enabled the formation of dense dopamine neuronal network architectures and developed biological profiles both similar and distinct from 2D culture systems in healthy and PD disease lines. 3D PD cultures showed elevated levels of α-synuclein and alterations in purine metabolite profiles. Furthermore, computational network analysis of transcriptome networks nominated several novel molecular interactions occurring in neurons from patients with mutations in LRRK2 and GBA.
Conclusion: The brain-like 3D system presented here is a realistic platform to interrogate molecular mechanisms underlying PD biology. The key advantages of silk-based bioengineering technology include long-term culture and the ability to incorporate multiple brain-relevant cell types to parse cell-cell interactions in development, disease, and aging.

overall_design: mRNA profiles of hiPSC-dopaminergic neurons from healhty subjects and Parkinson's Disease patients, cultured in 2D and 3D formats.

first: David

middle: L

last: Kaplan

first: Thomas

last: Nieland

first: Yosif

middle: M

last: Ganat

first: Daniel

last: Paull

first: Kapil

last: Devkota

first: Rebecca

last: Batorsky

first: Ming

last: Lei

first: Kyongbum

last: Lee

first: Lenore

last: Cowen

first: Gist

last: Croft

first: Scott

last: Noggle


title: Acute myeloid leukemia cells functionally compromise hematopoietic stem/progenitor cells inhibiting normal hematopoiesis through the release of extracellular vesicles

status: Public on Mar 11 2022

city: Rionero in Vulture

first: Luciana

last: De Luca

address: Via Padre Pio, 1

country: Italy

institute: IRCCS - CROB

summary: Acute myeloid leukemia (AML) is an aggressive and heterogeneous clonal disorder of hematopoietic stem/progenitor cells (HSPCs). It is not well known how leukemia cells alter hematopoiesis promoting tumor growth and leukemic niche formation. In this study, we investigated how AML deregulates the hematopoietic process of HSPCs through the release of extracellular vesicles (EVs). First, we found that AML cells released a heterogeneous population of EVs (AML-EVs) containing microRNAs involved in AML pathogenesis. Notably AML-EVs were able to influence the fate of HSPCs modifying their transcriptome. In fact, a gene expression profile of AML-EV-treated HSPCs identified approximately 923 down and 630 up-regulated genes involved in hematopoiesis/differentiation, inflammatory cytokine production and cell movement. Indeed, most of the downregulated genes are targeted by AML-EV-derived miRNAs. Furthermore, we demonstrated that AML-EVs were able to affect HSPCs phenotype, modifying several biological functions, such as inhibiting cell differentiation and clonogenicity, activating inflammatory cytokine production and compromising cell movement. Indeed, a redistribution of HSPC populations was observed in AML-EV treated cells with a significant increase in the frequency of common myeloid progenitors and a reduction in granulocyte-macrophage progenitors and megakaryocyte-erythroid progenitors. This effect was accompanied by a reduction in HSPC colony formation. AML-EV treatment of HSPCs increased the levels of CCL3, IL1B and CSF2 cytokines, involved in the inflammatory process and in cell movement, and decreased CXCR4 expression associated with a reduction of SDF-1 mediated-migration. In conclusion, this study demonstrates the existence of a powerful communication between AML cells and HSPCs, mediated by EVs, which suppresses normal hematopoiesis and potentially contributes to create a leukemic niche favorable to neoplastic development.

overall_design: NOT PROVIDED; REQUESTED

first: Giovanni

last: Calice

first: Stefania

last: Trino


title: Expression data from ovalbumin (OVA) induced asthma model

status: Public on Feb 22 2022

city: Yanji

first: guanghai

last: yan

address: No. 977, Gongyuan Road

department: Department of Anatomy, Histology and Embryology

institute: guanghai yan

summary:
MiRNAs are involved in the pathogenesis of bronchial asthma and are involved in the regulation of airway inflammation, airway remodeling and airway hyperreactivity. In this experiment, we constructed OVA asthma model and identified the differentially expressed miRNAs in asthma and normal models by microarray technology, providing a preliminary basis for future studies on the mechanism of asthma.
We used microarrays to detail the global program of gene expression in asthma models and identify miRNAs that are differentially expressed in this process.

overall_design: Ovalbumin (OVA) induced asthma model was established in female BALB/c mice. Briefly, mice were sensitized with 200 μL of sensitization solution (OVA 10 μg + Al(OH)3 1mg) by intraperitoneal injection on days 1, 7, and 14. From day 21, mice were challenged with 3% OVA nebulization for 30 min three times a week until day 56. For control, mice were intraperitoneally injected with 200 μL saline on days 1, 7, and 14, and were challenged with the same amount of normal saline from day 21 to day 56.

first: Guanghai

last: Yan

first: Hongmei

last: Piao


title: Hsa_circ_0066351 acts as a prognostic and immunotherapeutic biomarker in colorectal cancer

status: Public on Jun 15 2022

city: Chang Sha

first: Shan

last: Zeng

address: 87 Xiangya Road, Changsha city, Hunan Province, China

institute: Xiangya Hospital, Central South University

summary: Circular RNA (circRNA), a novel class of non-coding RNA, has been reported in various diseases, especially in tumors. However, the key signatures of circRNA-competitive endogenous RNA (ceRNA) network are largely unclear in colorectal cancer (CRC). We first characterized circRNAs profile by using circRNA-seq analysis from real-word dataset. The expression level of hsa_circ_0066351 in CRC tissues and cell lines was detected by quantitative real-time PCR. Then, cell proliferation assay was used to confirm the proliferation function of hsa_circ_0066351. Next, Cytoscape was used to construct circRNA–miRNA–mRNA networks. Last but not least, the landscape of hsa_circ_0066351–miRNA–mRNA in CRC had been investigated in the bulk tissue RNA-Seq level and single-cell Seq level. We proved that hsa_circ_0066351 was significantly downregulated in CRC cell lines and tissues (P < 0.001), and was negatively associated with distant metastasis (P < 0.01). Significantly, the expression of hsa_circ_0066351 was associated with better survival in patients with CRC. Function assays showed that hsa_circ_0066351 could inhibit CRC cells proliferation. In addition, a ceRNA network, including hsa_circ_0066351, two miRNAs, and ten mRNAs, was constructed. Our analyses showed that these ten mRNAs were consistently downregulated in pan-cancer and enriched in tumor suppressive function. A risk score model constructed by these ten downstream genes also indicated that they were related to the prognosis and immune response in CRC. In conclusion, we demonstrated that a novel circRNA (hsa_circ_0066351) inhibited CRC prol

overall_design: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.      Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

first: Hong

last: Shen

first: Changjing

last: Cai


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and sh-KIAA1211 cells

status: Public on Feb 10 2022

city: NANJING

first: zhang

last: juan

address: CHANGLE ROAD 68#

institute: Nanjing First Hospital

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: mRNA profiles of Control and sh-KIAA1211 cells were generated by deep sequencing, in triplicate, using illumina Novaseq™ 6000. After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome. The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and allgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Results:  The sequencing of transcriptome and bioinformatics analysis was performed using Illumina Novaseq™ 6000 by Lianchuan Biotechnology Company (Hangzhou, China). The screening criteria for differential genes is that the gene transcription expression was increased or decreased by two times, and the P-value was less than 0.05.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Yuhan

last: Chang

first: Juan

last: Zhang

first: Xiaowei

last: Wei

first: Qiong

last: Jia


title: Single cell RNA transcriptome landscape in mouse RPE layer after CRISPR administration

status: Public on Mar 01 2022

city: Shanghai

first: Sikai

last: Ling

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

summary: To detect whether gene editing will lead to editing specific changes in cell state and microenvironment. We depicted a landscape in mouse RPE layer after CRISPR administration after single cell RNA transcriptome sequencing.

overall_design: The experiment was divided into three groups: mice were injected with PBS, RLPs, empty LPs respectively. One mouse in each group.

first: Yujia

first: Xujiao

last: Zhou

first: Jiaxu

last: Hong


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and TRCs(3D)

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: mRNA profiles of Control and TRCs were generated by deep sequencing, in triplicate, using illumina Novaseq™ 6000. After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome. The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and allgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Results: The sequencing of transcriptome and bioinformatics analysis was performed using Illumina Novaseq™ 6000 by Lianchuan Biotechnology Company (Hangzhou, China). The screening criteria for differential genes is that the gene transcription expression was increased or decreased by two times, and the P-value was less than 0.05.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of Control and TRCs


title: Double-negative T cell therapy alone or in combination with oral UDCA alleviates primary biliary cholangitis in mice

status: Public on Feb 28 2022

city: Beijing

first: Chunpan

address: No. 95 Yong-An Road

institute: Beijing Friendship Hospital

summary: Methods: The DNT cells incubation with anti-CD3/CD28 antibodies were stimulated with UDCA (60uM) for 48 hours, then transcriptome sequencing studies were performed on DNT cells RNA.Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced by the University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=1.41 and pvalue <= 0.05 between UDCA treated and control DNT cells were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.

overall_design: DNT cells mRNA profiles of control and UDCA stimulated were generated by deep sequencing in duplicate, using Illumina instrument.

first: Hua

last: Jin

first: Xiaonan

last: Du

first: Changying

last: Li

first: Xiaotong

last: Han

first: Xinyan

last: Zhao

first: Dan

last: Tian

first: Yanmeng

first: Tingting

last: Lv

first: Sha

last: Chen

first: Guangyong

last: Sun

first: Dong

first: Jidong


title: Single-cell RNA-seq analysis of macrophages extracted from mouse alveolar bone subjected to orthodontic force

status: Public on Feb 01 2022

city: Nanjing

first: Bin

last: Yan

address: 140Hanzhong Road

institute: Nanjing Medical University

summary: Exploring the transcriptome heterogeneity of macrophages during orthodontic force-induced alveolar bone remodeling

overall_design: The transcriptomes of alveolar macrophages after force application in a mouse model of tooth movement and without force application (control) were determined by single cell RNA sequencing (scRNA-Seq)

first: Hao

last: Xu


title: Single-nuclear gene expression profiles of cells of human myocardial tissue obtained after heart transplantation.

status: Public on Jun 07 2022

city: Nashville

first: Kaushik

last: Amancherla

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: We used single-nuclear RNA sequencing (snRNA-seq) to analyze the diversity of cells in human myocardium and to compare cell types between patients with chronic rejection (cardiac allograft vasculopathy; CAV) and those without.

overall_design: Human myocardial tissue was obtained by endomyocardial biopsy (at the time of right heart catheterization) for post-transplant patients without CAV. Human myocardial tissue from patients with severe CAV was obtained at the time of re-do heart transplantation.


title: cuc2-identification-Dynamic and specificity of CUP-SHAPED COTYLEDON transcription factors during leaf development

status: Public on May 18 2022

first: Véronique

last: BRUNAUD

summary: ngs2014_39_leafnet2-cuc2-identification-Identification of CUC2 targets-10-days old 35S::CUC2-GR Arabidopsis transgenic line grown in liquid culture have been treated for 6 hours with DEXAMETHASONE 10µM or Mock.

overall_design: 6 samples with 3 biological replicats. treated vs untreated comparison

first: Zakia

last: Tariq

first: Nicolas

last: Arnaud

first: Ludivine

last: Taconnat-Soubigou


title: Transcriptomics analysis reveals the molecular mechanisms of the  antibacterial activity of gallium nitrate against Acinetobacter baumannii isolated from bloodstream infections

status: Public on Jan 27 2022

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

summary:
Purpose: The aim of this study was to explore the antibacterial effect and molecular mechanism  of gallium nitrate [Ga(NO 3 ) 3 ] against Acinetobacter baumannii from bloodstream  infection.
Methods: A total of 40 A. baumannii with different antimicrobials susceptibility patterns were isolated from bloodstream infections. In vitro antibacterial effect of Ga(NO 3 ) 3 was analyzed by micro-dilution method and time-kill assay. The effect of ferric chloride/heme on the antibacterial effect of Ga(NO 3 ) 3 was evaluated.  Transcriptome sequencing was performed to elucidate the antibacterial mechanism of gallium nitrate. Mouse infection model was conducted to explore the in vivo efficacy of gallium nitrate .
Results: Ga(NO 3 ) 3 exhibited excellent antibacterial effect in RPMI 1 640 medium containing 10% human serum (MICs ranged from 0.06 μg/mL to 0.125 μg/mL),  whereas its antibacterial effect was weakened by exogenous ferric chloride/heme.  Ga(NO 3 ) 3 inhibited A. baumannii growth in a dose- and time- dependent manner.  Ga(NO 3 ) 3 exerted antibacterial effect by up-regulating the expression of genes associated with biosynthesis and transport of siderophore and disrupting multiple iron  dependent metabolism processes. Ga(NO 3 ) 3 significantly reduced bacterial load in the neutropenic mouse thigh infection model.
Conclusions: This study revealed that Ga(NO 3 ) 3 had excellent antibacterial activity both in vivo and in vitro . It might be a potential drug for treating bloodstream infections of A. baumannii

overall_design: mRNA profiles of A. baumannii BM2333 wildtype and Ga(NO3 )3-treated BM2333

first: Yao

first: Kaihang

last: Yu


title: barley responses to nitrate limitation-BarIEy Stress Tolerance

status: Public on Jan 24 2022

summary: ngs2020_19_arimnet-barley responses to nitrate limitation-What are the molecular mechanisms taking place in barley under nitrate limitation?-Barley were grown on sand under 0.5 mM nitrate (Low nitrate= LN) or 5 mM nitrate (high nitrate = HN)

overall_design: 18 samples with 3 biological replicats. dose response,genotype comparison

first: José

last: Caius

first: Alia-

last: Dellagi


title: effect of ethylene rna-seq-RNA-seq ± Ethylene

summary: ngs2018_10_ethylene-effect of ethylene rna-seq-what are the effects of ethylene on mRNA metabolism during germination-seeds were imbibed at 25°c in darkness ± C2H4 and RNA was extracted after 6, 16 and 24 h of imbibition

overall_design: 21 samples with 3 biological replicats. treated vs untreated comparison

first: Christophe

last: Bailly

first: Alex-avon

last: Alaunay

first: RANA

last: Jurdak


title: Dorsal root ganglion single-cell RNA-seq dataset of painful diabetic peripheral neuropathy rat, diabeitc rats, and health rats

status: Public on Dec 31 2021

first: Han

last: Zhou

address: No.639 Zhizaoju Road

department: Neurosurgery

institute: Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Painful diabetic peripheral neuropathy (PDPN) is a common complication of diabetes mellitus (DM).   As one of the most disturbing symptoms, mechanical allodynia (MA) in PDPN remains largely unexplored. This dataset contains single-cell RNA sequencing results from rat dorsal root ganglion (DRG). The goal of this experiment was to investigate the transcriptional changes of distinct cell types in the DRG along MA development.

overall_design: Diabetic rats were induced by injected streptozotocin (STZ) on Day 0. We grouped diabetic rats according to the 50% paw withdrawal threshold (PWT) on Day 28. Rats with PWT ≤ 8 g were selected into the PDPN group and rats with PWT ≥ 15g were selected into the DM group. Rats in normal group (N group) were injected vehicle on Day 0. This experiment contains 8 samples (4 PDPN, 2 DM and 2 N), each of which combined bilateral L5 DRG collected from one male rat.

first: Wenchuan

last: Zhang

first: Xiaosheng

last: Yang


title: Cellular Atlas of Human Heart Failure

status: Public on Jan 28 2022

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

summary: Heart failure represents a major cause of morbidity and mortality worldwide. Single cell transcriptomics have revolutionized our understanding of cell composition and associated gene expression across human tissues. Through integrated analysis of single cell and single nucleus RNA sequencing data generated from 45 individuals, we define the cell composition of the healthy and failing human heart. We identify cell specific transcriptional signatures of heart failure and reveal the emergence of disease associated cell states. Intriguingly, cardiomyocytes converge towards a common disease associated cell state, while fibroblasts and myeloid cells undergo dramatic diversification. Endothelial cells and pericytes display global transcriptional shifts without changes in cell complexity. Collectively, our findings provide a comprehensive analysis of the cellular and transcriptomic landscape of human heart failure, identify cell type specific transcriptional programs and states associated with disease, and establish a valuable resource for the investigation of human heart failure.

overall_design: Single cell n=7 (2 donor, 5 DCM), single nuclei n=38 (25 donor, 13 DCM).

first: Andrew

last: Koenig

first: Irina

last: Shchukina

first: Prabhakar

last: Andhey

first: Konstantin

last: Zaitsev

first: Lulu

last: Lai

first: Junedh

last: Amrute

first: Geetika

last: Bajpai

first: Andrea

last: Bredemeyer

first: Gabriella

last: Smith

first: Cameran

last: Jones

first: Emily

last: Terrebonne

first: Stacey

last: Rentschler

first: Maxim

middle: N

last: Artyomov


title: Integrated chromatin accessibility and transcriptome landscapes of 5-Fluorouracil-resistant colon cancer cells

status: Public on Dec 17 2021

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: 5-Fluorouracil (5-FU) is one of the most effective and widely used chemotherapeutic drugs in the treatment of colon cancer. Yet chemoresistance is a common feature of colon cancer, resulting in poor prognosis and short survival. Dynamic reprogramming of chromatin accessibility allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression via direct transcription factor activation and regulatory element-binding. To better understand the regulatory network underlying 5-FU resistance in colon cancer cells, we explored the systematic alterations of chromatin accessibility and transcript expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with transcriptome sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in 5-FU-resistant HCT15 (HCT15-FR) cells. A total of 3175 differentially expressed mRNAs (DEGs), lncRNAs (DELs) and miRNAs (DEMs) related to 5-FU resistance were identified, including dramatically up-regulated IL33, H19, miR-17-5p, significantly down-regulated AKR1B10, LINC01012, miR-125b-5p, and potential chromatin modifiers such as INO80C, HDAC6 and KDM5A. A competitive endogenous RNAs (ceRNAs) regulatory network was established based on information about interactions among DEGs, DELs and DEMs, suggesting that H19, HOXA11-AS and NEAT1 might function as ceRNAs associate with 5-FU resistance in HCT15 cells. By integrating with transcriptome data, 9868 DARs were identified in HCT15-FR cells compared to control, which were positively (r = 0.58) correlated with their nearest DEGs and DELs. The up-regulated genes related to 4937 increased chromatin-accessible regions were significantly enriched in signaling pathways of MAPK, FOX and WNT, while the 4931 decreased chromatin-accessible regions were considered to be involved in declined biosynthesis of amino acids and nucleotide sugars, signaling pathways of Notch, and HIF-1. Analyses of the DAR sequences revealed that, besides AP-1 family, the TF DNA-binding motifs of FOX and KLF family members were highly enriched in hyper- and hypo-accessible regions, respectively. Moreover, relationships of critical TFs and their potential targets associated with DARs were identified, such as FOXA1, RUNX2, KLF3 and GRHL2. These data provided clear insights and valuable resources for an improved understanding of the non-genetic landscape of 5-FU-resistant colon cancer cells based on chromatin accessibility and transcript levels, which allowed for genome-wide detection of TF-binding sites, potential cis-regulatory elements and therapeutic targets.

overall_design: Genome-wide profiling of chromatin accessibility and gene expression in parental and 5-FU-resistant colon cancer cells. In total, 12 samples were analyzed. mRNA+lncRNA-seq_HCT15_1, mRNA+lncRNA_HCT15_2, smRNA-seq_HCT15_1, smRNA_HCT15_2 were 4 biological replicates and served as the control group. mRNA+lncRNA-seq_HCT15-FR_1, mRNA+lncRNA_HCT15-FR_2, smRNA-seq_HCT15-FR_1, smRNA_HCT15-FR_2 were 4 biological replicates and served as the treatment group. ATAC-seq_HCT15_1 and ATAC-seq _HCT15_2 were 2 biological replicates and served as the control group. ATAC-seq_HCT15-FR_1 and ATAC-seq_HCT15-FR_2 were 2 biological replicates and served as the treatment group.


title: The cGAS-STING pathway drives type I IFN immunopathology in COVID-19

status: Public on Jan 07 2022

city: Lausanne

first: Jeremy

last: Di Domizio

address: Av Boveresses 155

country: Switzerland

institute: CHUV

summary: we profiled the inflammatory transcriptome of ten COVID-19 skin manifestations from patients with moderate-to-severe disease and compared the resultant signatures with those obtained from skin lesions of patients with cutaneous lupus erythematosus.

overall_design: Inflammation-oriented transcriptomics was performed on RNA extracted from skin biopsies using NanoString technologies


title: ngs2017_12_ddm1-Hypomethylation and drought stress on transcriptome

status: Public on Nov 22 2021

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

summary: ngs2017_12_ddm1-ngs2017_12_ddm1-Rôle of poplar DDM1 on genes expression under water availability variation-Effect of hypomethylation and drought on genes expression

overall_design: 6 samples with 3 biological replicates. normal vs rnai mutant comparaison

first: José

last: Caius

first: Stéphane

last: Maury

first: Ludivine

last: Taconnat-Soubig


title: eauptic_carences - Characterization of the ionomic signatures of plants submitted to nutritional deficiencies and some potentially involved mechanism

status: Public on Nov 17 2021

summary: ngs2020_16_carences-eauptic_carences- What are the molecular processes associated with macronutrient deficiencies in B. napus roots? What are metabolic pathway involved in root remobilization? -Root samples of N, Mg, P, S, K and Ca deprivations was harvested after 10 days of deprivations, and root samples of Cl, Mn and Co deprivations was havested after 22 days of deprivations.

overall_design: 33 samples with 3 biological replicats. treated vs untreated comparison

first: Stéphanie

last: Pateyron

first: Etienne

last: Delannoy

first: Philippe

last: Etienne

last: Taconnat-Soubigou


title: Gene expression of Ovarian Cancer

status: Public on Nov 19 2021

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

summary: We report RNA sequencing data from 2 primary ovarian tumor, 2 omemtum and 1 normal ovary.

overall_design: Examination of transcriptomics of High Grade Serous ovarian cancer

first: Elaine

last: Stur


title: CD19-CAR T cells undergo exhaustion epigenetic programming in patients with acute lymphoblastic leukemia

status: Public on Nov 08 2021

city: Memphis

first: Tian

last: Mi

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: Zebley et al. show that CD8+ CD19-CAR T cells undergo genome-wide DNA methylation changes during an anti-tumor response in patients with B-cell acute lymphoblastic leukemia (ALL). Post-infusion CAR T cell differentiation involves acquisition of DNA methylation programs associated with effector function, repression of memory potential, and transition toward exhaustion.

overall_design: 4 Pre-infusion samples, 13 GMP samples, 4 week1 after GMP samples, 5 week2 after GMP samples, 3 week3 after GMP samples, 1 week4 after GMP sample.

first: Caitlin

last: Zebley

first: Stephen

last: Gottschalk

first: Ben

last: Youngblood


title: Transcriptional regulation by Aire in medullary thymic epithelial cells revisited

status: Public on Oct 13 2021

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

summary: The deficiency of Aire, a transcriptional regulator whose defect results in the development of autoimmunity, is associated with reduced expression of tissue-restricted self-Ags (TRAs) in medullary thymic epithelial cells (mTECs). Although the mechanisms underlying Aire-dependent expression of TRAs need to be explored, the physical identification of the target(s) of Aire has been hampered by the low and promiscuous expression of TRAs. We have tackled this issue by engineering mice with augmented Aire expression. Integration of the transcriptomic data from Aire-augmented and Aire-deficient mTECs revealed that a large proportion of so-called Aire-dependent genes, including those of TRAs, may not be direct transcriptional targets downstream of Aire. Rather, Aire induces TRA expression indirectly through controlling the heterogeneity of mTECs, as revealed by single-cell analyses. In contrast, Ccl25 emerged as a canonical target of Aire, and we verified this both in vitro and in vivo. Our approach has illuminated the Aire?s primary targets while distinguishing them from the secondary targets.

overall_design:
FACS-sorted mTEChigh from one mouse at eight weeks of age were prepared for scRNA-seq analyses, TECs WT and TECs 3xAireKI.

ATAC-seq analysis for FACS-sorted mTECs from mice at eight weeks of age

first: Hitoshi

last: Nishijima

first: Minoru

last: Matsumoto

first: Ryuichiro

last: Miyazawa

first: Kazuyoshi

last: Hosomichi

first: Nobuko

last: Akiyama

first: Taishin

first: Koichi

last: Tsuneyama

first: Junko

last: Morimoto

first: Mitsuru


title: Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing

city: Pittsburgh

first: Robert

last: Ferris

address: 5500 Center Ave

institute: University of Pittsburgh

summary: Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the heterogeneity, signatures of unique cell populations, and cell-cell interactions of suppressive non-immune and immune cell populations in 6 human papillomavirus (HPV)+ and 12 HPV- HNSCC patient tumor and matched peripheral blood specimens using single-cell RNA sequencing (scRNAseq). Using this dataset of 134,606 cells, we show cell type-specific signatures associated with inflammation and HPV status, describe the negative prognostic value of fibroblasts with elastic differentiation specifically in the HPV+ TME, predict therapeutically targetable checkpoint receptor-ligand interactions, and show that tumor-associated macrophages are dominant contributors of PD-L1 and other immune checkpoint ligands in the TME. We present a comprehensive single-cell view of cell-intrinsic mechanisms and cell-cell communication shaping the HNSCC microenvironment.

overall_design: PBL, CD45+ and CD45- samples  from 18 treatment naïve patients were analyzed in this study

first: Aditi

last: Kulkarni

first: Cornelius

last: Kurten

first: Lazar

last: Vujanovic


title: Human Respiratory Syncytial Virus Non-Structural Protein NS1 enters the nucleus to disrupt gene transcription (RNA-seq)

status: Public on Oct 12 2021

city: St. Louis

first: Jacqueline

last: Payton

state: MO

department: Pathology and Immunology

summary: Human respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections in young children, the elderly, and immunocompromised individuals. Prior exposure to RSV affords little protection and many are susceptible to reinfection throughout life. Virally encoded non-structural (NS) protein 1 (NS1) is thought to modulate host responses in the cytosol. Here, we describe the nuclear localization of NS1 during RSV infection and a corresponding nuclear role in modulating host transcription. In support, we show that a significant proportion of NS1 is partitions to the nucleus and that NS1 alone is necessary and sufficient to translocate into the nucleus. NS1 co-localizes with exportin XPO1 and inhibition of XPO1 results in NS1 accumulation in the nucleus. Furthermore, nuclear NS1 is chromatin-associated and co-immunoprecipitates with Mediator complex proteins. Chromatin-immunoprecipitation demonstrates enrichment of NS1 binding overlapping Mediator and interferon-stimulated transcription factor binding sites that lie within regulatory elements of genes differentially expressed during RSV infection. Mutation of the unique alpha helix in NS1 enhances its repressive effect on host gene expression. Together, these data suggest that nuclear NS1 may alter host responses to RSV infection by binding at the promoters and enhancers of host immune response genes and disrupting host transcriptional regulators. Our study identifies yet another regulatory layer of interactions with RSV proteins that shapes host response to RSV and potentially impacts long-term immunity to RSV.

overall_design: RNA-seq and ChIP-seq (anti-HA and anti-Mediator) profiling of A549 cell line mock-infected or infected with hRSV A2 strain or transfected with HA-tagged NS1.

first: Daisy

middle: W

last: Leung


title: Human Respiratory Syncytial Virus Non-Structural Protein NS1 enters the nucleus to disrupt gene transcription (ChIP-seq)


title: Organ-differential Regulation of Vascular Development by DEAD-box Helicase 24

status: Public on Oct 08 2021

city: Zhuhai

first: Fangbin

last: Chen

state: Guangdong

address: Meihua East Road No.52

institute: Sun Yat-sen University

summary: The goal of this study is to understand the molecular mechanisms by which DDX24 regulates vascular development in an organ-specific manner. To this end, we performed RNA sequencing on HUVECs and HCMECs transfected with either DDX24 siRNA or control siRNA and compared the expression levels of genes involved in angiogenesis

overall_design: mRNA profiles were generated from HUVECs and HCMECs transfected with either DDX24 or control siRNA. Total RNA was extracted from collected cells, and cDNA libraries were constructed for sequencing. Samples were prepared in duplicate and sequenced using the Illumina NovaSeq 6000 platform

first: Zhaohua

last: Deng

first: Hong

last: Shan

first: Huanhuan

last: He


title: Bromodomain Containing Protein 4 (BRD4) Regulates Inducible Expression Of Its Interactome In The Innate Response To Respiratory Syncytial Virus

status: Public on Oct 01 2021

city: Middleton

first: Allan

last: Brasier

state: WI

address: 715 Highland

institute: university of Wissconsin

summary: We examine the effect of a selective BRD4 inhibitor n the epithelial response to RSV infection.  Wild type human small airway epithelial cells were infected in the absence or prescend of ZL0454.  24 h later, RNA was extracted and  subjected to short read illumina RNA Seq.

overall_design: wild type small airway epithelial cells were mock or RSV infected for 24 h prior to RNA seq.  Cells were treated in the absence or presence of the BRD4 inhibitor, ZL0454

first: Xiaofang

last: Xu


title: Identification of new snoRNAs in human muscle cells

status: Public on Sep 28 2021

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

department: LBD

institute: Sorbonne Université, CNRS, Paris, France

summary: Small non-coding RNAs (sncRNAs) represent an important class of regulatory RNAs involved in the regulation of transcription, RNA splicing or translation. Among these sncRNAs, small nucleolar RNAs (snoRNAs) mostly originate from intron splicing in humans and are central to posttranscriptional regulation of gene expression. Yet, the characterization of the complete repertoire of sncRNAs in a given cellular context and the functional annotation of the human transcriptome are far from complete. Here, we report the large-scale identification of sncRNAs in the size range of 50 to 200 nucleotides, without a priori on their biogenesis, structure and genomic origin, in the context of normal human muscle cells. We provided a complete set of experimental validation of novel candidate snoRNAs by evaluating the prerequisites for their biogenesis and functionality, leading to their validation as genuine snoRNAs. Interestingly, we also found intergenic snoRNAs, which we showed are in fact integrated into candidate introns of unannotated transcripts or degraded by the Nonsense Mediated Decay pathway. Hence, intergenic snoRNAs represent a new type of landmark for the identification of new transcripts that have gone undetected because of low abundance or degradation after the release of the snoRNA.

overall_design: Identification of new snoRNAs with the medium RNAseq and of their host genes with the total RNAseq

first: Claire

last: Francastel


title: Human Respiratory Syncytial Virus Non-Structural Protein NS1 enters the nucleus to disrupt gene transcription

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

overall_design: Refer to individual Series


title: Transcriptome analysis of isogenic Neural stem cell for LRRK2 G2019S mutation.

status: Public on Sep 08 2021

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

summary: We report the transcriptome data produced from isogenic neural stem cells with normal LRRK2 gene, or LRRK2 G2019S mutation. After gene correction from patient-derived iPSCs with LRRK2 G2019S, the isogenic lines were diffrentiated toward neural stem cells. To reflect on aging effect, theses cells were harvested to the early (passage number 1) or late stage (passage number 13), without replicate. Also, they were prepared at the early stage (passage number 3), triplicate.

overall_design: Two RNA seq data from early (passage 1) and late stage (passage 13) of LRRK2 G2019S-mutant neural stem cells or LRRK2 gene corrected neural stem cells. Triplicate RNA seq data from early stage (passage 3) of  LRRK2 G2019S-mutant neural stem cells or LRRK2 gene corrected neural stem cells, respectively.

first: Seo-Young

last: Lee

first: Sun-Ku

last: Chung


title: Single cell RNA sequencing (scRNA-Seq) deciphering pathological alterations in streptozotocin-induced diabetic retinas

status: Public on Aug 24 2021

first: Qihuang

last: Jin

address: 85 Wujin Road

department: Department of Ophthalmology

institute: Shanghai General Hospital

summary: Diabetic retinopathy (DR) is an irreversible and progressive diabetic complication leading to visual impairment, even blindness. Due to the delicate and complicated structure of the retina, the pathology of DR has not been completely elucidated yet. We constructed a transcriptome atlas of >14,000 single cells from healthy and streptozotocin (STZ)-induced diabetic murine retinas to decipher pathological alterations of DR. We found four stress-inducible genes Cirbp, Rmb3, Mt1 and Mt2 commonly induced in most types of retinal cells. Bipolar cells were little affected both in number and gene expression. There existed two subtypes of Müller cells, the Fos-expressing subtype and the no-marker subtype, and the latter lost more in DR. A large number of genes were deregulated in diabetic vascular endothelial cells (ECs), and the differential expression genes were paired to the pathways functioning in metabolism, shear stress and vascular permeability. These pathways were mapped by more differential expression genes in a subpopulation of ECs specifically presented in diabetic retinas (diabetic retinal ECs, DRECs). Moreover, several inflammation pathways were activated in DRECs, and the most significant one is the IL-17 signaling pathway. According to the EC markers, DRECs were mainly capillary ECs, confirmed by immunofluorescent staining of S100a9, a target gene of the IL-17 signaling pathway. This study deciphered pathological alterations of DR, and provided clues for new potential targets for DR therapy.

overall_design:
The mouse DR model was established by introperitoneal injection of STZ. 25 weeks later, the mice were then sacrificed and retinal single cell suspensions were prepared. The cell suspensions from 3 healthy or 3 diabetic retinas were pooled together. The labaries for scRNA-Seq were construted by the 10X Chromium Single Cell Platform. The final libraries were sequenced on an Illumina Nova6000 instrument using 150-base-pair paired-end reads.

UPDATE [04-16-2025] The processed data file was replaced. The new file GSE178121_counts_matrix.csv includes counts for both Samples GSM5380581 and GSM5380582.

first: Fang

last: Zhang

first: Licheng

last: Sun


title: Low Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy

status: Public on Aug 13 2021

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

summary: The development of approaches for inflaming cold tumors is critical for increasing response to immunotherapy. Here we report that low-dose radiotherapy (LDRT) in mice promotes tumor T-cell inflammation and enables responsiveness to combinatorial immunotherapyin an interferon-dependent manner. Treatment efficacy relied upon mobilizing both adaptive and innate immunity, and depended on both cytotoxic CD4+and CD8+T cells. LDRTinduced predominantly CD4+cells which exhibited features of exhausted effector and cytotoxic cells, with a subset expressing NKG2D and exhibiting proliferative capacity, and a novel subset of dendritic cells with activated phenotype that expressed the NKG2D ligand Rae1. Finally, tumor immune rejection was critically dependent on the NKG2D pathway. We translated these findings toa phase I clinical trial. Like in mice, combinatorial treatmenttriggered peripheral T-cell mobilization and resulted in important tumor T-cell infiltration, predominantly of CD4+cells and with Th1 signatures, observed only in patients with immune desert tumors who responded to a novel combination of LDRT, low dose cyclophosphamide and immune checkpoint blockade therapy.These results suggest the novel possibility of rationally combining LDRT with immune checkpoint therapy for the treatment of cold tumors, based on the simultaneous activation of antitumoral innate and adaptive immunity

overall_design: Transcriptomics data of human tumors from 7 patients undergoing low dose radiotherapy with matched pre- and post- biopsies for 6 patients.

first: Fernanda

last: Herrera

first: Melita

last: Irving

first: George

last: Coukos


title: Single-cell RNA-Seq of blood cells between an irradiated patient and non-irradiated healthy men

status: Public on Aug 11 2021

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

summary: This study aims to compare mRNA expression between irradiated and non-irradiated people’s blood by single-cell RNA-Seq. In this study, the blood was isolated from patients or healthy persons. The Control group of blood were collected from ten different persons without radiation and mixed for RNA-seq. The blood of irradiated patient was collected from a patient who was exposed to radiation.

overall_design: The Control group of blood were collected from ten different persons without radiation, while the blood of irradiated patient was collected from patient who was exposed to radiation.

first: Shuyu

first: Yan

last: Tao

first: Daojiang

last: Yu


title: Auxin-sugar antagonist effect on budburst

status: Public on Jun 21 2021

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

summary:
Project : Sugar-Auxine_Rose
ngs2017_11_rosex2-auxin sugar antagonist effect on budburst
Study of the antagonistic effect between sugar and auxin on the bud burst of the axillary bud of the rose bush - Identification of the molecular network involved in the antagonistic effect between sugar and auxin on the budburst of the vegetative budworm of the rose bush

overall_design: 12 samples with 2 biological replicates. treated vs untreated comparison

first: Alexandra

last: Avon-Launay

first: SOULAIMAN

last: Sakr

first: Ludivine

last: Taconnat-Soubigou


title: eauptic one-Effet of water shortage on the whole foliar elemental content (ie. Ionome)

status: Public on Jan 26 2022

summary: ngs2020_07_eauptic-eauptic one-How rapeseed transcriptome is affected by a short or a maintained water shortage and relationships betwenen genes expression and ionome variations .-Rapeseed not vernalized for a study at the vegetative stage. Brassica napusleaf blades samples which were grown at 80% of the field capacity (control) or during a moderate (50%) or a severe water shortage (25%), short (t1) or prolonged (t2).

overall_design: 24 samples with 3 biological replicats. treated vs untreated comparison

first: Stéphanie

last: Pateyron

first: Etienne

last: Delannoy

first: Philippe

last: Etienne


title: Gene expression profiling of colorectal cancer liver metastases (CRLM).

status: Public on Jul 27 2021

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have performed gene expression profiling of surgically resected liver metastases by exon-resolution microarrays, and identified a metastasis-oriented subtyping framework consisting of 5 de novo transcriptomic subtypes (LMS1-5).

overall_design: This series consists of 283 CRLM samples from 171 patients, analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Seyed

middle: H

last: Moosavi

first: Ina

last: Eilertsen

first: Ragnhild

last: Lothe


title: Integrated Profiling Reveals Low Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy

first: David

last: Barras

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


status: Public on Jun 12 2021

first: Xiangning

last: Xue

address: 4200 Fifth Ave

department: Department of Biostatistics

summary: Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC

overall_design: Compare transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC

first: Ryan

last: Logan


title: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination

status: Public on Aug 02 2021

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology

summary: Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by ‘writer’ and ‘eraser’ enzymes, respectively. Nucleosomal PTMs are recognised by a variety of ‘reader’ proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite’s bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.

overall_design: This dataset shows the genomic association of 71 YFP-tagged proteins and an untagged control. There are three replicates for BDF6, CRD1 and DMT; one replicate for ELP3a, NAT2 and SET10; and two replicates for the remaining 65 YFP-tagged proteins and for the untagged control.

first: Desislava

middle: P

last: Staneva


title: Transcriptome profiles of colonic stem cells of WT and AhR deficient mice

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: Francis Crick Insititue

summary: We analysed intestinal (colon) organoids from wildtype and AhR deficient mice to identify AhR dependent functions in intestinal stem cells

overall_design: Orgnaoids were prepared from colonic crypts of WT and AhR deficient mice and maintained in either stem cell condition or differentiated into epithelial subsets. RNAseq was performed on total RNA.


title: CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

status: Public on Jun 04 2021

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

summary: The eleven zinc finger (ZF) protein CTCF regulates topologically associating domain (TAD) formation and transcription through selective binding to thousands of genomic sites. We replaced endogenous CTCF in mouse embryonic stem (ES) cells with GFP-tagged wildtype or mutant proteins lacking individual ZFs. We examined the various ES cell lines using next generation sequencing methods (ChIP-Seq, RNA-Seq, MedSeq, HiC) in order to identify additional determinants of CTCF positioning and function.

overall_design:
1) ChIP-Seq of CTCF in mouse ES cells expressing GFP-CTCF or mutant proteins lacking individual ZFs 1, 8, 9, 10 or 11. Seven ChIP-Seq libraries were prepared using rabbit polyclonal antibodies against CTCF (home made). As control we used pre-immune serum.
2) RNA-Seq of mRNA derived from mouse ES cells expressing GFP-CTCF (GC) or a CTCF mutant protein lacking ZF8 (d8). RNA-Seq libraries were prepared from two GC lines (GC1, GC2) and three d8 lines (d8-1, d8-2, d8-3). Triplicate samples were isolated, except in the case of d8-3, where duplicates were isolated.
3) MedSeq of LpnPI-digested genomic DNA from mouse ES cells expressing GFP-CTCF (GC) or a CTCF mutant protein lacking ZF8 (del8). MedSeq libraries were prepared from two GC ES lines (GC1, GC2) and three del8 ES lines (d8-1, d8-2, d8-3). Two technical replicates were analyzed from each line.


title: Petals in ranunculaceae - Characterization of the petal gene network in Nigella damascena (Ranunculaceae)

status: Public on Jun 03 2021

first: Véronique

last: BRUNAUD

summary: ngs2013_09_aap-ideev-petals in ranunculaceae-Identification of putative NdAP3-3 target genes-Developmental and genetic origin of shape diversity and evolutionary role.

overall_design: 12 samples with 3 biological replicats. genotype comparaison

last: Taconnat

first: Sandrine

last: Balzergue

first: Catherine

last: Damerval


title: The immune atlas of human deciduas with unexplained recurrent pregnancy loss

city: Shenzhen

first: Lisha

last: Mou

address: NO.3002 Sungang Road, Futian district

department: Institute of Translational Medicine

institute: Shenzhen Second People's Hospital

summary: We profiled the transcriptomes of about 14,000 CD45+ single cells from 3 normal and 3 URPL deciduas within 8-10 gestational weeks. The cellular composition revealed six major subsets of immune cells including dNK, T cell, macrophage, dendritic cell (DC), mast cell, and B cell in the decidua.We identified previously unknown variations of immune cells including the decreased proportion of CSF1+CD59+ KIRs-expressing dNK subset and the increase of activated DC subset in URPL deciduas.

overall_design: Profiling the transcriptomes of about 14,000 CD45+ single cells from 3 normal and 3 URPL deciduas using single-cell RNA Seq.

first: Pengfei

last: Chen

first: Liying

last: Zhou

first: Jiying

first: Ying

last: Lu

first: Chaoxia

last: Cao

first: Shuangli

last: Lv

first: Zhihong

last: Wei

first: Jiao

first: Xuefeng

last: Deng

first: Changchun

last: Zeng

first: Huiyun

last: Wang

first: Zuhui

last: Pu

first: Ruiying

last: Diao


title: Longitudinal profiling of the whole blood transcriptional response of human volunteers to repeated malaria challenge

status: Public on May 25 2021

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: We took a systems immunology approach to analyse the evolution of the human immune response to the first three infections of life in a re-challenge model of falciparum malaria. Ten volunteers were infected up to three times with Plasmodium falciparum in 4- to 8-month intervals. Remarkably, parasite densities and the dynamics of blood-stage infection were not altered over the course of three homologous infections. To track the development of immunity in real-time we used whole blood RNA-sequencing to analyse each volunteer’s transcriptional response throughout infection and convalescence (up to 9 time points per volunteer per infection).

overall_design:
Whole blood samples were collected from volunteers participating in controlled human malaria reinfection trials (vac063a/b: ClinicalTrials.gov NCT02927145, vac063c: ClinicalTrials.gov  NCT03906474) and preserved in Tempus reagent. RNA was extracted using the Tempus Spin RNA isolation reagent kit. Libraries were constructed using the TruSeq Stranded mRNA library protocol and sequenced on an Illumina NovaSeq 6000 platform.
-- longitudinal study: six volunteers received three malaria infections (1039, 1040, 1061, 1068, 1075, 6032), 4 volunteers two infections (1065, 1067, 806, 818) and 3 volunteers only a single infection (313, 315, 320)
-- their whole blood transcriptome was analysed at 5 to 9 time points time per infection covering baseline (before infection), several time points during infection (common time points include 6- and 8-days after malaria challenge (C6 and C8 respectively) and diagnosis), after parasite clearance (6-days after drug treatment, T6) and memory (45-days after challenge)

first: Diana

last: Muñoz-Sandoval

first: Philip

last: Spence


title: microdissection data of 3 vascular bundles stages - Brachypodium Vascular ontogeny

status: Public on Apr 28 2021

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

summary: ngs2015_19_anr-jc-bravo-microdissection data of 3 vascular bundles stages-what genes regulate vascular differentiation -Total RNA from microdissected Vascular Bundles at 3 different stages are compared together. They are also compared to the transcriptome with ground tissue. Plant were grown during 15 days. Meristems were sectionned with a freezing microtome. Appropriate vascular bundles were microdissected and catupulted in tubes and appropriates buffer for RNA extraction. There are 3 biological repetitions per stages and for the ground tissue control.

overall_design: 12 samples with 1 biological replicats. tissue differentiation, time course

first: Ludivine

last: Taconnat

last: Soubigou-taconnat

first: Richard

last: Sibout

first: Sandrine

last: Balzergue


title: Effect of the deletion of the lncRNA Neat1 on the rhythmic gene expression in the GH4C1 cell line

status: Public on May 05 2021

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

institute: CNRS-AMU

summary: The goal of this study was to determine the effect of the deletion of the lncRNA Neat1 on the rhythmic gene expression in the GH4C1 cell line

overall_design: GH4C1 sommatolactotroph pituitary cells (ATCC_ CCL-82.2™, Molsheim, France) were grown in HamF10 medium supplemented with 15% horse serum and 2% fetal calf serum.   To synchronize cells between themselves, GH4C1 cells were transferred to fresh medium.  Cells were harvested after this fresh medium replacement (T0) every 4 h from T10 to T34.   At each time point, total RNA was prepared, and RNA was isolated using NucleoSpin®RNA XS (Macherey-Nagel).

first: Audrey

last: Jaq

first: Denis

last: Becquet

first: Severine

last: Guillen

first: Benedicte

last: Boyer

first: Maria-Montserrat

last: Goutierrez

first: Laure

last: Fourel

first: Jean-Louis

last: Franc


title: CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells

first: Niels

last: Galjart

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

overall_design: Refer to individual Series


title: RNA-sequencing analysis of the CD4+ T cell response to a first-in-life infection and malaria re-challenge

last: Ivens

summary: Human volunteers received either their first, second or third homologous Plasmodium falciparum infection and six days after parasite clearance (at the peak of the adaptive immune response) we flow-sorted naïve, effector memory and regulatory CD4+ T cells for bulk RNA-sequencing. Transcriptional profiling of the T cell response at this time point allowed us to measure the outcome of critical cell-cell interactions within the inflamed spleen during the first three infections of life.

overall_design:
T cells were isolated directly ex vivo from the blood of volunteers participating in a controlled human malaria reinfection trial (vac063c: clinicaltrials.gov NCT03906474). Effector memory, naive and regulatory CD4 T cells were flow sorted into Trizol and total RNA was extracted using a modified phenol-chloroform protocol. Libraries were constructed using the Nextera XT DNA Library Preparation kit and sequenced on an Illumina NextSeq 550 platform.
- 11 volunteers: n = 3 first, n = 2 second, n = 6 third malaria infection
- 2 time points: baseline before malaria infection and 6-days after drug treatment T6
- 3 flow sorted CD4 T cell subsets: effector memory (Tm), naive (Tn) and regulatory (Tr)
- RNA-sequencing: 66 samples

first: Wiebke

last: Nahrendorf


title: Nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants

status: Public on Apr 27 2021


title: Profiling the human immune response to Plasmodium falciparum during the first three infections of life

first: Alasdair

summary:
Controlled human malaria infection is a powerful experimental medicine tool to understand the human immune response to a first ever malaria infection. Here we have taken this approach a step further and conducted the first human malaria reinfection trial in the modern era. Volunteers were challenged up to three times with Plasmodium falciparum in 4- to 8-month intervals. Remarkably, parasite densities and the dynamics of blood-stage infection were not altered over the course of three homologous infections.
Using whole blood RNA-sequencing we tracked the host immune response through time and found that the emergency myeloid response, which triggers systemic inflammation and the global recruitment of T cells into lymphoid tissues, is not altered by repeated infection.
Six days after parasite clearance, when the innate response subsides, T cells return to the circulation and reflect the outcome of critical cell-cell interactions within the inflamed spleen. By transcriptionally profiling flow sorted CD4+ T cell subsets after their release from the tissue we could show that TH1 polarised effector response in naïve hosts is tolerised upon re-challenge to avoid collateral tissue damage. Instead, a subset of specialised cytokine-producing CD4+ T cells are activated to promote essential protective immune functions.
Together these data indicate that innate and adaptive immune responses can be uncoupled in malaria and illustrate that human hosts prioritises damage limitation (tolerance) over parasite clearance (resistance) to quickly acquire clinical immunity.


title: RNaseI-RIPseq for rfl8-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

summary: blanc09_ripseq_rfl8-rnasei-ripseq for rfl8-Which mitochondrial transcripts are bound by RFL8 protein? -The RNaseI-RIPseq approach to find the in vivo binding sites of RFL8 protein on mitochondrial mRNAs via co-immunoprecipitation of 3HA tag fused in C-terminal of RFL8 protein

overall_design: 4 samples with 2 biological replicates. normal vs transgenic comparison

first: Hakim

last: Mireau


title: An androgen receptor switch underlies lineage infidelity to drive neuroendocrine prostate cancer

status: Public on Jul 15 2021

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: We generate transcription factor, histone modification and ATAC cistromes in castration-resistant prostate cancer (CRPC) and treatment-induced neuroendocrine prostate cancer (tNEPC) specimens.

overall_design: ChIP-seq for AR, PRC2 subunits, and the histone marks H3K27Me3 and H3K27Ac, ATAC-seq for measuring chromatin accessibility, and RNA-seq for transcriptome profiling.

first: Alastair

last: Davies

first: Shaghayegh

last: Nouruzi

first: Dwaipayan

last: Ganguli

first: Takeshi

last: Namekawa

first: Daksh

last: Thaper

first: Simon

last: Linder

first: Fatih

last: Karaoğlanoğlu

first: Meltem

last: Omur

first: Soojin

last: Kim

first: Sahil

last: Kumar

first: Olena

last: Sivak

first: Chiara

last: Bostock

first: Jennifer

last: Bishop

first: Marlous

last: Hoogstraat

first: Suzan

last: Stelloo

first: Henk

last: van der Poel

first: Andries

last: Bergman

first: Musaddeque

last: Ahmed

first: Ladan

last: Fazli

first: Haojie

last: Huang

first: Wayne

last: Tilley

first: David

last: Goodrich

first: Felix

middle: Y

last: Feng

first: Martin

last: Gleave

first: Housheng

last: He

first: Faraz

last: Hach

first: Wilbert

last: Zwart

first: Himisha

last: Beltran

first: Luke

last: Selth