title: The application of second-generation sequencing in congenital pulmonary airway malformations

city: Guangzhou

first: Gang

last: Zhang

state: Guangdong

address: NO.63, Duobao road,Liwan district,Guangzhou city,Guangdong prov.

department: pediatric surgery

institute: Third Affiliated Hospital of Guangzhou Medical University

summary:
Objective: To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology.
Methods: Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis.
Results: Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes.
Conclusion: The whole transcript of CPAM shows obvious gene up- and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.

overall_design: CPAM samples (n=4) and control samples (n=5) were used for  RNA-Seq

last: Yu

first: Chun

first: Xiao


title: IkappaBzeta Controls IL-17-triggered Gene Expression Program in Intestinal Epithelial Cells that Prevents Expansion of SFB and Attenuates Autoimmune Disorders

status: Public on Dec 07 2022

city: Ota-ku

first: Soh

last: Yamazaki

state: Tokyo

address: 5-21-16 Omorinishi

department: Biohemistry

country: Japan

institute: Toho University School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: IkappaBzeta Controls IL-17-triggered Gene Expression Program in Intestinal Epithelial Cells that Prevents Expansion of SFB and Attenuates Autoimmune Disorders [ilea]

summary: Control of gut microbes is crucial for not only local defense in the intestine but also proper systemic immune responses.  Although intestinal epithelial cells (IECs) play important roles in cytokine-mediated control of enterobacteria, the underlying mechanisms are not fully understood.  Here we show that deletion of IkappaBzeta in IECs in mice leads to dysbiosis with marked expansion of segmented filamentous bacteria (SFB), thereby enhancing Th17 cell development and exacerbating autoimmune inflammatory diseases.  Mechanistically, the IkappaBzeta deficiency results in Paneth cell loss and impaired expression of IL-17-inducible genes involved in IgA production.  The Paneth cell loss is caused by aberrant activation of IFN-gamma signaling and a failure of IL-17-mediated recovery from IFN-gamma-induced damage.  Thus, the IL-17R–IkappaBzeta axis in IECs contributes to the maintenance of intestinal homeostasis by serving as a key component in a regulatory loop consisting of the gut microbiota and immune cells

overall_design: Total RNA was extracted from the ilea of two pairs of Nfkbizfl/flVil1-Cre and co-housed gender-matched littermate controls (Nfkbizfl/fl), and the gene expression profiles were analyzed by microarray analysis.

first: Hiroyasu

last: Nakano


title: IkappaBzeta Controls IL-17-triggered Gene Expression Program in Intestinal Epithelial Cells that Prevents Expansion of SFB and Attenuates Autoimmune Disorders [jejunum]

overall_design: Total RNA was extracted from the jejuna of Nfkbizfl/flVil1-Cre and controls, and the gene expression profiles were analyzed by RNA-seq analysis.


title: RAS-dependent ROS signaling in C. elegans.

city: Montreal

first: Robyn

last: Branicky

state: Quebec

address: 1205 Docteur Penfield Ave,, Stewart Bldg, W5/26

department: Biology

country: Canada

institute: McGill University

summary: Mitochondrial superoxide produced by low concentrations of the pro-oxidant paraquat increases C. elegans lifespan. We found that paraquat acts by intensifying RAS-dependent ROS signaling (RDRS) to alter the expression of >50% of the genome and control animal composition and physiology. We show that RDRS is regulated by negative feedback from SOD-1-dependent conversion of superoxide into cytoplasmic hydrogen peroxide, which in turn acts on a redox-sensitive cysteine (C118) of the RAS homologue LET-60ras. Preventing C118 oxidation by replacement with serine, or mimicking oxidation by replacement with aspartic acid, leads to opposite changes in the expression of thousands of genes. We show that paraquat acts through RDRS to exacerbate and accelerate gene expression changes that are normally observed at the end of post-embryonic development. The identities of the genes affected by paraquat suggest that RDRS stimulation extends lifespan by increasing turnover and repair while moderating damage from metabolic activity.

overall_design: Three biological replicates per condition were analysed; RNA was isolated individually from each replicate. C118S and C118D were sequenced in separate experiments and therefore contain their own WT controls for comparison (N2_Control_replicate 1 - replicate 3 are the WT controls used for C118S and N2_Control_replicate 4 – replicate 6 are the WT controls used for C118D). Bacteria grown on Nematode Growth Media (NGM) plates were transferred to experimental NGM plates for Paraquat (PQ) experiments (for both the PQ-treated and untreated controls). In contrast, the bacterial culture was seeded directly onto plates for developmental experiments. Therefore, the N2_gravid adults, N2_young adults and N2_L4 larvae samples should be compared to each other rather than to the N2_Control samples.

first: Ju-Ling

last: Liu

first: Siegfried

last: Hekimi


title: Single-Cell Transcriptomic Atlas of Penile Corpus Cavernosum Aging

first: qi

middle: wei

address: No.600 Tianhe Road

department: Urology

country: China

institute: Third Affiliated Hospital of Sun Yat-Sen University

summary:
Purpose: Molecular mechanisms of penile corpus cavernosum aging and male age-related erectile dysfunction (ED) remain unclear. Here we profiled young and old rat penile corpus cavernousm by single-cell RNA sequencing (scRNA-seq).
Methods:To map the single-cell transcriptomic landscape of penile corpus cavernosum during aging, we performed uniform manifold approximation and projection (UMAP), differential gene expression analysis (DGEs), pseudotime analysis and single-cell entropy algorithm to dissect cellular composition and transcriptional heterogeneity. For validation analysis, we further performed immunofluorescence studies on key molecules involved during penile corpus cavernosum aging.
Results: After stringent filtering,transcriptomes of 14,879 single cells (8,557 young and 6,322 old) derived from penile corpus cavernosum of 5 young (3 months) and 5 old (23 months) rats were analyzed subsequently. Clustering analysis of cell-type specific gene expression identified 19 cell types, such as smooth muscle cells, endothelial cells, fibroblasts,myofibroblasts and immune cells.Transcriptomic analyses revealed that transcriptional alterations across all cell types exhibited distinct properties rather than universally consistent. DGEs analysis demonstrated that genes related to extracellular matrix organization were highly expressed. Among these cell types, fibroblasts showed apparent heterogeneities. By performing pseudotime and single-cell entropy analysis on fibroblasts, we observed the age-associated decrease of entropy, and aged fibroblasts were found to adopt senescent secretory phenotype, as evidenced by the high expression of genes associated with the senescence-associated secretory phenotype (SASP). Since eliminating senescent cells or SASP were demonstrated to improve health and life span, we further investigated the distinct senescence-related gene expression signatures across all cell types during aging.
Conclusions: We plotted a cellular atlas of penile corpus cavernosum, and revealed the molecular alterations of aging cells, especially fibroblasts. Our work will deepen the understanding of the heterogeneity among certain cell types during penile corpus cavernosum aging and provide novel entry points for the age-associated ED treatment.

overall_design: Single cell sequencing of cells derived from penile corpus cavernosum of 5 young (3 months) and 5 old (23 months) male Sprague-Dawley rats

first: Yulong

last: Song

first: Qiwei

first: Cheng

last: Hu

first: Yun

last: Luo


title: ChIP-seq analysis of GLABRA2 transcription factor DNA-binding sites in wild-type and mutant Arabidopsis seedlings

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

country: USA

institute: University of kansas medical center

summary: GLABRA2 (GL2) is a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor that is critical for the differentiation of the epidermis in the plant model Arabidopsis. HD-Zip IV transcription factors are characterized by the presence of a lipid sensing domain known as START (for STeroidogenic Acute Regulatory (StAR)-related lipid Transfer). Genome-wide ChIP-seq assays were performed with seedlings expressing EYFP-tagged GL2 wild-type and mutant proteins to test whether the START domain is dispensible for DNA binding in vivo. These experiments included three START domain mutants (gl2_∆ST (listed here as gl2_dSTART), gl2_Amo, and gl2_E375G;R392M) as well as a mutant deleted for the six terminal amino acids of the HD and the entire leucine zipper (gl2_∆HD6;∆ZLZ (listed here as gl2_dZip)). Data analysis revealed DNA binding proficiency for wild-type GL2 and for all three START domain mutants whereas little or no binding was detected for gl2∆HD6;∆ZLZ and the gl2-5 null mutant control. Genomic distributions of the binding sites were similar for wild-type GL2 and the START domain mutants. Most of the ChIP-seq hits were mapped to promoter or intergenic regions, consistent with the role of GL2 as a transcriptional regulator. The relative positions of the binding sites to the transcription start sites were also similar. Gene ontology (GO) classification revealed overlapping functional classes of target genes bound by wild-type GL2 and the START domain mutants.

overall_design: Chip-seq analysis to identify genome-wide transcription factor binding sites of wild-type GL2 and five mutant versions thereof in 10-day-old Arabidopsis seedlings.

first: Aashima

last: Khosla

first: Kathrin

last: Schrick


title: Specialized functions and sexual dimorphism explain the functional diversity of the myeloid populations during glioma progression

status: Public on Dec 06 2022

city: Warsaw

first: Pawel

last: Segit

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) used to dissect myeloid cell identities and states in murine experimental gliomas (GL261).

overall_design: CITE-seq sequencing analysis of 6 groups: female control (3 samples), female tumor D14 (14 days post implantation, 3 samples), female tumor D21 (21 days post implantation, 3 samples), male control (3 samples), male tumor D14 (14 days post implantation, 3 samples), male tumor D21 (21 days post implantation, 3 samples). Samples were hashed.

first: Natalia

last: Ochocka

first: Kamil

last: Wojnicki

first: Salwador

last: Cyranowski

first: Julian

last: Swatler

first: Karol

last: Jacek

first: Wieslawa

last: Grajkowska

first: Bozena

last: Kaminska


title: Transcriptomic reveals the ferroptosis features of host response in a mouse model of Zika virus infection

first: zheng

last: wenjiang

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

summary:
Background: Zika virus (ZIKV) is a neurotropic flavivirus. The outbreak of ZIKV in 2016 created a global health emergency. However, the underlying pathogenic mechanisms remain elusive.
Methods: We investigated the host response features of in vivo replication in a mouse model of ZIKV infection, by performing a series of transcriptomic and bioinformatic analyses of ZIKV and mock-infected brain tissue.
Results: Tissue damage, inflammatory cells infiltration and high viral replication were observed in the brain tissue of ZIKV infected mice. RNA-Seq of the brain indicated the activation of ferroptosis pathways. Enrichment analysis of ferroptosis regulators revealed their involvement in pathways such as mineral absorption, fatty acid biosynthesis, fatty acid degradation, PPAR signaling pathway, peroxidase and adipokinesine signalling pathway. We then identified 12 interacted hub ferroptosis regulators (CYBB, HMOX1, CP, SAT1, TF, SLC39A14, FTL, LPCAT3, FTH1, SLC3A2, TP53 and SLC40A1) that were related to the differential expression of CD8+ T cells, microglia and monocytes. CYBB, HMOX1, SALT and SLAC40A1 were selected as potential biomarkers of ZIKV infection. Finally, we validated our results using RT-qPCR and outside available datasets.
Conclusions: For the first time, we proposed a possible mechanism of ferroptosis in brain tissue infected by ZIKV in mice and identified the four key ferroptosis regulators.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the brain and liver tissues of zika virus-infected mice and control mice.

first: Wenjiang

last: Zheng

first: Qian

last: Yan

first: Chengxin

first: Peng

last: Wu

first: Hongfa

last: Zhuang

first: Huiting

last: Huang

first: Yong

last: Jiang

first: Shaofeng

last: Zhan

first: Xiaohong

first: Geng

last: Li

first: Peiwen

last: Zhou

first: Yanni

last: Lai

first: Zizhao

last: Lao


title: iMbody - a nanobody for i-Motif research

city: Sydney

first: Samuel

last: Ross

state: NSW

address: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

summary: i-Motifs (iMs) are four-stranded structures formed by certain cytosine-rich nucleic acids. They may be involved in regulation of cellular processes such as transcription. In addition, the pH dependency of iMs makes them suitable for certain nanobiotechnological applications. Probes that recognize these structures with high specificity and affinity can significantly advance the iM research field. Here we report the generation of an iM specific nanobody (iMbody) and describe its applications for the in vitro characterization of a potential iM-forming oligonucleotide, strand-specific pull-down of iMs present in the human genome at near physiological pH and temperature followed by sequencing, and visualization of iMs in the nuclei of human cells. Utilization of iMbody could be beyond above-mentioned applications and it can be used to investigate iMs in other organisms. The plasmid encoding iMbody for the bacterial expression is available via Addgene (Plasmid #184496).

overall_design: i-Motif specific nanobody (iMbody) was used to perform strand-specific pull-down of i-Motifs present in the genomic DNA purified from K562 cells followed by high-throughput sequencing. Pull-down was performed at pH 7.2 ± 0.1 and 37 °C. Two replicates included in the study.

first: Mahdi

last: Zeraati

middle: E


title: Gene expression in microglia cells related to the development of post-traumatic stress disorder (PTSD)

city: Tampa

first: chengqi

last: wang

address: 4202 E Fowler Ave

institute: University of South Florida

summary: The research was conducted by in-vitro experiments on microglial cells, performed by Wildman lab and Uddin research group in the College of Public Health at the University of the South Florida. The experiments mimic the trauma-related immune environments by utilizing stress hormones. Stress hormones can modify individual internal environment during times of stress, mobilizing energy sources, increasing heart rate, and downregulating metabolic processes

overall_design: In this experiment, we adopt dexamethasone and hydrocortisone as stress hormones, which serve as treat- ments on microglial cells. In addition, we include alcohol as an additional treatment to distinguish whether gene expression is changed solely because of a random treat- ment (i.e. alcohol) as opposed to stress hormones treatments. Microglial cells were grown in media supplemented with one of the following treatments: dexamethasone (dex), hydrocortisone (cort), alcohol (vehicle) or control (only media). After the microglia cells were exposed to different treatments for three days, the RNA-seq data was extracted from microglial cells on day 3 and on the final day of washout (day 6). Our goal is to detect the genes in microglia cells which are differentially expressed when exposed to stress hormones. In addition, we investigate whether the dosage of the stress hormone affects the genes’ expression levels.

first: Wildman

last: Derek

first: Uddin

last: Monica


title: Magnesium modulates Bacillus subtilis cell division frequency

city: College Station

first: Jennifer

last: Herman

state: Texas

address: 300 Olsen blvd

department: Biochemistry & Biophysics

institute: Texas A&M University

summary: By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates Bacillus subtilis division frequency without affecting growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media and in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 4.0 mM, with little or no detectable change in labile, intracellular Mg2+ based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed enhanced expression of a large number of SigB-regulated genes and activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple growth rate from division frequency and identify transcriptional changes suggesting cell division is accompanied by the general stress response and an enhanced demand to sequester and/or increase uptake of iron, Mn2+, and Zn2+.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of three biological repeats with or without Mg supplement at exponential stage.

first: Tingfeng

last: Guo


title: Epigenetic biomarkers to track differentiation of pluripotent stem cells [RNA-Seq]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that may be indicative for differentiation capacity, as well as lineage-specific differentiation scores to monitor either directed differentiation, or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.

overall_design: 3 iPSC lines were differentiated into the three germ layer with directed differentiation. Additionally, cells (4 cell lines) were also used to generate embryoid bodies (EBs) for undirected differentiation (4 and 7 days). DNA and RNA was isolated for Illumina Methylation BeadChips and RNA-seq.

first: Marco

last: Schmidt

first: Kira

last: Zeevaert

first: Mohamed

middle: H

last: Elsafi Mabrouk

first: Roman

last: Goetzke


title: Epigenetic biomarkers to track differentiation of pluripotent stem cells [methylation array]

type: Methylation profiling by genome tiling array

last: Mabrouk


title: Epigenetic biomarkers to track differentiation of pluripotent stem cells


title: In vivo genome editing using novel AAV-PHP variants rescues motor function deficits and extends survival in a SOD1-ALS mouse model

city: Cambridge

first: Maria

middle: I.

last: Zavodszky

state: MA

address: 225 Binney Street

institute: Biogen

summary: CRISPR-based gene editing technology represents a promising approach to deliver therapies for inherited disorders, including amyotrophic lateral sclerosis (ALS). Toxic gain-of-function superoxide dismutase 1 (SOD1) mutations are responsible for ~20% of familial ALS cases. Thus, current clinical strategies to treat SOD1-ALS are designed to lower SOD1 levels. Here, we utilized AAV-PHP.B variants to deliver CRISPR-Cas9 guide RNAs designed to disrupt the human SOD1 (huSOD1) transgene in SOD1G93A mice. A one-time intracerebroventricular injection of AAV.PHP.B-huSOD1-sgRNA into neonatal H11Cas9 SOD1G93A mice caused robust and sustained mutant huSOD1 protein reduction in the cortex and spinal cord, and restored motor function. Neonatal treatment also reduced spinal motor neuron loss, neuromuscular junction (NMJ) denervation and muscle atrophy, diminished axonal damage and preserved compound muscle action potential throughout the lifespan of treated mice. SOD1G93A treated mice achieved significant disease-free survival, extending lifespan by more than 110 days. Importantly, a one-time intrathecal or intravenous injection of AAV.PHP.eB-huSOD1-sgRNA in adult H11Cas9 SOD1G93A mice, immediately before symptom onset, also extended lifespan by at least 170 days. We observed substantial protection against disease progression demonstrating the utility of our CRISPR editing preclinical approach for target evaluation. Our work not only uncovered key parameters (e.g., AAV capsid, Cas9 expression) that resulted in improved efficacy compared similar approaches but can also serve to accelerate drug target validation.

overall_design: Comparative gene expression profiling to quantify SOD1 suppression and off-target effects following AAV-PHP.B-U6-sgSOD1-5 treatment of a HeLa cell line stably expressing the CRISPR Cas9 nuclease. Total number of samples: 40. Samples were collected at two timepoints: 48 and 72 hrs post-transduction. There were three treatment groups: (1) untransduced, (2) transduced with sgLACZ (1000K MOI), (3) transduced with sgSOD1-5 (1000K MOI). Each treatment group had four biological replicates. In addition, samples from treatment groups 1 and 2 had two technical replicates, each.

first: Yi

middle: A

last: Chen

first: Mark

middle: W

last: Kankel

first: Sam

last: Hana

first: Shukkwan

middle: K

last: Lau

middle: I

first: Olivia

last: McKissick

first: Nicole

last: Mastrangelo

first: Jessica

last: Dion

first: Bin

last: Wang

first: Dan

last: Ferretti

first: David

last: Koske

first: Sydney

last: Lehman

first: Kathryn

last: Koszka

first: Patrick

last: Cullen

first: Helen

last: McLaughlin

first: Mei

last: Liu

first: Eric

last: Marshall

first: Attila

last: Fabian

first: Galina

last: Marsh

first: Stefan

last: Hamann

first: Michael

last: Craft

last: Sebalusky

first: Moore

last: Arnold

first: Rachelle

last: Driscoll

first: Adam

last: Sheehy

last: Luo

first: Sonia

last: Manca

first: Chao

last: Sun

first: Kirsten

last: Sigrist

first: Alexander

last: McCampbell

first: Christopher

last: Henderson

first: Shih-Ching

last: Lo


title: M2-like macrophages in the injured-kidney cortex promoted kidney cancer progression via the direct pro-tumor effect and the inhibition of CD8 T cell infiltration

city: Tokyo

first: Taisuke

last: Ishii

address: 7-3-1 Hongo, Bunkyo-ku

department: Division of Nephrology and Endocrinology

institute: The University of Tokyo

summary:
In this study, we aimed to evaluate the effect of M2-like macrophages in the injured kidney on kidney cancer progression.
As an acute kidney injury to chronic kidney disease model, we used unilateral ischemia-reperfusion injury (uIRI).
And we inoculated RenCa cells, which are murine kidney cancer cell line, into renal subcapsule 14 days after uIRI (uIRI-Can) and compared uIRI-Can to RenCa cells inoculated into sham-operated renal subcapsule (Sham-Can) 20 days after inoculation.
To identify gene characteristics of M2-like macrophages that are commonly detected both in the uIRI kidney cortex and uIRI-Can, we sorted Ly6Clow macrophages from 4 groups, uIRI kidney cortex, sham kidney cortex, uIRI-Can, and Sham-Can, and conducted RNA-Seq.
This study revealed the characteristic gene expression of M2-like macrophages which were commonly detected in the injured kidney cortex and kidney cancer progressed on the injured kidney. And this could be a future therapeutic target of macrophage-targeted therapy.

overall_design: Using cell sorter, Ly6Clow macrophages were sorted from uIRI-Can, Sham-Can, uIRI kidney cortex, and sham kidney cortex.   And total RNA-seq was conducted to detect the feature of gene expression of uIRI-Can and uIRI kidney cortex compared to Sham-Can and sham kidney cortex, respectively.


title: Mitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate post-mitotic gene reactivation. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the significance and importance of their bookmarking function. Here, we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover an unexpected redundancy among members of the protein superfamily of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly the most rapidly and strongly reactivated ones. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.

overall_design: ES cells were arrested in mitosis and the binding profile of Nr5a2 analysed by ChIP-seq and compared to asynchronous ells. Mitotic cells were also release into the next interphase with or without Esrrb/Nr5a2 degradation for RNA-seq analysis 20, 30, 40, 50, 60, 90 and 120' post-release. All experiments were done in triplicates.


title: RNA-seq analysis identifies differentially expressed genes regulated by PM2.5 exposure on HNEpC cells

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of  Human Nasal Epithelial Cells (HNEpC) (C-12620, PromoCell, Heidelberg, Germany) after exposure to PM2.5 for 24 hours.

overall_design: Comparison of mRNA expression profiles between PM2.5 exposed HNEpC cells and control cells.

first: Weitian

last: Zhang


title: Transcriptome analysis of piperonylic acid-treated, Meloidogyne graminicola-inoculated rice roots [6 and 24h after treatment]

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

country: Belgium

institute: Ghent University

summary: We used mRNA sequencing to study the effects of foliar piperonylic acid treatment on the transcriptome of rice plants (cv. Nipponbare) and infection by M. graminicola to gain insights in the molecular basis of piperonylic acid-induced disease resistance against this nematode

overall_design: mRNA sequencing of the root systems of rice seedlings treated with piperonylic acid or a mock treatment 13 days post transplantation

first: Tina

last: Kyndt


title: Comparative transcriptome analysis of rice roots treated with the resistance inducers piperonylic acid, acibenzolar-S-methyl and beta-aminobutyric acid

summary: We used mRNA sequencing to study the effects of foliar treatment with piperonylic acid, acibenzolar-S-methyl or beta-aminobutyric acid on the root transcriptome of rice plants (cv. Kitaake) in order to find conserved systemic responses to distinct resistance-inducing stimuli

overall_design: mRNA sequencing of the root systems of rice seedlings treated with piperonylic acid, beta-aminobutyric acid, acibenzolar-S-methyl or a mock treatment


title: m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast [pho92D_ime4D]

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate correct translation and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae cells. Wild type, PHO92 deletion or IME4 deletion cells were used for RNA-Seq libraries, respectively.

first: Radhika

last: Varier

first: Theodora

last: Sideri

first: Harshil

last: Patel

middle: J


title: m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast [ime1D_ndt80D]

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae cells. Wild type, IME1 deletion or NDT80 deletion cells were used for RNA-Seq libraries, respectively.


title: Transcriptome analysis of piperonylic acid-treated, Meloidogyne graminicola-inoculated rice roots

overall_design: mRNA sequencing of the root systems of rice seedlings treated with piperonylic acid or a mock treatment 7 and 13 days post transplantation and inoculated with M. graminicola 14 days post transplantation


title: m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast [iCLIP_miCLIP-seq]

summary: During meiosis, in Saccharomyces cerevisiae, N6-methyladenosine (m6A) modified transcripts are induced, of which the function is unknown. Here, we uncover the role of the m6A reader Pho92. Cross-linking immunoprecipitation (CLIP) revealed that Pho92 associates with meiotic mRNAs in both m6A dependent and independent manner. Incidentally, Pho92 resides in the nucleus during early meiosis and associates with nascent RNAs, which is mediated through its interaction with Paf1C. Transcripts bound by Pho92 show elevated translational efficiency while cells lacking Pho92 display a small, but notable, increase in mRNA levels but not in protein levels, suggesting role of Pho92 in translation and decay. We show that Pho92 associates with ribosomes where it promotes the decay of m6A modified transcripts, contingent on active translation and the CCR4-NOT complex. We propose that m6A reader Pho92 is loaded co-transcriptionally to promote translation and subsequent decay fate of m6A modified transcripts, which ensures gamete fitness.

overall_design: iCLIP and miCLIP analysis of Saccharomyces cerevisiae cells entering meiosis. iCLIP was performed for Pho92 and Gis2 tagged cells. To indentify m6A depending binding we used wild type and ime4 deletion mutant for the analysis. miCLIP was performed in WT and ime4 deletion strain.

first: Charlotte

last: Capitanchik


title: miR from peripheral blood mononuclear cells' (PBMCs') exosome

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: The results (significance versus foldchange) showed 183 up- and 195 downregulated miR in the oxygen-glucose deprivation-PBMCs compared to normoxic PBMCs

overall_design: The comparison of isolated exosome miRNA from peripheral blood mononuclear cells conditioned media between normoxic condition and oxygen-glucose deprivation.

first: Yutaka

last: Otsu

first: Masato

last: Kanazawa


title: m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast.

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

overall_design: Refer to individual Series


title: m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast [Polysome]

overall_design: RNA-Seq analysis of mRNAs from total fraction and  polysome bound fraction in Saccharomyces cerevisiae cells entering yeast meiosis. We comapred the wild type to Pho92 deletion mutant.


title: The IL32/BAFF axis supports prosurvival dialog in the lymphoma ecosystem and is disrupted by NIK inhibition

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: We demonstrated that the microenvironment-dependent secretion of IL32β was controlled by the CD40L/NFKB2 axis whereas its tumor specificity was the consequence of IL32 promoter hypomethylation in MCL. Through the secretion of IL32β, the tumor was able to corrupt its microenvironment through the polarization of monocytes into specific MCL-associated macrophages, which in turn favor tumor survival. We next highlighted that while IL32β-stimulated macrophages secreted several protumoral factors, they supported tumor survival through a soluble dialog, mostly driven by BAFF. Finally, we demonstrated the efficacy of selective NIK/alternative-NFkB inhibition to counteract both microenvironment-dependent induction of IL32β and BAFF-dependent survival of MCL cells.

overall_design: RNA from monocytes, monocyte-derived macrophages (Mf) and T cells stimulated with (rh)IL32β (100 ng/ml) for 24H were extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends. Triplicat made for each cell type.

first: Salome

last: Decombis

first: Antonin

last: Papin

first: Celine

last: Bellanger

first: Clara

last: Sortais

first: Christelle

last: Dousset

first: Yannick

last: Le Bris

first: Thiphanie

last: Riveron

first: Stéphanie

last: Blandin

first: Philippe

last: Hulin

first: Benoit

last: Tessoulin

first: Mathieu

last: Rouel

first: Steven

last: Le Gouill

first: Agnes

last: Moreau-Aubry

first: Catherine

last: Pellat-Deceunynck


overall_design: Peripheral Blood (PB) MCL cells  were separated from other mononuclear cells using anti-human CD19-conjugated magnetic beads  with purity >90%. For comparison with normal naive CD5+ B cells, cord blood B cells (NBC) were isolated and cultured using the same protocol. MCL and CD5+ B cells were cultured with growth factors (interleukin-10 [IL10]: 50 ng/mL, B-cell activating factor [BAFF]: 50 ng/mL, insulin-like growth factor-1 [IGF1]: 10 ng/mL, interleukin-6 [IL6]: 1 ng/mL) on adherent CD40L-expressing cells  for 7 days.


title: Transcriptomic analysis of Xanthomonas campestris pv. campestris wild type vs two mutant

city: Nanning

first: Yan-Hua

last: Qi

state: China

address: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of L

institute: Guangxi university

summary: To gain an understanding of the regulatory role of PilG and PilH in Xcc a set of global gene expression profiles,we performed transcriptome analysis.Transcriptome analyses that showed PilG and PilH regulating many genes involved chemotaxis and flagellar biosynthesis.Taken this data together it is clear the impact of PilG and PilH on the expression of specific genes at the transcriptional level accounts for the phenotypes seen in the ΔpilG and ΔpilH strains.

sample_organism: Xanthomonas campestris pv. campestris str. 8004

overall_design: Two biological replicates from control and two  mutants were analyzed one day after the inoculation in NYGB (a total of 6 samples).

first: Li

last: Huang

first: Guo-Fang

last: Liu

first: Ming

last: Leng

first: Guang-Tao

last: Lu


title: RNA-seq analysis of differentially expressed genes in response to Neocarzinostatin and Hydrogen Peroxide

city: Minneapolis

first: Eric

last: Batchelor

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: In this study we identified differentially expressed genes in hTERT-HPNE cells in response to two distinct cellular stressors over time.  1) Neocarzinostatin induced DNA double strand breaks and 2) Oxidative stress induced through hydrogen peroxide treatment.  Using these data sets we identified specific genes involved in differential cell fate determination in response to these stresses.

overall_design: 400 ng/ml NCS treatment and 300 uM hydrogen peroxide treatment for 0, 4, 8, and 24 hours

first: Ryan

middle: L

last: Hanson


title: Multimodal measurement of the transcriptome and proteome in single cells using nanoSPLITS

status: Public on Dec 05 2022

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

summary: We report the development of a method (nanoSPLITS) capable of performing global proteome and transcriptome measurements from the same single-cell.

overall_design: RNAseq and scRNAseq data of mouse C10 cells treated with RO-3306 or untreated after nanoSPLITS.

middle: M

first: Meng

last: Markillie

first: Hugh

middle: D

last: Mitchell

first: Kristin

last: Engbrecht

first: William

middle: B

last: Chrisler

first: Ying

last: Zhu


title: Mir-130a potentiates the reparative properties of human endothelial colony forming cells facing hypoxia via VEGFR2 and STAT3

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

summary: Hypoxia controls reparative angiogenesis. MiRNAs are master regulators of gene expression in hypoxia and angiogenesis. However, we do not yet have a clear understanding of how hypoxia-induced miRNAs modulate vasoreparative processes. Here, we identify miR-130a as a mediator of the hypoxic response in human primary endothelial colony forming cells (ECFCs), a well-characterized subtype of endothelial progenitor. Under hypoxic conditions, miR-130a overexpression enhances ECFC pro-angiogenic capacity in vitro and potentiates their vasoreparative properties in vivo. Mechanistically, miR-130a orchestrates upregulation of VEGFR2, activation of STAT3-dependent transcription, and accumulation of HIF1α via translational inhibition of DDX6. These findings unveil a new role for miR-130a in hypoxia, whereby it modulates the VEGFR2/STAT3/HIF1α axis to increase the vasoregenerative capacity of ECFCs.

overall_design: hypoxia response in ECFCs

first: Jasenka

last: Guduric-Fuchs

first: Reinhold

last: Medina


title: CIRBP safeguards against chemotherapeutics-induced cardiac apoptosis and cardiotoxicity via dampening OGF/OGFR signal

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

summary:
Background: Albeit with well-recorded cytoprotective function, the study of stress protein CIRBP coping with cardiotoxicity during chemotherapy remains obscured. Here we report that CIRBP plays a critical role in safeguarding against chemo-induced cardiac apoptosis and dysfunction.
Methods: Treating the immortalized human ventricular myocytes (T0519) and neonatal rat ventricular myocytes (NRVMs) with three regular chemotherapeutics (DOX/Cisplatin/5-FU), and DOX-induced cardiotoxic mouse model were leveraged to explore the cardioprotection of CIRBP during chemotherapy. We took advantage of AAV9 carrying CIRBP or shCIRBP expressive cassette under cTNT promoter to interfere with cardiac CIRBP expression. A conjoint analysis of transcriptomics and proteomics was performed within T0519 to identify the latent effector of CIRBP in regulating cardiomyocyte apoptosis. By contrast with the pan-opioid receptor Alvimopan (ALV), OGFR blocker Naltrexone (NTX) was introduced to disrupt CIRBP-OGFR signaling in an attempt to provide new insight in formulating efficacious cardioprotective scheme for tumor patients.
Results: We discovered that CIRBP deficiency is involved in in-vivo and in-vitro cardiomyocyte apoptosis triggered by chemotherapeutic agents. Ectopic delivery of CIRBP in mouse myocardium significantly mitigates doxorubicin-induced cardiac apoptosis and malfunction. Opioid growth factor receptor (OGFR) was further highlighted as CIRBP downstream effector responsible for cardiomyocyte chemotherapeutical apoptosis. Mechanistically, CIRBP interacts with OGFR mRNA and represses OGFR expression by reducing mRNA stability. CIRBP-mediated cytoprotection against doxorubicin-induced apoptosis relies largely on the regulation of CIRBP on OGFR. Naltrexone, an antagonist targeting OGFR of potency as well as certain opioid receptors, successfully rescues CIRBP ablation-rendered susceptibility to cardiac apoptosis and dyshomeostasis when exposed to DOX; while another antagonist Alvimopan, merely acting on opioid receptors, does not.
Conclusions: Taken together, our results demonstrate that CIRBP confers myocardium resistance to chemotherapy-induced cardiac apoptosis and dysfunction via dampening OGF/OGFR axis, shedding new light on the cardioprotection of tumor patients subjected to chemotherapy.

overall_design: Three mRNA profiles of NC and CIRBP knockdown in Immortalized human cardiomyoctes (T0519)

first: Cihang

first: Xiaolei

last: Cheng

first: Junyue

last: Xing

first: Jun

last: Li


title: Fabrication of hard tissue using dental cells derived from hiPSCs

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

summary: To analyze the transcriptomic differences between hiPSC and hiPSC-derived dental epithelial cells (hDEC), and between hiPSC and hiPSC-derived dental mesenchymal cells (hDMCs)

overall_design: Comparative gene expression profiling analysis of RNA-seq data between hiPSC and hDECs, and between hiPSC and hDMCs

first: Eun-Jung

last: Kim


title: Differential gene expression of human periodontium-derived mesenchymal stem cells

city: Bangkok

first: Supreda

middle: Suphanatachat

last: Srithanyarat

address: 34 Henri-Dunant Rd. Pathumwan District

department: Periodontology

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

summary: Mesenchymal stem cells (MSCs)  isolated from human gingival tissue and periodontal ligament (PDL)  have shown potential for periodontal regeneration. Although PDL-MSCs have been recognized as the best choic for cell-based periodontal regeneration, isolation of PDL-MSCs required tooth extraction which is impractical for clinical use. Supracrestal gingival connective tissue (SG) is a part of gingival tissue which located closely to PDL and can be harvested without tooth extraction. Here, the characteristics of MSCs derived from SG was evaluated. Differential gene expression profiles of hSG-MSCs, hPDL-MSCs, and human marginal gingival tissue (MG)-derived MSCs were compared.  Results demonstrated that hSG-MSCs had a more similar gene expression profile to the hPDL-MSCs than the hMG-MSCs, suggested a potential candidate cell source of SG for future peridontal tissue engineering.

overall_design: hSG-MSCs, hPDL-MSCs, hMG-MSCs from 5 subjects were cultured in complete medium. Total RNA of each cell type was isolated and RNA sequencing was performed. Differential gene expression and pathway enrichment was also performed.

first: Thanaphum

last: Osathanon

first: Manutsanun

last: Choosiri

first: Nppadol

last: Sa-Ard-IIam


title: Selective inhibitors of autophagy reveal new link between the cell cycle and autophagy and lead to discovery of novel synergistic drug combinations

city: New York City

first: Agata

last: Kurowski

state: NY

address: 1180 5th Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: Autophagy is a conserved metabolic pathway that is central to many diseases. Recently, there has been a lot of interest in targeting autophagy with small molecule inhibitors as a possible therapeutic strategy. However, many of the compounds used for autophagy are non-selective. Here, we explored the inhibition of autophagy in pancreatic cancer cells using established selective small molecule inhibitors and discovered an unexpected link between the autophagy pathway and progression through the cell cycle. RNA-Seq analysis revealed that treatments with inhibitors that have different autophagy pathway targets block cell replication and activate other metabolic pathways to compensate for the blockade in autophagy. An unbiased screen looking for known drugs that might synergize with autophagy inhibition revealed new combination treatments that might provide a blueprint for therapeutic approaches to pancreatic cancer. The drugs quizartinib and THZ1 showed a strong synergistic effect in pancreatic cells with autophagy inhibition.

overall_design: Biological triplicates of treated PANC-1 cells with two different selective autophagy inhibitors, ULK100 and VPS34in1 and DMSO treated cells as control.

first: Kisa

last: Sung

first: Carisse

last: Lansiquot

first: Kanny

last: Wan

first: Samarjit

last: Patnaik

first: Martin

last: Walsh

first: Michael

last: Lazarus


title: Operon complexity in Rhodobacter capsulatus revealed by integration of dRNA-seq and RNA-seq data

city: St John's

first: Marc

middle: Patrick

last: Grüll

state: Newfoundland

address: 230 Elizabeth Ave

institute: Memorial University of Newfoundand

summary: We report a complex operon architecture for R. capsulatus: operons with multiple TSSs and TTSs, genomic regions of high transcriptional activity and novel transcripts. In addition, we present a new 5' and 3' targeted sequencing method for the Ion Torrent PGM. TEX+ and TEX- indicates if the dRNA-seq library was treated with Terminator 5'-Phosphate-Dependent Exonuclease or not. Treatment with TEX degrades every RNA that does not have a 5'-PPP.

sample_organism:
Rhodobacter capsulatus SB 1003
Rhodobacter capsulatus DE442

overall_design: Prediction of transcriptional units and  analysis of operon complexity

middle: P

first: Lourdes

last: Peña-Castillo

last: Mulligan

first: Andrew

last: Lang


city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Transcriptomic analysis of DSG2-W2A mouse heart tissue. In DSG2-W2A mice, adhesion of the desmosomal molecule desmoglein-2 (DSG2) is abrogated via mutation of its’ major interaction mechanism (so-called "tryptophan swap" (Harrison, Brasch et al. 2016)). Adult DSG2-W2A mut/mut mice resemble the phenotype of Arrhythmogenic Cardiomyopathy (ACM or ARVC) with biventricular fibrosis, impaired systolic output function and arrhythmia. This phenotype was present in mutant mice analysed at the age of 9 weeks compared to 5-days old hearts, which showed no morphological alterations.

overall_design: Ventricular mRNA profiles of 5-day and 9-weeks old wild type (wt) and Dsg2-W2A homozygouse mutant (mut) mice

first: Volker

last: Spindler

first: Camilla

last: Schinner

first: Florian

last: Geier


title: long read RNA-seq from adrenal gland (ENCSR295PVQ)

status: Public on Dec 04 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ENC4_227 - B6Cast F1 PND25_Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection [RNA-seq]

city: San Diego

first: Edgar

middle: Mauricio

last: Barajas-Mora

address: 9500 Gilman Dr, La Jolla, CA

department: Molecular BIology

institute: UCSD

summary: Antigen receptor loci are organized into variable (V), diversity (D), and joining (J) elements that rearrange to generate diverse antigen receptor repertoires. Here, we identified an enhancer (E34) in the immunoglobulin kappa locus (Igκ) that instructed rearrangement of Vκ genes located in a sub-topologically associating domain (subTAD), including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. E34 promoted the deposition of active histone marks across the E34 subTAD to instruct its nuclear repositioning from a V(D)J recombination-repressive compartment to a permissive one. E34-induced nuclear repositioning of the E34 subTAD promoted Vκ-Jκ interactions assisted by enhancer-associated epigenetic marks and de novo CTCF binding. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. These data show how enhancer-instructed chromatin topology mechanically pulls specific Vκ and Jκ genes into close physical proximity to generate distinct antibody repertoires to combat bacterial infection.

overall_design: Examination of histone modification, RNA, chromatin accesibility, CTCF binding, and chromatin conformation in pre-B cell from wild-type and enhancer-deleted mice in the V gene region of the Igk locus.

first: Cornelis

last: Murre


title: long read RNA-seq from HL-60 (ENCSR278ZPI)

summary:
HL-60 derived M2A macrophages (12hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR280VKU)

summary:
5xFAD cortex het Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection [ATAC-seq]

overall_design: Examination of histone modification, RNA, chromatin accesibility, CTCF binding, and chromatin conformation in  the V-gene region of the Igk locus in pre-B cell from wild-type and enhancer-deleted mice.


title: long read RNA-seq from OCI-LY7 (ENCSR700SUP)

summary:
ENC4_503, ENC4_504 OCI-LY7 rep1 human non-Hodgkin lymphoma

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Randomized phase-1 trial of antigen-specific tolerizing immunotherapy with peptide/calcitriol liposomes in ACPA+ rheumatoid arthritis

city: Woolloongabba

first: Ranjeny

last: Thomas

address: 37 Kent St

institute: University of Queensland Diamantina Institute, Translational Research Institute

summary: Antigen-specific regulation of autoimmune disease is a major clinical research goal. In seropositive rheumatoid arthritis (RA), T cells help to autoreactive B cells matures the citrullinated antigen-specific immune response, generating RA-specific V-domain glycosylated anti-citrullinated (Cit) protein antibodies (VDG ACPA) before arthritis onset. Repeated low or escalating antigen doses administered under “sub-immunogenic” conditions generally favors tolerance. The aims of this study were to explore the safety, pharmacokinetics, immunological and clinical effects of s.c. DEN-181, comprising liposomes encapsulating self-peptide collagen II259-273 (CII) and NF-KB inhibitor 1,25-dihydroxycholecalciferol (calcitriol)

overall_design: scRNA-seq and scTCR-seq of CD45+ immune cells flow-sorted from PBMC of 4 participants in the clinical trial at day1 baseline and 28 days post-dosing (n=1 per dose level including placebo)

first: Amee

last: Sonigra

first: Hendrik

last: Nel

first: Pascale

last: Wehr

first: Nishta

last: Ramnoruth

first: Swati

last: Patel

first: Karin

last: van Schie

first: Max

last: Bladen

first: Ahmed

last: Mehdi

first: Joanne

last: Tesiram

first: Meghna

last: Talekar

first: Jamie

last: Rossjohn

first: Hugh

last: Reid

first: Frederik

middle: E

last: Stuurman

first: Helen

last: Roberts

first: Phillip

last: Vecchio

first: Ian

last: Gourley

first: Mark

last: Rigby

first: Stephane

last: Becart

first: Rene

last: Toes

first: Hans

middle: U

last: Scherer

first: Kim-Ahn

last: Cao

first: Kim

last: Campbell


title: PAS-seq from GM12878 (ENCSR275KDL)

first: ENCODE

last: DCC

summary:
GM12878 QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR271ULH)

summary:
ENC4_217 - B6Cast F1 PND4_Female 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptional control of cone photoreceptor diversity by a thyroid hormone receptor

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary:
Purpose: To define the cone photoreceptor diversity and underlying transcriptional controls in mouse retina
Methods: Individual retinal cone cells were isolated by micro-manipulator from dissociated pieces of superior/inferior retina from heterozygous (or homozygous) Thrb-b2Cre:Ai6 mice.  Single cell libraries were constructed for RNA-seq analysis.  Thrb-b2Cre;Rosa26-Sun1Gfp mice were used to isolate cone nuclei for ATAC-seq analysis.  Thrb-HAB mice were used to identify TRb2 genomic binding sites using ChAP-seq analysis.
Results: Developmental analyses of individual cones revealed a network of gradient genes.  Many of these gradient genes are regulated by TRb2, a thyroid hormone receptor that has been associated with color visual impairment.
Conclusions: The results suggest that TRb2 controls chromatin remodeling and transcriptional plasticity in the cone lineage to promote diversity.

overall_design: Derived a Thrb-b2Cre driver to isolate M and S opsin-enriched cones, which are distributed in counter-gradients over the mouse retina.

first: Aramaki

last: Michihiko

first: Wu

last: Xuefeng

first: Liu

last: Hong

first: Forrest

last: Douglas


title: long read RNA-seq from adrenal gland (ENCSR698DOB)

summary:
ENC4_219 - B6Cast F1 PND10_Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from aorta (ENCSR700EBI)

summary:
W61 aorta ENC4_88

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from K562 (ENCSR917JIA)

summary:
OnT dRNA of K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection [Hi-C]

first: Edgar

last: Barajas-Mora

first: Cornelis

last: Murre


title: Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection

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

overall_design: Refer to individual Series


title: long read RNA-seq from HepG2 (ENCSR724HQB)

summary:
ONT dRNA of HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection [CUT&RUN]


title: long read RNA-seq from mucosa of descending colon (ENCSR997RFW)

summary:
ENC4_77 W76 mucosa of descending colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from H1 (ENCSR271KEJ)

summary:
LRGASP H1 ES

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Gene expression profile at single nuclei level of cerebellar neurons (Purkinje cells) and glia (Bergmann glia, velate astrocytes and oligodendrocytes) in a transenic mouse model of Spinocerebellar Ataxia Type 1 (SCA1)

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

summary: Cerebellar glia are affected in SCA1. We used single nuclei RNA sequencing (snRNA-seq) to analyze the gene expression changes in glia in response to neuronal dysfunction in SCA1.

overall_design: Cerebellar nuclei were isolated from 12 weeks old SCA1 mice and Wild type (WT) sex matched littermate controls and analyzed using snRNAseq.

first: Marija

last: Cvetanovic


title: long read RNA-seq from layer of hippocampus (ENCSR972DID)

summary:
ENC4_439, ENC4_440 hippocampus_B6Cast F1_2 months_male_5_ENC4_cDNA511

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from A673 (ENCSR989ZYL)

summary:
ENC4_509 , ENC4_510 A673 rep1 human Ewing sarcoma (bone or soft tissue sarcoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PAS-seq from F121-9 (ENCSR944IAR)

summary:
ES QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR964OKW)

summary:
ENC4_381a, ENC4_382a B6Cast F1 PND4_Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR942UFC)

summary:
adrenal gland BL6 male

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR938RPH)

summary:
ENC4_495, ENC4_496 heart_B6Cast F1 PND 2 months Female 03 heart_ENC4_cDNA607, cDNA608

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR930GRQ)

summary:
HL-60 derived M2A macrophages (24hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from PC-9 (ENCSR916JDV)

summary:
ENC4_501, ENC4_502 PC-9 rep1 human lung adenocarcinoma

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR926OGQ)

summary:
Hippocampus from 6 mo C57BL/6 male

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR920WYI)

summary:
ENC4_391a, ENC4_392a B6Cast F1 PND14 Females Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR909NPF)

summary:
ENC4_437, ENC4_438 hippocampus_B6Cast F1_2 months_female_6_ENC4_cDNA510

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR462COR)

summary:
RUSH brain E3348003

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR862DMK)

summary:
ENC4_465, ENC4_466 B6Cast F1 PND 2 months Male 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR437WYC)

summary:
ENC4_397a, ENC4_398a B6Cast F1 PND36_ Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR861RCH)

summary:
ENC4_467, ENC4_468 B6Cast F1 PND 2 months Female 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR893GCO)

summary:
ENC4_229 B6Cast F1 PND25_ Female 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cardiac atrium (ENCSR424QFN)

summary:
ENC4_60 W73 left cardiac atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR411ZHA)

summary:
Control hippo Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR842KTN)

summary:
ENC4_481, ENC4_482 heart_B6Cast F1 PND14 3x Males 03 heart_ENC4_cDNA593, cDNA_594

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR454ECK)

summary:
ENC4_223 - B6Cast F1 PND14_3x Males 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR410XGE)

summary:
ENC4_497, ENC4_498 heart_B6Cast F1 PND 18-20 months Male 03 heart_ENC4_cDNA609, cDNA610

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR845IUJ)

summary:
ENC4_401a, ENC4_402a B6Cast F1 PND 2 months_Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR885NRP)

summary:
ENC4_239 B6Cast F1 PND 18-20 months_Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR463IDK)

summary:
RUSH brain E5194210

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from posterior vena cava (ENCSR853YZN)

summary:
W71 posterior vena cava ENC4_101

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR402DOZ)

summary:
ENC4_389a, ENC4_390a B6Cast F1 PND14 Males Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR398SKD)

summary:
HL-60 derived M1 macrophages (72hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR818JQK)

summary:
ENC4_395a, ENC4_396a B6Cast F1 PND25_ Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR852HRM)

summary:
ENC4_237 - B6Cast F1 PND 2 months_Female 03 _Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR404AEI)

summary:
5xFAD hippo 8 mo Male

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left colon (ENCSR450GAR)

summary:
W73 left colon ENC4_87

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PAS-seq from H1 (ENCSR813AOB)

summary:
H1 QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR370BHF)

summary:
ENC4_403a, ENC4_404a B6Cast F1 PND 2 months_Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR791CDT)

summary:
ENC4_393a, ENC4_394a B6Cast F1 PND25_Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR375EOW)

summary:
ENC4_493, ENC4_494 heart_B6Cast F1 PND 2 months Male 03 heart_ENC4_cDNA605, cDNA606

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from MCF 10A (ENCSR813UIT)

summary:
ENC4_515, ENC4_516 MCF10A rep1 human female pre-neoplastic mammary epithelial cells

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from lower lobe of right lung (ENCSR323XND)

summary:
W78 lower lobe of right lung ENC4_83

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR754VEZ)

summary:
ENC4_387a, ENC4_388a B6Cast F1 PND10_Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PAS-seq from WTC11 (ENCSR322MWL)

summary:
WTC11 QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR267XBT)

summary:
ENC4_499, ENC4_500 heart_B6Cast F1 PND 18-20 months Female 03 heart_ENC4_cDNA611, cDNA612

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR791JQO)

summary:
ENC4_453, ENC4_454 B6Cast F1 PND14 3x Males 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR735IBE)

summary:
adrenal gland BL6 female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR734WEK)

summary:
ENC4_385a, ENC4_386a B6Cast F1 PND10_Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR697ASE)

summary:
RUSH brain E7948794

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR309XOR)

summary:
ENC4_240 - B6Cast F1 PND 18-20 months_Female 03 _Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from right cardiac atrium (ENCSR728TXV)

summary:
W76 right cardiac atrium ENC4_84

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR257YUB)

summary:
RUSH brain E4368365

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR316ZTD)

summary:
RUSH brain E6207143

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from psoas muscle (ENCSR243DYK)

summary:
W80 psoas muscle ENC4_86

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR690QHM)

summary:
RUSH brain E6341028

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR649MEZ)

summary:
ENC4_235 B6Cast F1 PND 2 months_Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR205QMF)

summary:
RUSH brain E5115600

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR242UEB)

summary:
ENC4_231 B6Cast F1 PND36_ Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR665XLM)

summary:
ENC4_221 - B6Cast F1 PND10_Female 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from endothelial cell of umbilical vein (ENCSR687RWI)

summary:
ENC4_505, ENC4_506 HUVEC rep1 primary human umbilical vein endothelial cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PAS-seq from endodermal cell (ENCSR198UNH)

summary:
H1-DE QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR223AZQ)

summary:
ENC4_407, ENC4_408 B6Cast F1 PND 18-20 months_Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR187TGD)

summary:
ENC4_483, ENC4_484 heart_B6Cast F1 PND14 3x Females 03 heart_ENC4_cDNA595, cDNA_596

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR169YNI)

summary:
RUSH brain E7461192

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from F121-9 (ENCSR172GXL)

summary:
LRGASP Mouse ES

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR631KNS)

summary:
ENC4_455, ENC4_456 B6Cast F1 PND14 3x Females 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR159ICU)

summary:
HL-60 derived M2A macrophages (72hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PAS-seq from layer of hippocampus (ENCSR147WNH)

summary:
Mouse hippocampus QuantSeq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR152PAT)

summary:
ENC4_443, ENC4_444 hippocampus_B6Cast F1_18 - 20 months_male_6_ENC4_cDNA515

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR628IMW)

summary:
ENC4_469, ENC4_470 B6Cast F1 PND 18-20 months Female 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR146ZFC)

summary:
ENC4_413, ENC4_414 hippocampus_B6CastF1_PND14_3x female_4,5,6_ENC4_cDNA497

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from endodermal cell (ENCSR127HKN)

summary:
LRGASP H1 definitive endoderm

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR121FDE)

summary:
HL-60 derived M1 macrophages (12hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR116DUT)

summary:
ENC4_405, ENC4_406 B6Cast F1 PND 18-20 months_Male Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR588IRT)

summary:
ENC4_399a, ENC4_400a B6Cast F1 PND36_Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from upper lobe of right lung (ENCSR096QUP)

summary:
ENC4_82 W78 upper lobe of right lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from Calu3 (ENCSR583KCB)

summary:
ENC4_513, ENC4_514 Calu-3 rep1 human non-small cell lung cancer (epithelial)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from astrocyte (ENCSR071IHY)

summary:
ENC4_207, ENC4_208 - PGP1 derived astrocytes

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR084MKR)

summary:
ENC4_233 - B6Cast F1 PND36_Female 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR583KAF)

summary:
HL-60 derived M1 macrophages (24hr)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR060OTU)

summary:
5xFAD hippo het Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from Caco-2 (ENCSR580IDG)

summary:
ENC4_511, ENC4_512 Caco-2 rep1 human colorectal adenocarcinoma (epithelial)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from cardiac septum (ENCSR549ELD)

summary:
W61 cardiac septum ENC4_92

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR550KPM)

summary:
ENC4_471, ENC4_472 B6Cast F1 PND 18-20 months Male 03 L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from HL-60 (ENCSR546DFO)

summary:
HL-60 derived M0 macrophages

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from left cerebral cortex (ENCSR131CES)

summary:
Control cortex Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR512EWP)

summary:
ENC4_215 B6Cast F1 PND4_Male 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from gastrocnemius (ENCSR524XLA)

summary:
ENC4_383a, ENC4_384a B6Cast F1 PND4_Female Gastrocnemius

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR026WRM)

summary:
ENC4_415, ENC4_416 hippocampus_B6CastF1_PND14_3x male_7,8,9_ENC4_cDNA499

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR530ZLE)

summary:
ENC4_225 - B6Cast F1 PND14_3x Females 03_Adrenals

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from layer of hippocampus (ENCSR472CHU)

summary:
ENC4_441, ENC4_442 hippocampus_B6Cast F1_18 - 20 months_female_6_ENC4_cDNA513

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from middle frontal area 46 (ENCSR094NFM)

summary:
RUSH brain E4368365

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from chondrocyte (ENCSR470HYQ)

summary:
ENC209, ENC210, ENC211 - H9 derived chondrocytes

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from mammary epithelial cell (ENCSR998KIZ)

summary:
ENC4_507, ENC4_508 HMEC rep1 primary human mammary epithelial cells

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from adrenal gland (ENCSR563RLX)

summary:
ENC4_29 W61 adrenal gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptome of soybean reproductive tissues from plants subjected to water deficit, heat stress and a combination of water deficit and heat stress.

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

institute: The Division of Plant Sciences and Technology

summary: Soybean plants were subjected to water deficit, heat stress, and combination of water deficit and heat stress. Flower parts, sepal, anther, ovary and stigma were collected from 8-10 different plants at R1 stage growing under three above mentioned stress conditions, and under control conditions 10 days after initiation of the stresses. Differential gene expression compared to control was studied using RNAseq method.

overall_design: Soybean plants (16-18 days old) were subjected to water deficit, heat stress, and combination of water deficit and heat stress and flower parts were collected in liquid nitrogen. Total RNA was isolated and mRNA profile were generated by deep sequencing using NovaSeq 6000 PE150.

first: Ranjita

last: Sinha

first: Sai

last: Induri

first: María

last: Peláez-Vico

first: Sidharth

last: Sen

first: Trupti

last: Joshi

first: Felix

last: Fritschi


title: long read RNA-seq from WTC11 (ENCSR507JOF)

first: ENCODE

last: DCC

summary:
LRGASP WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RNA sequencing of HUVECs stimulated with VEGF, OSM+VEGF, or CNTF+CNTFR+VEGF with or without STAT3 knock-down

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

summary: The role of STAT3 signaling  induced by stimulation of IL-6 cytokine family members such as OSM and CNTF on the angiogenic response of endothelial cells is still not fully understood. To assess the impact of this pathway on angiogenesis, this study compares human umbilical vein endothelial cells (HUVECs) with or without STAT3 knock-down introduced by siRNA and stimulation with VEGF, OSM+VEGF and CNTF+VEGF in the presence of the CNTF receptor (CNTFR).

overall_design: mRNA profiles of HUVECs stimulated with VEGF (n=4), OSM+VEGF (n=4), or CNTF+CNTFR+VEGF (n=4) for 24h transfected with control siRNA. The samples were compared to HUVECs transfected with STAT3 siRNA and incubated by the same cytokines for 24 (n=4 each).

first: Felicitas

last: Bucher


title: Intralesional TLR4 agonist treatment strengthens the organ defense against colonizing cancer cells in the brain

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

institute: Institute of Bioinformatics

summary: Brain metastasis in breast cancer remains difficult to treat and its incidence is increasing. Therefore, the development of new therapies is of utmost clinical relevance. Recently, toll-like receptor (TLR) 4 was correlated with IL6 expression and poor prognosis in 1 215 breast cancer primaries. In contrast, we demonstrated that TLR4 stimulation reduces microglia-assisted breast cancer cell invasion. However, the expression, prognostic value, or therapeutic potential of TLR signaling in breast cancer brain metastasis have not been investigated. We thus tested the prognostic value of various TLRs in two brain-metastasis gene sets. Furthermore, we investigated different TLR agonists, as well as MyD88 and TRIF-deficient microenvironments in organotypic brain-slice ex vivo co- cultures and in vivo colonization experiments. These experiments underline the ambiguous roles of TLR4, its adapter MyD88, and the target nitric oxide (NO) during brain colonization. Moreover, analysis of the gene expression datasets of breast cancer brain metastasis patients revealed associations of TLR1 and IL6 with poor overall survival. Finally, our finding that a single LPS application at the onset of colonization shapes the later microglia/macrophage reaction at the macro-metastasis brain-parenchyma interface (MMPI) and reduces metastatic infiltration into the brain parenchyma may prove useful in immunotherapeutic considerations.

overall_design: We collected samples from 17 patients with brain metastases and characterized them by RNA-Seq. To investigate the impact of TLRs, CCL2, and IL6 in brain metastasis patients, we correlated the expression levels of genes in the metastatic tissue with patient outcome using the gene expression data obtained by RNA-Seq.

first: Tobias

last: Pukrop

first: Raquel

last: Blazquez

first: Han

middle: N

last: Chuang

first: Britta

last: Wenske

first: Laura

last: Trigueros-Lopez

first: Renato

last: Liguori

first: Fulvia

last: Ferrazzi

first: Tommy

last: Regen

first: Martin

last: Proescholdt

first: Veit

last: Rohde

first: Markus

last: Riemenschneider

first: Christine

last: Stadelmann

first: Annalen

last: Bleckmann

first: Tim

last: Beißbarth

first: Denise

last: van Rossum

first: Uwe

last: Hanisch


title: Peripheral Blood Gene Expression Signatures in Patients with Rheumatoid Arthritis

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Observational study in cohort of patients with Rheumatoid Arthritis.

overall_design: Comparisons were made between active/inactive patients and those with and without current methotrexate treatment.

first: Nancy

last: Olsen

first: Rayford

last: June


title: Mettl3 regulates late retinogenesis

status: Public on Dec 02 2022

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

institute: Zhongshan Ophthlamic Center

summary: Mettl3 was conditionally knocked out from retinal progenitor cells. Metll3 deficient retinas exhibited disrupted cell cycle during late retinogenesis and abnormality in retinal architecture and physiology.

overall_design: 2 control and 2 Mettl3-conditional knockout retinas (from the same litter at postnatal day 7) were dissociated into single cells, and processed using 10X Genomics Chrominum to prepare scRNAseq libraries. 2 control retinas were mixed together as one control sample, and 2 mutant retinas were processed together as one mutant sample.


title: Mouse retina m6A epitranscriptome

status: Public on Dec 03 2022

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: m6A epitranscriptome of postnatal day 6 mouse retina was sequenced using MeRIP-seq.

overall_design: 40 p6 C57BL/6J mouse retinas were collected into TRIzol, and processed for MeRIP-seq.


title: Effects of substrate stiffness on the polarization states of murine bone marrow-derived neutrophils

city: Shanghai,

first: Ting

last: Jiang

address: Quxi Road No. 500

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: The substrate stiffness plays an important role in mediating the cellular behavior. Neutrophils predominate the early inflammatory response and initiate the regeneration. The neutrophil activation can be regulated by physical cues. However, it is not known how neutrophils respond to substrate stiffness, which is of significant importance in determining the outcomes of engineered tissue mimics. Herein, a three-dimensional culture system made of hydrogel for bone marrow-derived neutrophils was developed to explore the effects of varying stiffness (1.5, 2.6, and 5.7 kPa) on neutrophil phenotype and polarization states.

overall_design: Murine bone marrow-derived neutrophils were encapsuled and cultured in GelMA hydrogel with different stiffnesses (1.5, 2.6, and 5.7 kPa) for 2 days. Then the hydrogel was lysed and released the cells, which were collected. RNA was extracted and differential gene expression was examined by RNAsequencing. Three experimental groups were set up in this study accoding to the substrate stiffness: Low (1.5kpa), middle (2.6kpa), high (5.7kpa). The group Low was set as control. Three replicates of RNA samples per experimental group were analyzed.

first: Ningjuan

last: Ouyang

first: Guohua

last: Tang


title: Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer's disease

status: Public on Dec 01 2022

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: Alzheimer's disease (AD) is one of the neurodegenerative diseases and characterized by the appearance and accumulation of amyloid-β (Aβ) aggregates and phosphorylated tau with aging. We performed scRNAseq of immene cells in the brain from WT and AD mice.

overall_design: CD45+ immunce cells in the brain from C57BL/6J and APPNL-G-F mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Ryusei

last: Kaneko

first: Ako

last: Matsui


title: Gene expression profiling analysis of laryngeal cancer

city: Xi’an, Shaanxi Province

first: SHEN

last: YAN

address: NO. 98 West Fifth Road

institute: Xi’an Jiaotong University

summary:
To investigate the metabolic mechanisms of laryngeal cancer.
We then performed gene expression profiling analysis using data obtained from ten tumor tissue samples and ten nontumor tissue samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for laryngeal cancer and adjacent normal tissues.

first: Xin

last: Huang

first: Shen

last: Yan

first: Hongying

last: Ruan


title: Transcriptome analisys of scl28-3

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary: The Arabidopsis SCARECROW-LIKE28 transcription factor promotes progression through G2/M, modulates division plane orientation and promotes post-mitotic cell expansion. To define the networks regulated by SCL28, we performed transcriptome profiling of wild-type and scl28-3 root tips.

overall_design: Total RNA was isolated from root tips (∼2 mm) in three biological replicates from wild-type or scl28-3 plants using RNeasy plant mini kit (QIAGEN, http://www.qiagen.com). Approximately 300 root tips from 6-days-old plants were collected for each biologica replicate

middle: R

first: Camila

last: Goldy