title: Transcriptional changes over time during growth of Streptomyces venezuelae on MYM and MYMG

status: Public on Aug 19 2023

city: Hamilton

last: Shepherdson

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote different growth behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

overall_design: Streptomyces venezuelae mRNA profiles from two media conditions at three timepoints; two replicates each. Changes in gene expression compared using DeSeq2

first: Marie

middle: A

last: Elliot


title: IFN-λ signaling protects mice from severe HSV-1 skin disease

status: Public on Sep 11 2023

city: Chapel Hill

first: Drake

last: Philip

state: North Carolina

address: 104 Airport Drive

country: USA

institute: University of North Carolina-Chapel Hill

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Acute and long-term exercise adaptation of adipose tissue and skeletal muscle in humans: a matched transcriptomics approach after 8-week training-intervention

status: Public on Aug 09 2023

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary: The participants performed an 8-week supervised aerobic endurance exercise intervention program. Biopsies of both adipose tissue and skeletal muscle were collected at associated timepoints and a matched analysis was performed.

overall_design: We performed gene expression microarray analysis in human muscle biopsies from subjects after acute exercise before and after training interventions

first: Simon

middle: I

last: Dreher

first: Martin

last: Irmler

first: Olga

last: Pivovarova-Ramich

first: Katharina

last: Kessler

first: Karsten

last: Jürchott

first: Carsten

last: Sticht

first: Louise

last: Fritsche

first: Patrick

last: Schneeweiss

first: Jürgen

last: Machann

first: Andreas

middle: F

last: Pfeiffer

last: Hrabe de Angelis

middle: L

last: Birkenfeld

last: Peter

middle: M

last: Niess

first: Cora

last: Weigert

first: Anja

last: Moller


title: Investigating the role of Bax/Bak as a driver of inflammation in aging

status: Public on Aug 16 2023

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Senescent cells drive age-related tissue dysfunction partially via the induction of a chronic senescence-associated secretory phenotype (SASP). Mitochondria are major regulators of the SASP; however, the underlying mechanisms have not been elucidated. Mitochondria are often essential for apoptosis, a cell fate distinct from cellular senescence. During apoptosis, widespread mitochondrial outer membrane permeabilization (MOMP) commits a cell to die. Here, we find that MOMP occurring in a subset of mitochondria is a feature of cellular senescence. This process, called minority MOMP (miMOMP), depends on the formation of BAX and BAK macropores leading to the release of mitochondrial DNA (mtDNA) into the cytosol, which in turn activates the cGAS-STING pathway, a major regulator of the SASP. Importantly, we found that inhibition of MOMP in vivo decreases inflammatory markers and improves healthspan in aged mice. Our results reveal, unexpectedly, that apoptosis and senescence are regulated by similar mitochondrial-dependent mechanisms, and that sub-lethal mitochondrial apoptotic stress is a major driver of the SASP. We also provide proof-of-concept that inhibition of miMOMP-induced inflammation may be a new therapeutic avenue to improve healthspan.

overall_design:
Aged mice (20 months old) were treated with the Bax inhibitor, BAI1, three times a week for three months. The drug was delivered by IP injections.

(April 13, 2024) Update:  The old processed files were aggregated matrix using Cellranger aggr by combining two samples together. To make it more clear and easy to access, the processed data were updated with the matrix for each sample separately.

first: Stella

last: Victorelli

first: Nicholas

last: Pirius

first: Joao

last: Passos


title: Developmental self-reactivity determines the pathogenic Tc17 differentiation potential of naive CD8+ T cells by adjusting endogenous SMAD3 expression

status: Public on Aug 15 2023

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

summary: The differentiation of naive CD8+ T cells into effector cells is important for establishing immunity. However, the effect of heterogeneous naive CD8+ T cell populations is not fully understood. Here, we demonstrate that steady-state naive CD8+ T cells are composed of functionally heterogeneous subpopulations that differ in their ability to differentiate into type 17 cytotoxic effector cells (Tc17) in inflammatory disease models. The differential ability of Tc17 differentiation was not related to T-cell receptor (TCR) diversity and antigen specificity but was inversely correlated with self-reactivity acquired during development. Mechanistically, this phenomenon was linked to differential levels of intrinsic TCR sensitivity and basal SMAD3 expression, generating a wide spectrum of Tc17 differentiation potential within naive CD8+ T cell populations. These findings suggest that developmental self-reactivity can determine the fate of naive CD8+ T cells to generate functionally distinct effector populations and achieve immense diversity and complexity in antigen-specific T-cell immune responses.

overall_design:
To investigate the genomic characteristics of the three different naive CD8+ T cell subsets, CD5low Ly6C-, CD5hi Ly6C-, and CD5hi Ly6C+, we cultured each subset in Tc17 polarizing condition.
We then perfomed gene expression profiling analysis using data obtained from RNA-seq of each subset.

first: Gil-Woo

last: Lee

first: Sung-Woo


first: Johannes

last: Beckers

overall_design: We performed gene expression microarray analysis in human muscle biopsies from subjects before and after exercise training interventions

first: Simon

last: Dreher

first: Martin

last: Irmler

first: Olga

last: Pivovarova-Ramich

last: Kessler

last: Jürchott

last: Sticht


title: Effect of Trim21 knockdown on MAPK and ERBB signaling pathways

status: Public on Aug 08 2023

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

summary: To investigate Trim21 knockdown on the gene expression of downstream effectors of MAPK and ERBB pathways, we established HPAC cell lines with Trim21 knockdown.

overall_design: We then performed gene set analysis using data obtained from RNA-seq (Trim21 knockdown vs scramble)

first: Kian

last: Lim


title: Skin - Gut axis

status: Public on Aug 07 2023

city: San Diego

first: Tatsuya

last: Dokoshi

state: California

address: 9500 Gilman

department: Department of Dermatology

institute: Univeristy of California, San Diego

summary: Analysis of the gut single cell and spacial sequencing after skin HA digestion as a model of skin inflammation

overall_design: Control and skin HA digestion with or without DSS challenge


title: Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells

city: West Lafayette

first: Kyle

last: Cottrell

state: IN

address: 201 S University Street

department: Medicine

institute: Purdue University

summary: Sensing of double-stranded RNA (dsRNA) is an important component of innate immunity. Proteins like PKR and MDA5 recognize dsRNA and activate various pathways to fight viral infection. In addition to viral dsRNA, many endogenous RNAs containing double-stranded regions can be misrecognized as immunogenic. The RNA editing enzyme ADAR1, specifically its p150 isoform, has been shown to suppress activation of PKR and MDA5 through its A-to-I editing activity. While the cytoplasmic ADAR1-p150 isoform has been well established within this role, the functions of the nuclear ADAR1-p110 isoform are less understood. To address this knowledge gap, we utilized proximity labeling by APEX2 to identify putative ADAR1-p110 interacting proteins. We identified 110 proteins across three breast cancer cell lines that either interact with p110 or are within close proximity. Many of these proteins have known roles in RNA metabolism. Nine of the identified proteins belong to the DEAD or DEAH box families of RNA helicases, including DHX9. DHX9 is overexpressed in breast cancer, with expression closely correlated with that of p110. By co-immunoprecipitation we confirmed that p110 interacts with DHX9. Knockdown of DHX9 in several triple-negative breast cancer cell lines caused cell death and activation of the dsRNA sensor PKR. In two cell lines that are refractory to knockdown of ADAR1, the combined knockdown of DHX9 and ADAR1 caused a substantial increase in PKR activity, where knockdown of either alone had no effect. Knockdown of DHX9 and ADAR1 caused activation of the type I IFN pathway, RNase L and NF-KB signaling. Activation of these proteins and pathways was not seen with individual knockdown of ADAR1 or DHX9. Activation of PKR following combined knockdown of ADAR1 and DHX9 could be rescued by expression of p110, p150, DHX9, and catalytically inactive DHX9. Additionally PKR activation could be rescued by the dsRBM of DHX9, revealing an important role for dsRBMs in suppressing PKR activation. Together these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways.

overall_design: Gene expression analysis using RNAseq data from two cell lines (MCF-7 and SK-BR-3) transduced with shRNAs against ADAR1 or DHX9, alone or in combination. Two replicates for each condition.

first: Sua

last: Ryu

first: Jason

middle: D

last: Weber


title: A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella

status: Public on Aug 05 2023

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: Flagellum plays a crucial role in the invasion process of Salmonella, while also functioning as a significant antigen to trigger host pyroptosis. The regulation of flagella biogenesis is essential for both pathogenicity and immune escape of Salmonella. Here, we identified the conserved and unknown function protein STM0435 as a new flagellar regulator. ∆stm0435 strain exhibit higher pathogenicity in both cellular and animal infection experiments compared to wild-type Salmonella. Conjoint analysis of proteomics and transcriptomics demonstrated that almost all the ﬂagellar genes were dramatically increased in a ∆stm0435 strain compared to wild-type Salmonella. Microscale thermophoresis assay showed that the purified STM0435 protein bound c-di-GMP with a ~194 µM KD affinity. The crystal structures of  apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137 and D138 of STM0435 are essential for c-di-GMP binding. Mutant that is unable to bind to c-di-GMP loses its ability to regulate motility, indicating that STM0435 affected the Salmonella ﬂagellar biogenesis process by binding to c-di-GMP.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Salmonella typhimurium ATCC 14028s and Salmonella typhimurium ATCC 14028s (STM0435 knock-out),and each set has 3 repetitions .

first: Weiwei

last: Wang

first: Bingqing

last: Li

first: Yuanji

last: Dai

first: Ruirui

last: Liu


title: Analysis of the lncRNA 2610035D17rik interactions with other RNAs using RIP and RNAseq techniques.

city: Jupiter

first: Sathya

last: Puthanveettil

state: Florida

address: 120 Scripps way

department: Neuroscience

institute: UF Scripps Biomedical Research

summary: The goal of our study was to assess whether the lncRNA 2610025D17rik regulates the function of other RNAs throguh its direct interaction. To carry-out this we performed the RIP techniques using probes that includes de full sequence of this lncRNA and sequence the final products by RNAseq.

overall_design: Hippocampus from C57BL/6 male mice were isolated and the tissue was homogenized and incubated with biotenilated probes of sense and antisense sequenes of 2610035d17rik. After pull-down the complexes the RNA was isolated and send for sequencing.

first: I

last: Espadas Villanueva

first: S


title: Contextual fear conditioning induced transcriptional changes in hippocampal CA1 neurons

summary: The goal of our study was to assess whether the experience can regulate specific lncRNAs within the hippocampus and their role in associative memory. To address this, we carried out unbiased analyses of gene expression in CA1-hippocampal neurons to identify lncRNA changes induced by contextual fear conditioning (CFC).

overall_design: C57BL/6 male mice were placed in a contextual fear conditioning chamber for the following training: context+shock, shock alone, and context alone. One hour after training, brains were isolated and CA1 dissected using laser capture microdissection (LCM)


title: Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cell therapies have yielded durable clinical benefits for patients with cancer but have been accompanied by unexpected side effects of treatment, including neurotoxicity. Currently, we lack a comprehensive understanding of the mechanisms of toxicity observed in patients receiving cell therapies, including encephalitis caused by human herpesvirus 6 (HHV-6) that has been repeatedly reported. Here, via comprehensive viral RNA data mining, we examine the landscape of human latent viral reactivation, revealing that HHV-6B can become reactivated in human CD4+ T cells in standard in vitro cultures. Using single-cell sequencing, we identify a rare population of HHV-6 'super-expressors' (~1 in 360-10,000 cells) that possess high viral transcriptional activity in chimeric antigen receptor (CAR) T cell culture before spreading rapidly to infect other cells in vitro. Through the reanalysis of single-cell sequencing data from FDA-approved cell therapy products, we identify the presence of CAR+, HHV-6 super-expressor T cells in human patients in vivo. Together, our study implicates cell therapy products as the source of lytic HHV-6 repeatedly reported in clinical trialsand has broad implications for the design, screening, and interpretation of unexpected toxicities in cell therapies.

overall_design: In vitro T cells were stimulated with aCD3/aCD28 beads and cultured in IL2 over time before single-cell genomics were performed

first: Emma

last: Yin

first: Ansuman

last: Satpathy


title: Understanding differential expression of genes during EBV lytic cycle reactivation by employing high throughput RNA-sequencing

status: Public on Aug 03 2023

city: Kolkata

first: Samaresh

last: Malik

state: West Bengal

address: Street-358, Action Area-1, Newtown

department: Institute of Health Sciences

country: India

institute: Presidency University

summary: To understand the changes in global transcriptomic landscape during the EBV lytic cycle reactivation from lymphoblastoid cell lines (LCLs), RNA-seq was performed. By examining the transcriptomic changes, we obtained valuable insights into the molecular events and regulatory mechanisms involved in EBV reactivation into lytic cycle replication. The study also enhances our knowledge of the complex interplay between EBV and the host cells during its lytic cycle.

overall_design: EBV reactivation into lytic replication was induced by treating two LCL clones (LCL#1 and LCL#89) using sodium butyrate (3mM) and 12-O-tetradecanoylphorbol-13-acetate (TPA; 20ng/ml). Total RNA was isolated 48 and 72 h post-treatment and subjected to cDNA preparation followed by RNA-Seq analyses using Ion S5 XL platform.

first: Abhik

last: Saha


title: Whole transcriptome analysis of EBV infected peripheral blood mononuclear cells (PBMCs)

summary: In order to gain insights into the intricate molecular alterations taking place following Epstein-Barr virus (EBV) infection in primary B-cells, we employed RNA-Seq to investigate the dynamic changes occurring within the cell transcriptome during the early stages of EBV infection (0, 2, and 4 days post infection).  By analysing the transcriptomic data generated, our objective was to find novel pathways and mechanisms that may play pivotal roles in the EBV-induced transformation of B-cells, particularly during early stage of B-cell activation.

overall_design: Peripheral blood mononuclear cells (PBMCs) were infected with wild type GFP-tagged EBV (B95.8 strain) and total RNA was isolated post 2 and 4 days of infection. Uninfected PBMCs were taken as experimental control.

first: Shatadru

middle: G

last: Roy


title: GM-CSF signaling strength determines opposing innate memory phenotypes at different stages of myelopoiesis

status: Public on Aug 01 2023

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

summary: Inflammatory responses must be tightly coordinated with the activation of emergency myelopoiesis to produce potent myeloid cells that fight infection without causing self-damage. Here we show that GM-CSF programs myeloid committed progenitors to produce trained macrophages (increased cytokine response), but programs the upstream non-committed LKS+ progenitors to produce tolerized macrophages (decreased cytokine response). In myeloid progenitors, GM-CSF strongly activates STAT5, ERK and Akt-mTOR signaling pathways which are essential to establish a training program, whereas in LKS+ progenitors GM-CSF induces NF-κB translocation to the nucleus to establish a tolerization program. These differences arise from higher GM-CSF receptor expression in myeloid progenitors compared to LKS+ cells. We demonstrate that β-catenin regulation of NF-κB nuclear translocation is central in this process. Glycogen synthase kinase 3 (GSK3) inactivation by strong ERK and PI3K-Akt signaling increases cytoplasmic β-catenin levels to block NF-κB nuclear translocation in myeloid progenitors. In contrast, when ERK and PI3K-Akt signaling is weak, active GSK3 decreases β-catenin to allow NF-κB nuclear translocation in LKS+ progenitors. Finally, GM-CSF-induced LKS+ tolerization can be reversed and takes place in several murine models of trained immunity and in human CD34+ CD38– progenitors. Our study reveals that in addition to activating myelopoiesis, GM-CSF also programs early and immediate myeloid progenitors to produce opposing immune memory phenotypes. We propose that the inflammatory response from immediate myeloid progenitors may be balanced by the tolerized phenotype of early progenitors, thus providing a mechanism for appropriate resolution of inflammation and protection against prolonged cytokine storm.

overall_design: 10X Genomics single-cell ATAC-seq from two murine hematopoietic stem cell populations (LKS progenitors and CD34+ myeloid progenitors) treated with two conditions for 24h (M-CSF and M-CSF + GM-CSF)

first: Paula

last: Guerrero

first: Cristina

last: Bono

first: María

last: Sobén

first: Andrea

last: Guiu

middle: J

first: M

last: Gil

first: Alberto

last: Yáñez


title: Resident microglia and infiltrating macrophages inflammatory, metabolic and sex-dependent gene-regulatory dynamics in the neonatal hippocampus after hypoxia-ischemia.

status: Public on Jul 26 2023

city: Solna

first: Daniel

last: Ramsköld

address: Solnavägen 9

department: Dept of Cell and Melecular Biology

country: Sweden

institute: Karolinska Institutet

summary: Neonatal hypoxia-ischemia (HI) is a major cause of perinatal death and long-term disabilities worldwide. Post-ischemic neuroinflammation, characterized by resident and infiltrating immune cells, plays a pivotal role in HI pathophysiology. However, the specific modulatory roles of resident microglia and blood-derived macrophages remain poorly understood. In the present study, we investigated the temporal dynamics of microglia (CX3CR1GFP/+) and infiltrating macrophages (CCR2RFP/+) in the hippocampi of mice subjected to HI at postnatal day (PND) 9. We reveal an increase of CX3CR1GFP+ resident cells in the injured hippocampi soon after HI, peaking at three days post injury. In contrast, infiltration of CCR2RFP/+ cells peaked one day after HI and gradually decreased over time. Transcriptomic signatures of CX3CR1GFP/+ and CCR2RFP/+ cells isolated from hippocampi showed a partial convergence at day 3, through cell type - specific dynamics. Using inflammatory pathway and transcription factor analyses, we identify a distinct post-ischemic response in CCR2RFP/+ cells characterized by differential gene expression in sensome, homeostatic, matrisome, lipid metabolic and inflammatory molecular signatures as consequence of HI. Finally, we identified a sexual dimorphism in CX3CR1GFP/+ cells, where microglia unique genes in males but not in females returned to homeostatic levels comparable to controls three days after HI. In conclusion, our results indicate that CX3CR1GFP/+ and CCR2RFP/+ cells have diverse roles in orchestrating the inflammatory cascade after HI, and that infiltrating macrophages drive post-ischemic inflammation.

overall_design: After 1 day or 3 days after experimentally induced hypoxia and ischemia, hippocampi were isolated and disassociated. CX3CR1GFP+/CD11b+ (resident microglia) and CCR2RFP+/CD11b+ cells (infiltrating macrophages) were selected by anti-CD11b magnetic beads and flow cytometry. As control, microglia were also collected from age-matched animals where hypoxia-ischemia was not induced.

first: Elena

last: Di Martino

first: Julianna

last: Kele


title: H3K27me3 ChIP-seq on 16 days after pollination endosperm of cultivated barley

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

summary: To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a chromatin immunoprecipitation of H3K27me3 followed by high-throughput sequencing (ChIP-seq) in barley endosperm at 16 days after pollination.

overall_design: The endosperm was manually dissected at 16 days after pollination, chromatin was immunoprecipitated with anti-H3K27me3 antibody, processed into the DNA libraries, and sequenced on an Illumina platform

first: Martin

last: Kovacik

first: Anna

last: Nowicka

first: Jana

last: Zwyrtková

first: Beáta

last: Strejčková

first: Isaia

last: Vardanega

first: Eddi

last: Esteban

first: Asher

last: Pasha

first: Kateřina

last: Kaduchová

first: Maryna

last: Krautsova

first: Marie

last: Červenková

first: Jan

last: Šafář

first: Nicholas

last: Provart

first: Rüdiger

last: Simon


title: Single-cell RNA sequencing reveals the transcriptomic characteristics of peripheral blood mononuclear cells in hepatitis B vaccine non-responders

status: Public on Jul 30 2023

city: lanzhou

first: xiao

middle: dong

last: xie

state: Gansu

address: 1 wujiayuan west street, qilihe district, lanzhou city

department: clinical laboratory

institute: The first people's hospital of Lan Zhou

summary:
The emergence of a vaccine against hepatitis B has proven to be an important
milestone in the prevention of this disease; however, 5%–10% of vaccinated
individuals do not generate an immune response to the vaccine, and its
molecular mechanism has not been clarified. In this study, single-cell RNA
sequencing was performed on peripheral blood mononuclear cells (PBMCs)
from three volunteers with a high immune response (HR) and three with no
immune response (NR) to the hepatitis B vaccine. We found that the antigenpresenting activity scores of various antigen-presenting cells, the mitogenactivated protein kinase (MAPK) pathway activity scores of naive B cells, and the cell activity scores of three types of effector T cells were significantly
decreased, whereas the cytotoxicity scores of CD3highCD16lowKLRG1high
natural killer T (NKT) cells were significantly increased in the NR group
compared with those in the HR group. Additionally, the expression levels of
some classical molecules associated with distinct signaling pathways—including
HLA-B, HLA-DRB5, BLNK, BLK, IL4R, SCIMP, JUN, CEBPB, NDFIP1, and TXNIP—
were significantly reduced in corresponding subsets of PBMCs from the NR
group relative to those of the HR group. Furthermore, the expression of several
cytotoxicity-related effector molecules, such as GNLY, NKG7, GZMB, GZMM,
KLRC1, KLRD1, PRF1, CST7, and CTSW, was significantly higher in
CD3highCD16lowKLRG1high NKT cells derived from non-responders. Our study provides a molecular basis for the lack of response to the hepatitis B vaccine,
including defective antigen presentation, decreased T cell activity, and reduced
IL-4 secretion, as well as novel insight into the role of NKT cells in the immune
response to the hepatitis B vaccine.

overall_design: Single-cell RNA sequencing was performed on peripheral blood mononuclear cells (PBMC) from 6 volunteers without any disease, including 3 volunteers with high immune response (HR) to hepatitis B vaccine (HBsAb >1000 mIU /ml) and 3 volunteers with no immune response (NR) to hepatitis B vaccine (HBsAb<10mIU/ml). HBsAb testing and sample collection were performed 1 month after hepatitis B vaccination according to the 0 , 1 , and 6 month schedule.

first: Meie

last: Zhao

first: Chunxia

last: Wang

first: Peiqiang

last: Li

first: Tao

last: Sun

first: Jing

first: Shasha

last: Zhang

first: Qinglong

last: Ma

first: Fengdie

first: Wenjing

last: Shi

first: Maoning

first: Yapeng

first: Yunyan

last: Pan

first: Hui

first: Xiaodong

last: Xie


title: Barley seed developmental series

first: Ales

last: Pecinka

summary: To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination.

overall_design: Three main seed tissues (embryo, endosperm, and seed maternal tissues) were manually dissected at five developmental time points 4, 8, 16, 24 and 32 days after pollination (DAP). 4 DAP embryo and 32 DAP seed maternal tissues samples were omitted due to their minute size and dry nature, respectively. The total RNA was extracted, processed into the polyA-enriched libraries, and sequenced on the Illumina platform.

first: Martin

last: Kovacik

first: Anna

last: Nowicka

first: Jana

last: Zwyrtková

first: Beáta

last: Strejčková

first: Isaia

last: Vardanega

first: Eddi

last: Esteban

first: Asher

last: Pasha

first: Kateřina

first: Maryna

first: Marie

first: Jan

first: Nicholas


title: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice

status: Public on Jul 31 2023

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of microglia from forced microglia turnover and control mouse brain

status: Public on Jul 25 2023

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: Microglia are important immune cells in the brain. Microglia undergo a series of alterations during aging and increase the susceptibility to brain dysfunctions. However, the characteristics of microglia during the aging process are not fully understood. In this study, we mapped transcriptional and epigenetic profiles of microglia from 3- to 24-month-old mice. We observed unexpected gender divergences and identified age-dependent microglia (ADEM) genes in the aging process. We then compared characteristics between microglial aging and activation. To dissect the function of aged microglia excluding the influence from other aged brain cells, we established an accelerated microglial turnover model without directly affecting other brain cells. By this model, we achieved aged microglia in non-aged brains and confirmed that aged microglia per se contribute to cognitive decline. Collectively, we provide a comprehensive resource to decode the aging process of microglia, shedding light on how microglia maintain brain functions.

overall_design: After 3 rounds of PLX5622-CD diet treatment (3xDR), microglia were purified for sequencing.

first: Yanxia

last: Rao

first: Xiaoyu


title: The effect of auxin exposure on the adult Drosophila transcriptome

city: Bloomington

first: Lesley

middle: Nicole

last: Weaver

address: 1001 E. 3rd Street

department: Biology

institute: Indiana University

summary: Auxin is used to induce transgene expression or degrade proteins in Drosophila. Here we exposed three different genotypes to 0 mM or 10 mM auxin and measured changes in gene expression for both males and females. We found that auxin exposure significantly alters the transcriptome of adult Drosophila in all genotypes tested.

overall_design: To test the affects of auxin on the transcriptome, we fed 4-5 day old adult Drosophila to 0 mM or 10 mM auxin for 48 hours. We then processed whole body samples for RNA extraction and sequencing.

middle: N


title: Chromatin profile of Anthoceros agrestis

status: Public on Nov 10 2023

city: Ikoma

first: Tetsuya

last: Hisanaga

state: Nara

address: Takayama 8916-5

country: Japan

institute: Nara Institute of Science and Technology

summary: Bryophytes comprise mosses, liverworts and hornworts. The chromatin landscapes of mosses and liverworts are different, leaving open the question regarding the identity of the chromatin landscape of all bryophytes. To address this question we profiled five chromatin marks using a model hornworts, Anthoceros agrestis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone marks H3K9me1, H3K27me1, H3K4me3, H3K36me3 and H3K27me3 as well as H3.

first: Frederic

last: Berger


title: Regulatory changes associated with the head to trunk developmental transition [RNA-seq]

status: Public on Jul 24 2023

city: Oeiras

first: Patrícia

last: Duarte

address: Rua da Quinta Grande

country: Portugal

institute: Instituto Gulbenkian Ciência

summary: To investigate the mechanisms involved in the switch from head to trunk development, we compared the transcriptome profile from the posterior epiblast region of wild type mouse embryos at embryonic day (E)7.5 and E8.5.

overall_design: RNA-seq analysis of the posterior epiblast of wild type mouse embryos at embryonic (E)7.5 and E8.5

first: Rion

middle: B

last: Correia

first: Ana

last: Nóvoa

first: Moisés

last: Mallo


title: CRISPR/Cas9 dropout screen in two glioblastoma stem cell lines  with a domain-focused sgRNA library targeting 1387 human proteins involved in epigenetic regulation.

status: Public on Jul 21 2023

city: London

first: Helene

last: Damhofer

address: 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

summary: Poor survival and lack of response to current treatment modalities in adult human glioblastomas is attributed to the persistence of a subpopulation of glioma stem cells (GSCs). To identify novel approaches to therapeutically target GSCs, we performed CRISPR/Cas9 knockout screens in GSCs and identified the kinase TAK1 as an important selective survival factor in 50% of the tested GSCs. In sensitive cells, knockout of TAK1 leads to induction of caspase-dependent apoptosis via the RIPK1/Caspase 8/FADD complex due to constitutive, low-level secretion of tumor necrosis factor alpha (TNF-a) and stimulation of TNF receptor 1. Furthermore, we show that expression of genes involved in immune signaling and a mesenchymal signature predict the sensitivity and response of GSCs to TAK1 inhibition. In summary, we have identified TAK1 as a new therapeutic target for mesenchymal GBM and a potential gene signature for selection of patients benefitting from TAK1 targeted therapy.

overall_design: The domain-focused epigenetic sgRNA library was used in lentiviral pooled format to transduce Cas9-BSD expressing glioma stem cell lines (G166 and U3013) at ∼500-fold representation of the library at an MOI of 0.3. Two days after transduction, 1–2 μg/ml puromycin was added for 5 days. A portion of cells was harvested as day 0 time point after selection was completed. The rest of the cells were then passaged to maintain 500-fold representation and cultured for an additional 35–38 days (eight to ten cell doublings). During the screening period antibiotic selection for Cas9 and sgRNA expression was maintained at 2.5 μg/ml blasticidine and 0.5 μg/ml puromycin, respectively. Each screen was performed in two biological replicates. Drop-out of sgRNAs over the culture period was determined by comparing abundance of sgRNAs  between day 35 (G166) or day 38 (U3013) and day 0 by next-generation sequencing.

first: Kristian

last: Helin


title: TAK1 inhibition leads to RIPK1-dependent apoptosis in immune-activated cancers


title: Regulatory changes associated with the head to trunk developmental transition


title: Regulatory changes associated with the head to trunk developmental transition [ATAC-seq]

summary: To investigate the mechanisms involved in the switch from head to trunk development, we compared the chromatin accessibility profile from the posterior epiblast region of wild type and Raldh2 mutant mouse embryos

overall_design: ATAC-seq analysis of the posterior epiblast of wild type and Raldh2 mutant mouse embryos


title: Baseline RNA-sequencing data of 12 glioblastoma stem cell lines sensitive or resistant to TAK1 inhibition

overall_design: Comparative gene expression profiling analysis of baseline RNAseq data from 12 glioblastoma stem cell lines determined to be sensitive or restistant to TAK1 inhibition


title: Integrative methylome and transcriptome analysis reveals that Fusobacterium nucleatum promotes the expression of JAK3 in laryngeal cancer

status: Public on Jul 04 2023

city: shanghai

first: Xiaohui

last: Yuan

state: shanghai

address: 83 fenyang road

institute: Eye & ENT Hospital of Fudan University

type: Methylation profiling by genome tiling array


title: The subacromial bursa regulates rotator cuff tendon healing and is a target to augment tendon repair.

status: Public on Jul 07 2023

first: Stavros

last: Thomopoulos

state: NY

institute: Columbia University

summary: Rotator cuff injuries result in over 500,000 surgeries performed annually, an alarmingly high number of which fail. These procedures typically involve repair of the injured tendon and removal of the subacromial bursa. However, recent identification of a resident population of mesenchymal stem cells and inflammatory responsiveness of the bursa to tendinopathy indicate an unexplored biological role of the bursa in the context of rotator cuff disease. Therefore, we aimed to understand the clinical relevance of bursa-tendon crosstalk, characterize the biologic role of the bursa within the shoulder, and test the therapeutic potential for targeting the bursa. Proteomic profiling of patient bursa and tendon samples demonstrated that the bursa is activated by tendon injury. Using a rat to model rotator cuff injury and repair, tenotomy-activated bursa protected the intact tendon adjacent to the injured tendon and maintained the morphology of the underlying bone. The bursa also promoted an early inflammatory response in the injured tendon, initiating key players in wound healing. In vivo results were supported by targeted organ culture studies of the bursa. To examine the potential to therapeutically target the bursa, dexamethasone was delivered to the bursa, prompting a shift in cellular signaling towards modulating inflammation in the healing tendon. In conclusion, contrary to current clinical practice, the bursa should be retained to the greatest extent possible and provides a new therapeutically target for improving tendon healing outcomes.

overall_design: This study identified the role of the subacromial bursa in rotator cuff response to injury via the retention or removal of the subacromial bursa in rotator cuff injury setting. Rat rotator cuff tendon injury (supraspinatus tenotomy) were performed with or without subacromial bursectomy (removal of the subacromial bursa). The resulting bilateral supraspinatus tendons and remaining subacromial bursa were dissected for RNA-sequencing at 3 or 14 days post-operation. There were n=6 replicates per timepoint. Control bursa and supraspinatus tendon from non-operative rats were included for a non-injurious control; supraspinatus tendon samples were also internally controlled per rat.

first: Brittany

middle: P

last: Marshall

first: Beth

last: Ashinsky

first: Xavier

middle: E

last: Ferrer

first: Jennifer

last: Kunes

first: Astia

middle: C

last: Innis

first: Andrew

last: Luzzi

first: Lynn

last: Forrester

first: Kevin

last: Burt

first: Andy

last: Lee

first: Lee

last: Song

first: Lauren

last: Lisiewski

first: Rajesh

middle: K

last: Soon

first: Clark

middle: T

last: Hung

first: William

last: Levine

first: David

last: Kovacevic


title: Single-cell RNA-sequencing from stroma in a mouse submandibular salivary gland following 5-day deligation or control homeostatic

status: Public on Jul 01 2023

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

summary: The submandibular salivary gland stroma makes up only a small portion of the total salivary gland and the stromal response to salivary gland injury has been understudied. We used single-cell RNA-sequencing (scRNAseq) to analyze which cell types are present in deligated and homeostatic salivary glands, how the cell type abundance is altered during regeneration, and how the transcriptome of those cells is being altered. This will allow us to examine which cell types are important contributors torecovery from salivary gland ductal ligation injury.

overall_design: Submandibular salivary glands were dissociated into single cells followed by two rounds of magnetic activated cell sorting (MACs) to deplete for epithelial cells expressing EpCAM and red blood cells expressing Ter119. The samples then went through one round of dead cell removal using Miltenyi dead cell removal kit.

first: Amber

last: Altrieth

first: Suarez

last: Emily

first: Gabunia

last: Sergo

first: Deirdre

last: Nelson


title: Glutamine synthetase regulates the alternative metabolism of γ-aminobutyrate in oral squamous cell carcinoma

status: Public on Jul 06 2023

city: Lishui

first: Ming

middle: Guo

last: Cao

address: No 01, Rd Xueyuan Avenue

institute: Lishui University

summary: More than 90% of cancer cases in head and neck region are oral squamous cell carcinoma. Recent studies identified several tumor-specific metabolites for the screening or diagnosis of OSCC patients. However, the metabolic reprogramming of OSCC is not well understood. Here, we compared the metabolites between cancerous and paracancerous tissues of OSCC patients and investigated the metabolism of γ-aminobutyrate in OSCC derived cells. Our data revealed that the increase of γ-aminobutyrate was promoted by the synthesis of glutamate beyond the mitochondria, which was regulated by glutamine synthetase. This study is not only benefit for understanding the pathological mechanisms of OSCC, but also has application prospects for the diagnosis and therapy of OSCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CA-13 cells and PA-35 cells.

first: Shi-Lian

last: Wu

first: Guang-Yu

last: Zha

first: Ke-Bin

last: Tian

first: Jun

last: Xu

first: Ming-Guo


title: Transcriptome analysis reveals that Fusobacterium nucleatum promotes the expression of JAK3 in laryngeal cancer

first: Xiaohui

last: Yuan

summary: We perform an analysis of  transcriptome to understand the etiological mechanisms of F. nucleatum in laryngeal cancer.

overall_design: After laryngeal cancer cells were cocultured with F. nucleatum, whole genome-wide methylation and transcription were analyzed using DNA methylation arrays and RNA sequencing.


title: Trackable Intratumor Microdosing and Spatial Profiling Provide Early Insights into Activity of Investigational Agents in the Intact Tumor Microenvironment

status: Public on Jun 28 2023

city: Seattle

first: Rich

middle: A

last: Klinghoffer

state: WA

address: 530 Fairview Ave N

institute: Presage Biosciences

summary: Purpose: Cancer drug development is currently limited by a paradigm of preclinical evaluation that does not adequately recapitulate the complexity of the intact human tumor microenvironment (TME). To overcome this, we combined trackable intratumor microdosing (CIVOTM) with spatial biology readouts to directly assess drug effects in patient tumors in situ.  Patients and Methods: In a first-of-its-kind Phase 0 clinical trial, we explored the effects of an investigational stage SUMOylation Activating Enzyme (SAE) inhibitor, subasumstat (TAK-981) in 12 patients with head and neck carcinoma (HNC). Patients scheduled for tumor resection received percutaneous intratumor injections of subasumstat and vehicle control 1 to 4 days prior to surgery, resulting in spatially localized and graded regions of drug exposure (~1000-2000 microns in diameter). Drug-exposed (n=214) and unexposed regions (n=140) were compared  2  by GeoMx Digital Spatial Profiler, with evaluation at single cell resolution in a subset of these by CosMx Spatial Molecular Imager.  Results: Localized regions of subasumstat exposure revealed SUMO pathway inhibition, elevation of Type I interferon (IFN-I) response, and inhibition of cell cycle across all tumor samples. Single cell analysis by CosMx demonstrated cell cycle inhibition specific to the tumor epithelium, and IFN pathway induction commensurate with a TME shift from immune- suppressive to immune-permissive.  Conclusions: Pairing CIVO with spatial profiling enabled detailed investigation of response to subasumstat across a diverse sampling of native and intact TMEs. We demonstrate that drug mechanism of action can be directly evaluated in a spatially precise manner in the most translationally relevant setting: an in situ human tumor.

overall_design:
Total 354 areas of interest (AOIs) from 9 Head and Neck Carcinomas were sequenced using Digital Spatial Profiling (DSP) using GeoMX Nanostring, with the Cancer Transcriptome Altas (1812 genes). AOIs were asssessed for drug (subasumstat) exposure using MIL113 staining allowing comparison of drug exposed to non exposed AOIs.

*** FASTQ raw data files have been requested. ***

first: Jonathan

last: Derry

first: Connor

last: Burns

first: Jason

last: Frazier

first: Richard


title: An analysis of DNA methylome to understand the etiological mechanisms of F. nucleatum in laryngeal cancer

summary: After laryngeal cancer cells were cocultured with F. nucleatum, whole genome-wide methylation was analyzed using DNA methylation arrays.

overall_design: Bisulphite converted DNA from the 6 samples (Control group and F. nucleatum group) were analyzed on the Illumina Infinium MethylationEPIC(850K) BeadChip


title: Reduced CD8 T cell exhaustion in DR4 risk subjects is selectively augmented with therapy [whole blood]

status: Public on Jun 30 2023

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Exhausted CD8 T cells (TEX) are associated with worse outcome in cancer yet better outcome in autoimmunity. However, factors contributing to reduced TEX in autoimmunity are poorly  understood. We use two genetically related autoimmune diseases, type 1 diabetes (T1D) and rheumatoid arthritis (RA), to explore these factors. We identify a common human peripheral blood TIGIT+KLRG1+ CD8 TEX population: TIGIT+KLRG1+ CD8 TEX of healthy controls (HC), T1D, and rheumatoid arthritis (RA) subjects share EOMES signature genes, are increased with age and in chronic viral-specific cells and are hyporesponsive in vitro. Consistent with a genetic determinant, TIGIT+KLRG1+ TEX are stable within but vary between individuals. In HC and RA subjects (n>100/cohort), lower levels of EOMES transcriptional modules and TIGIT+KLRG1+ TEX were associated with RA HLA risk alleles (DR0401, 0404, 0405, 0408, 1001) even when considering disease status and CMV seropositivity. TIGIT+KLRG1+ TEX   significantly increased in RA HLA risk but not non-risk subjects treated with abatacept (CTLA4Ig); no change in TIGIT+KLRG1+ TEX was observed with adalimumab (anti-TNF) therapy. The DR4 association and selective modulation with abatacept suggests that therapeutic modulation of TEX may be more effective in DR4 subjects and TEX may be indirectly influenced by cellular interactions that are blocked by abatacept.

overall_design: Whole blood samples from seropositive RA patients and matched healthy controls

first: S

last: Long

first: Virginia

middle: S

last: Muir

first: Britta

last: Jones

first: Valerie

middle: Z

last: Wall

first: Katharina

last: Lambert

first: Alyssa

last: Ylescipidez

first: Stephan

last: Pribitzer

first: Jerill

last: Thorpe

first: Bryce

last: Fuchs

first: Alice

last: Wiedeman

first: Megan

last: Tatum

first: Hannes

last: Uchtenhagen

first: Cate

last: Speake

first: Bernard

last: Ng

first: Alexander

last: Heubeck

first: Troy

middle: R

last: Torgerson

first: Adam

last: Savage

first: Michael

last: Maldonado

first: Neelanjana

last: Ray

first: Vadim

last: Khaychuk

first: Jinqi

last: Liu

first: Peter

last: Linsley

first: Jane

middle: H

last: Buckner


title: Reduced CD8 T cell exhaustion in DR4 risk subjects is selectively augmented with therapy.

first: Stephanie

last: Osmond


title: A novel viral tool designed with enhancer-driven gene expression (EDGE) technology allows specific labelling of cell types in wild type rodents

status: Public on Sep 14 2023

city: Trondheim

first: Stefan

last: Blankvoort

address: Olav Kyrresgt 9

department: Kavli Institute for systems Neuroscience

country: Norway

institute: NTNU

summary: The mammalian brain contains an unimaginable number of neurons, who are all intricately connected to form complex neuronal circuits. Neurons that exhibit similar properties are often defined as belonging to the same cell-type, which can be determined for example by analysing the genetic profile of the cells. A key aspect of studying brain function on a circuit level is the ability to target specific cell types, but this necessitates sophisticated molecular and genetic tools. Here, we contribute to the ever-expanding toolkit of genetic targeting approaches, by utilizing Enhancer-Driven Gene Expression (EDGE) technology to create viral tools that allow specific targeting of cell populations in the hippocampus and parahippocampus of wild type mice. We also demonstrate the applicability of our tool in wild type rats, emphasising the versatility of this technology in cross-species studies. Cell-type specific targeting in wild type animals is something that could be of great benefit to the field, also in other species than mice where transgenic lines are not common.

overall_design: Bulk ChIP-seq against H3K27Ac for several brain regions, analyzed to find region specific putative enhancers

first: Maria

middle: L

last: Potenza

first: Miguel

middle: M

last: Carvalho

first: Joachim

last: Grimstvedt

first: Valentina

last: Di Maria

first: Rajeevkumar

last: Nair

first: Marcus

last: Flatset

first: Qiangwei

last: Zhang

first: Kristian

last: Moan

first: Francois

last: Pauzin

first: Laurent

middle: F

last: Thomas

first: Giulia

last: Quattrocolo

first: Clive

last: Bramham

first: Menno

last: Witter

first: Clifford

middle: G

last: Kentros


title: Gene expression changes in collagen10a1 (col10a1) medaka mutants

status: Public on Jun 26 2023

city: Singapore

first: Wen Hui

last: Tan

address: 14 Science Drive 4

country: Singapore

institute: National University of Singapore

summary: To elucidate molecular mechanisms contributing to the disease phenotype in col10a1 medaka (Oryzias latipes) mutants, we isolated col10a1:nlGFP cells from heterozygous col10a1 medaka mutants and wild-type siblings via fluorescence activated cell sorting (FACS) and performed RNA-seq. Comparison of the transcriptome profiles indicated elevated ER stress, dysregulated cell polarity and reduced ECM production in heterozygous col10a1 mutants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for col10a1:nlGFP-expressing cells in col10a1 medaka mutants and wild-type siblings. Two biological replicates were analyzed for heterozygous col10a1 mutants and three biological replicates were analyzed for wild-type siblings.

first: WenHui

first: Christoph

last: Winkler


title: Reduced CD8 T cell exhaustion in DR4 risk subjects is selectively augmented with therapy [CD8s]

first: Stephanie

last: Osmond

overall_design: KLRG1+/TIGIT+ partially exhausted CD8 T-cells and KLRG1-/TIGIT- CD8 T-cells were profiled from healthy individuals, individuals with type 1 diabetes, and individuals with renal cell carcinoma (RCC). Gene expression of KLRG1+/TIGIT+ partially exhausted CD8 T-cells from healthy individuals specific for flu or CMV antigens were also sorted using tetramers and profiled.

first: S

last: Long

first: Virginia

last: Muir

first: Britta

last: Jones

first: Valerie

last: Wall

first: Katharina

last: Lambert

first: Alyssa

last: Ylescipidez

first: Stephan

last: Pribitzer

first: Jerill

last: Thorpe

first: Bryce

last: Fuchs

first: Alice

last: Wiedeman

first: Megan

last: Tatum

first: Hannes

last: Uchtenhagen

first: Cate

last: Speake

first: Bernard

last: Ng

first: Alexander

last: Heubeck

first: Troy

last: Torgerson

first: Adam

last: Savage

first: Michael

last: Maldonado

first: Neelanjana

last: Ray

first: Vadim

last: Khaychuk

first: Jinqi

last: Liu

first: Peter

last: Linsley

first: Jane

last: Buckner


title: PRMT9-catalyzed SF3B2 methylation regulates RNA splicing and synapse development

status: Public on Aug 27 2023

city: Philadelphia

first: Yuanyuan

last: Wang

state: PA

address: 3720 Chestnut St, Apt 709

institute: UCLA

summary: Human genome encodes nine protein arginine methyltransferases (PRMT1–9), which catalyze three types of arginine methylation: monomethylation (MMA), asymmetric dimethylation (ADMA), and symmetric dimethylation (SDMA). These modifications can alter protein-protein and protein-nucleic acid interactions and play critical roles in transcription regulation and RNA metabolism. A few years ago, we characterized the newest member of the PRMT family–PRMT9 as a SDMA modifying enzyme and identified the splicing factor SF3B2 as its methylation substrate, linking its function to pre-mRNA splicing. However, the biological function of PRMT9 and the molecular mechanism by which PRMT9-catalyzed SF3B2 arginine methylation regulates pre-mRNA splicing remain largely unknown. Here, by charactering an intellectual disability patient-derived PRMT9 mutation (G189R) and establishing a Prmt9 conditional knockout (cKO) mouse model, we uncovered an important function of PRMT9 in neuronal development. We found that G189R mutation completely abolishes PRMT9 methyltransferase activity and destabilizes the protein by promoting its ubiquitination and proteasome degradation. PRMT9 loss in hippocampal neurons alters RNA splicing of ~1800 transcripts, which likely account for the abnormal synapse development and impaired learning and memory observed in the Prmt9 cKO mouse. Mechanistically, we discovered a critical protein-RNA interaction between the arginine 508 (R508) of SF3B2, the site that is exclusively methylated by PRMT9, and the pre-mRNA anchoring site, a cis-regulatory element located upstream of the branch point sequence (BPS). Additionally, we provide strong evidence that supports SF3B2 being the major and likely only substrate of PRMT9, thus highlighting the conserved function of PRMT9/SF3B2 axis in pre-mRNA splicing regulation.

overall_design: To identify differentially expressed and differentially spliced genes regulated by PRMT9, we performed RNA-seq analysis with polyA+ RNA samples prepared from age and gender matched littermates of wild type control and Prmt9 knockout mouse hippocampus tissues. Each group contains RNA samples from hippocampus of three individual mouse.

first: Lei

last: Shen

first: Xiaokuang

last: Ma

first: Zhihao

first: Yi

last: Zhang

first: Dimitri

last: Lin

first: Tharindumala

last: Abeywanada

first: Swanand

last: Hardikar

first: Taiping

last: Chen

first: Dalia

last: Barsyte-Lovejoy

first: Shenfeng

last: Qiu

last: Xing

first: Yanzhong

last: Yang


title: Precision RNAi using synthetic shRNAmir target sites

city: Vienna

first: Florian

last: Andersch

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

summary: Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient, inducible, and reversible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

overall_design: Quant-seq of RKO and HT-1080 human cell lines transduced with ARTi.6570, ARTi.6634, ARTi.6786 artificial short-hairpin RNA constructs or with empty vector control (+/- trametinib treatment) in biological triplicates.

first: Thomas

last: Hoffman

first: Alexandra

last: Hörmann

first: Maia

last: Corcokovic

first: Jakub

last: Zmaikovic

first: Matthias

last: Hinterndorfer

first: Jasko

last: Salkanovic

first: Fiona

last: Spritzer

first: Anna

last: Köferle

first: Katrin

last: Gitschtaler

last: Popa

first: Sarah

last: Oberndorfer

first: Michaela

last: Feller

first: Jan

last: Ruppert

first: Paolo

last: Chetta

first: Melanie

last: Wurm

first: Johannes

last: Zuber

first: Ralph

last: Neumüller


title: ChIP_Seq analysis in cultured hTSCs

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

summary: To detect the direct target genes of H4K20me1, H4K20me3, and H3K36me3  in hTSCs, hTSCs are collected and subjected to ChIP-Seq. After aligned to human hg38 by HISAT2, peaks are called by MACS2. Our results show that methylation of H4K20 mediated by PR-SET7 as the key regulator of hTSCs, indicating the essential role of  PR-SET7. This ChIP-Seq data provides fundamental information for our further physiological study of  PR-SET7.

overall_design: ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.


title: Function of CHG methylation dynamics in rice male gametogenesis

status: Public on Jun 24 2023

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

type: Methylation profiling by high throughput sequencing

summary: In this work, we analyzed DNA methylation in rice male meiocyte, microspore and sperm and studied the function of a set of chromatin regulators during the process. The results indicate that that DNA methylation remodeling started after meiosis of the male meiocytes and that non-CG, particularly CHG, methylation is dynamically remodeling during rice male gametogenesis. The work reveals distinct function of DNA methyltransfesaes and histone demethylase in the remodeling of CHG methylation and suggests that the CHG methylation remodeling has functional significance for male gametogenesis and fertilization.

overall_design: Germ cells were obtained by micromanipulation. DNA methylation and transcriptome libraries were constructed by scBS-seq and scRNA-seq techniques. In addition, a seedling DNA methylation library was constructed by directly extracting whole genome DNA.

first: Xue

last: Li

first: Bo

last: Zhu


title: MSK1 is required for the beneficial synaptic and cognitive effects of enriched experience across the lifespan

status: Public on Jun 20 2023

city: coventry

first: daniel

last: hebenstreit

address: gibbet hill rd

institute: university of warwick

summary: Positive experiences, such as social interaction, cognitive training and physical exercise, have been shown to ameliorate some of the harms to cognition associated with ageing. Animal models of positive interventions, commonly known as environmental enrichment, strongly influence neuronal morphology and synaptic function and enhance cognitive performance. While the profound structural and functional benefits of enrichment have been appreciated for decades, little is known as to how the environment influences neurons to respond and adapt to these positive sensory experiences. We show that adult and aged male wild-type mice that underwent a 10-week environmental enrichment protocol demonstrated improved performance in a variety of behavioural tasks, including those testing spatial working and spatial reference memory, and an enhancement in hippocampal LTP. Aged animals in particular benefitted from enrichment, performing spatial memory tasks at levels similar to healthy adult mice. Many of these benefits, including in gene expression, were absent in mice with a mutation in an enzyme, MSK1, which is activated by BDNF, a growth factor implicated in rodent and human cognition. We conclude that enrichment is beneficial across the lifespan and that MSK1 is required for the full extent of these experience-induced improvements of cognitive abilities, synaptic plasticity and gene expression.

overall_design: to examine the influence of experience and MSK1 on hippocampal gene expression in aged mice housed in standard or enriched conditions

first: Lorenzo

last: Morè

first: Lucia

last: Privitera

first: Daniel

middle: D

last: Cooper

first: Marianthi

last: Tsogka

first: J

last: Simon

first: C

last: Arthur

first: Bruno

last: Frenguelli


title: Tomato exocarp-specific promoter screen by RNA-seq of tomato cultivar Alisa Craig  exocarp, mesocarp and leaf

city: Guangzhou

first: Xue-Ming

last: Ruan

address: College of Life Sciences, Sun Yat-sen University, 135 Xingang West Road, Guangzhou

department: School Of Life Sciences

institute: Sun Yat-sen University

summary: In order to find the specific promoter of tomato exocarp, we extracted RNA extraction from the red ripe exocarp, red ripe mesocarp, mature green  exocarp,  mature green exocarp and leaf cells, and then performed RNA seq to find the differential genes from the Transcriptome data. Our data provides gene expression data for three tissues of tomato during the red ripe and mature green stages, laying the foundation for the search for differential genes

overall_design: We extracted RNA extraction from the red mature exocarp, red mature mesocarp, green mature exocarp, green mature exocarp and leaf cells, and then performed RNA seq to find the differential genes from the Transcriptome data.

first: Xue-ming

first: Jian-feng


title: Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [scRNAseq_Female]

status: Public on Jun 13 2023

city: San Francisco

first: Steven

middle: Anthony

last: Cincotta

address: 35 Medical Center Way

institute: UCSF

summary: While physiologic stress has long been known to impair mammalian reproductive capacity through hormonal dysregulation, mounting evidence now suggests that stress experienced prior to or during gestation may also negatively impact the health of future offspring. Rodent models of gestational physiologic stress can induce neurologic and behavioral phenotypes that persist for up to three generations, suggesting that stress signals can induce lasting epigenetic changes in the germline. Treatment with glucocorticoid stress hormones is sufficient to recapitulate the transgenerational phenotypes seen in physiologic stress models. These hormones are known to bind and activate the glucocorticoid receptor (GR), a ligand-inducible transcription factor, thus implicating GR-mediated signaling as a potential contributor to the transgenerational inheritance of stress-induced phenotypes. Here we demonstrate dynamic spatiotemporal regulation of GR expression in the mouse germline, showing expression in the fetal oocyte as well as the perinatal and adult spermatogonia. Functionally, we find that fetal oocytes are intrinsically buffered against changes in GR signaling, as neither genetic deletion of GR nor GR agonism with dexamethasone altered the transcriptional landscape or the progression of fetal oocytes through meiosis. In contrast, our studies revealed that the male germline is susceptible to glucocorticoid-mediated signaling, specifically by regulating RNA splicing within the spermatogonia, although this does not abrogate fertility. Together, our work suggests a sexually dimorphic function for GR in the germline, and represents an important step towards understanding the mechanisms by which stress can modulate the transmission of genetic information through the germline.

overall_design: To interrogate the role of the glucocorticoid receptor (GR) in female germ cells, we performed single cell RNA-seq on germ cells following genetic deletion of GR. To generate the GR deletion allele, mouse strain Nr3c1tm1.1Jda harboring a floxed allele of GR exon 3 was crossed to β-actin cre mice (Tmem163Tg(ACTB-cre)2Mrt) to generate a heterozygous deletion of GR. Mice with heterozygous deletion of GR were crossed to OCT4-GFP mice (Tg(Pou5f1-EGFP)2Mnn) to facilitate germ cell labeling. As the GR deletion allele is homozygous lethal at birth, mice were maintained as heterozygotes, and crossed to each other to generate embryos with homozygous deletion of GR for the experiment. To enrich for germ cells, fetal ovaries from GR deletion and WT controls were collected at E15.5, pooled according to genotype (n=2 GR deletion embryos, n=4 WT embryos), and were digested and FACS sorted for the OCT4-GFP transgene. OCT4-GFP positive germ cells were mixed back in with sorted OCT4-GFP negative somatic cells at a ratio of 60:40, and samples were submitted for single cell RNA-seq using the 10X Illumina platform.

first: Diana

middle: J

last: Laird


title: Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [TAGseq_KO_ALL]

overall_design: To investigate the role of glucocorticoid signaling in female germ cells, we performed RNA-seq on germ cells of the ovary following genetic deletion of the glucocorticoid receptor (GR). To generate embryos homozygous for the GR knockout allele (GR KO/KO), heterozygous females (GR KO/+) were crossed to heterozygous males also carrying an Oct4-GFP transgene (GR KO/+ ; Tg:Oct4 GFP/GFP) to facilitate FACS sorting of germ cells.  To generate embryos with a conditional deletion of GR (GR cKO/cKO), females homozygous for an exon 3 floxed GR allele (GR flox/flox) were crossed to similar males that were also heterozygous for the germ cell specific Oct4CreERT2 allele (GR flox/flox ; Oct4CreERT2+ ; Tg:Oct4 GFP/GFP). Pregnant dams were injected at E10.5 with 125 μg / g tamoxifen to induce recombination and deletion of GR exon 3 specifically in the germ cells. For both full body knockout and GR conditional deletion models, pregnant dams were dissected the morning of E17.5, genotyped, and Oct4 GFP+ germ cells were FACS sorted from individual embryos prior to performing low input 3' Tag-Seq.


title: Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [RNAseq_DEX_Female]

overall_design: To investigate the role of glucocorticoid signaling in female germ cells, we performed RNA-seq on germ cells and somatic cells of the ovary following administration of the glucocorticoid receptor agonist, dexamethasone (dex). Pregnant dams were dosed by IP with 10 μg dex / gram (or saline vehicle) at E12.5, E13.5, E14.5, and E15.5. Ovaries were harvested at E15.5, and germs cells (OCT4-GFP positive) and somatic cells (OCT4-GFP negative) were FACS sorted prior to performing bulk RNA-seq.


title: Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling [RNAseq_DEX_Male]

overall_design: To investigate the role of glucocorticoid signaling in male germ cells, we performed RNA-seq on germ cells and somatic cells of the testis following administration of the glucocorticoid receptor agonist, dexamethasone (dex). Pregnant dams were dosed by IP with 10 μg dex / gram (or saline vehicle) at E17.5 and E18.5, and postnatal pups were dosed subcutaneously at PN0 with the same dose. Testes were harvested at PN1, and germs cells (OCT4-GFP positive) and somatic cells (OCT4-GFP negative) were FACS sorted prior to performing bulk RNA-seq.


title: Y chromosome loss in cancer drives growth by evasion of adaptive immunity

status: Public on Jun 10 2023

city: los Angeles

first: Hany

last: Abdel-Hafiz

address: 110 N George Burns RD, DRoom 3057

department: Medicine/ Medical Oncology

institute: Cedars-Sinai Medical Center

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

overall_design: Refer to individual Series


title: Y chromosome loss in bladder cancer contributes to T cell exhaustion and sensitivity to immune checkpoint blockade [WES]

summary: Loss of the Y chromosome (LOY) is observed in several common cancer types, including 10-40% of bladder cancers, but the clinical and biological significance of this finding is unknown. Through genomic and transcriptomic studies, we report that low LOY gene signature scores correlate with poor prognoses in patients with bladder cancer. We then performed in-depth studies of natural occurring bladder cancer cells with LOY mutants as well as those with targeted deletion of Y chromosome by CRISPR/Cas9. Both Y+ and Y- tumors had similar growth kinetics in vitro, while Y- tumors grew faster than Y+ tumors in immune competent hosts in a T cell-dependent manner

overall_design: Whole Exome sequencing for MB49 parental , MB49 Y chromosome positive and MB49 Y chromosome negative cell lines.

first: Johanna

last: Schafer

first: Zihai

first: Dan

last: Theodorescu


title: Effect of constitutive AHR activation in skeletal muscle

status: Public on Jun 08 2023

city: Gainesville

first: Terence

middle: E.

last: Ryan

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

summary: To investigate the RNA differences in muscle with and without constitutive AHR activation. AAV9 was used to express either a green fluorescent protein (control) or mutant AHR protein that exhibits constitutive transcriptional activity

overall_design: Male C57BL6J mice were infected with AAV9 viruses encoding a GFP or constitutively active AHR driven by the human skeletal actin promoter to cause myofiber-specific expression. AAV's were injected into the gastrocnemius mucle of 5-month old mice and muscles were harvested 5 months later for RNA isolation

middle: E


title: Differential susceptibility of male and female germ cells to glucocorticoid-mediated signaling

status: Public on Jun 12 2023


title: sc-RNAseq of the day 4 zebrafish spinal cord

status: Public on Jun 07 2023

city: Portland

first: Paul

last: Brehm

state: OR

address: 3232 SW Research Drive

department: Vollum

institute: Oregon Health and Science University

summary: Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish.  Electrophysiological studies have shown that additional to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNAseq (scRNAseq) to identify molecular distinctions causal to the unique physiology of primary motoneuron (PMn) function, as well as associated specialized interneurons that are tailored specifically for mediation of the powerful escape response. Generating scRNA-seq datasets that provide both a wide overview of the cellular populations of the spinal cord and a granular view of the zebrafish motor neurons.

overall_design: Cells from the spinal cords of 150 tg(SAIG213a;EGFP) zebrafish were analyzed via scRNA-seq and populations of interneurons were identified based on established markers. For examination of Motor neurons we additionally preformed FACS on cells dissociated from spinal cords of 150 tg(mnx1:GFP) zebrafish.

first: Hua

last: Wen

first: Jimmy

last: Kelly


title: ELONGATED HYPOCOTYL (HY5) AND HY5 HOMOLOG (HYH) maintain shade avoidance suppression in sunlight

city: Bristol

first: Keara

last: Franklin

address: 24 Tyndall Avenue

department: School of Biological Sciences

institute: University of Bristol

summary: We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.

overall_design: Monitoring of gene expression in Arabidopsis thaliana wild type (Wassilewskija) individuals and hy5/hyh mutants under different light conditions.


title: Y chromosome loss in cancer drives growth by evasion of adaptive immunity [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MB49 Y chromosome positive and MB49 Y chromosome negative cell lines and tumors

last: Li


title: Placenta insufficiency caused by abnormal folate metabolism linked to fetal growth restriction across gestation and generations [RNA-Seq]

status: Public on Jun 06 2023

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

institute: Loke Centre for Trophoblast Research

summary: Folate is important for fetal development and growth, yet its role in placentation is understudied. Here we report that disrupting folate metabolism by the hypomorphic Mtrr mutation in mice causes morphological and functional defects in their placentas that correspond with early- and late-onset fetal growth restriction. Remarkably, Mtrr heterozygous males initiate inheritance of similar placenta phenotypes and fetal growth defects in their wildtype grandprogeny. An integrated genome-wide approach shows placental transcriptional change and epigenetic instability is caused by an intrinsic or ancestral Mtrr mutation, affecting genes important for placenta development and function (e.g., pregnancy specific glycoprotein (Psg)/Ceacams). Crucially, we establish a functional association between mouse placenta transcript levels and fetal size and identify a human PSG gene variant linked to birthweight. This study provides molecular insight into how folate metabolism influences placental development and attributes a potential multigenerational epigenetic mechanism to unexplained cases of fetal growth defects.

overall_design: RNA-seq from E10.5 mouse placentas to assess the intrinsic and ancestral effect of an Mtrrgt allele impairing folate metabolism

first: Claire

last: Senner

first: Malwina

last: Prater

first: Joanna

last: Rakoczy

first: Katerina

last: Menelaou

first: Panayiotis

last: Laouris

first: Simon

last: Tunster

first: Maria-Sofia

last: Kalogeropoulou

first: Louisa

last: White

first: Alexander

last: Anderson

first: Nisha

last: Padmanabhan

first: Robin

middle: N

last: Beaumont

first: Rachel

last: Freathy

first: Russell

last: Hamilton

first: Erica

last: Watson


title: One carbon metabolism is required for epigenetic stability in the mouse placenta

summary: One-carbon metabolism, including the folate cycle, has a crucial role in fetal development though its molecular function is complex and unclear. The hypomorphic Mtrrgt allele is known to disrupt one-carbon metabolism, and thus methyl group availability, leading to several developmental phenotypes (e.g., neural tube closure defects, fetal growth anomalies). Remarkably, previous studies showed that some of the phenotypes were transgenerationally inherited. Here, we explored the genome-wide epigenetic impact of one-carbon metabolism in placentas associated with fetal growth phenotypes and determined whether specific DNA methylation changes were inherited. Firstly, methylome analysis of Mtrrgt/gt homozygous placentas revealed genome-wide epigenetic instability. Several DMRs were identified including at theCxcl1gene promoter and at theEn2gene locus, which may have phenotypic implications. Importantly, we discovered hypomethylation and ectopic expression of a subset of ERV elements throughout the genome of Mtrrgt/gt placentas with broad implications for genomic stability. Next, we determined that known sperm DMRs in Mtrrgt/gt males were reprogrammed in the placenta with little evidence of direct or transgenerational germline DMR inheritance. However, some sperm DMRs were associated with placental gene misexpression despite normalisation of DNA methylation, suggesting the inheritance of an alternative epigenetic mechanism. Integration of published wildtype histone ChIP-seq datasets with Mtrrgt/gt sperm methylome and placenta transcriptome data point towards H3K4me3 deposition at key loci suggesting that histone modifications might play a role in epigenetic inheritance in this context. This study sheds light on the mechanistic complexities of one-carbon metabolism in development and epigenetic inheritance.

overall_design: MeDIP-seq (ie immunoprecipitation of methylated DNA followed by sequencing) on E10.5 wildtype placentas, Mtrrgt/gt placentas as well as F2 Mtrr+/+ placentas with an ancestral Mtrrgt allele

first: Ziqi

last: Dong

first: Miguel

last: Branco


title: Drug Resistance-Related Gene Targets and Molecular Mechanisms in the A2780 Paclitaxel-Resistant Cell Line of Epithelial Ovarian Cancer

status: Public on Jun 01 2023

first: Yongli

last: Zhang

address: Department of Cell biology and medical genetics, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, 280 Wai Huan Dong Road, University City of Guangzhou

institute: Guangdong Pharmaceutical University

summary: To investigate the gene targets associated with paclitaxel resistance in EOC, we cultured A2780 and paclitaxel resistant A2780 (A2780-Taxol) cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A2780 cells and its paclitaxel resistant.

first: Ruihui

last: Yang

first: Huainian

first: Zexin

last: Chen


title: Molecular analysis (meDIP-seq and RNA-seq) of E10.5 placenta from C57Bl/6J, Mtrrgt/gt and F2 Mtrr+/+ mice"

first: Loke CTR

last: Bioinformatics


title: Breast Cancer Stem Cells Regulated Metabolism Remodeling of Bulk Tumor Cells Drives Immune Evasion

city: hefei

first: linlin

last: yan

state: anhui

address: No. 96, Jinzhai Road

institute: University of Science and Technology of China

summary: Reprogramming of energy metabolism plays pivotal roles in cancer progression and immune surveillance. Here, we demonstrated that breast cancer cells showed positive feedback enhanced aerobic glycolysis in hypoxia condition. Further investigation suggested that breast cancer stem cells (BCSCs) induced by hypoxia stimulate aerobic glycolysis in bulk tumor cells. Cells cultured with hypoxic tumor cell- or BCSC-secretome exhibited similar gene expression patterns, with global remodeling of metabolism pathways, particularly glycolysis. BCSCs regulated glycolysis promoted breast cancer progression and evasion of immune surveillance. Screening of BCSC secretome identified MIF as a pivotal factor that potentiated glycolysis by increasing the expression of ALDOC. Breast cancer cell–intrinsic MIF depletion inhibited tumor progression and augmented intratumoral cytolytic CD8+ T cells and pro-inflammatory macrophages. Targeting MIF optimized immune checkpoint therapy of breast cancer in both syngeneic mouse models and humanized mouse model. Hence, this study delineates the contribution of BCSC regulated bulk tumor cell glycolysis in immune surveillance; and thereby proposes strategies to optimize immunotherapy in breast cancer.

overall_design: MCF-7 cells were seeded with the regular medium in monolayer culture under normoxia or hypoxia condition for 48 hours. The conditioned medium was centrifuged at 4,000 g for 3 minutes and filtered with a 0.22 μm filter unit (Millipore) to deplete any cell debris. The MCF-7 cells were cultured with the CM derived from normoxia cells or hypoxia cells for 48 hours, and the RNA was isolated and sequenced.

first: Linlin

last: Yan

first: Mingming

last: Wu

first: Tao

last: Zhu


title: Revealing the Pathogenesis of Keloids Based on the Status: Active vs Inactive

city: Seoul

first: Sejin

last: Oh

address: 81 Irwon-ro Gangnam-gu

institute: Samsung Medical Center

summary: Multiomics analysis demonstrated the distinct expression profile of active and inactive keloids. Clinically, these findings may provide the future appropriate directions for treatment of keloids depending on their activity and characteristics.

overall_design: We aimed to profile the transcriptomics of FBs and vascular endothelial cells (VECs) of keloids according to their clinical activity and location within the keloid lesion. Tissue samples were collected (keloid based on its activity (active and inactive), mature scar (MS) from keloid patients and normal scar (NS) from non-keloid patients). Multiomics assessment was performed by using single-cell RNA sequencing and multiplex immunofluorescence. Increased mesenchymal FBs was the main feature in keloid patients.

first: Jong Hee

last: Lee

first: Eunhye

last: Yeo


title: Small molecular ALA targets ELK1 to balance human neutrophil and erythroid differentiation

city: chengdu

first: Yong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

summary: Alpha lipoic acid is reported to inhibit neutrophil lineage determination by targeting transcription factor ELK1 in granulocyte-monocyte progenitors. Here, we provide new evidence of alpha lipoic acid in promoting erythroid differentiation by targeting transcription factor ELK1 in CD34+CD371– hematopoietic stem progenitor cells. Over expression of both L-ELK1 and S-ELK1 greatly inhibit erythroid cell differentiation, but not knocking down of ELK1. Thus,  RNAseq of CD34+CD123+CD38+CD371– HSPCs is performed to dissect the molecular mechanism of ELK1 in blocking erythrocyte differentiation.

overall_design: Two thousand  of pCCL-L-ELK1-GFP, pCCL-S-ELK1-GFP and pCCL-GFP overexpressing lentiviral transduced CD34+CD123+CD38+CD371-HSPCs are sorted to generated dsDNA (PMID: 20203668). DNA libraries are constructed as previous reported (PMID: 29434353,27720903,32725842) and sequenced using theIllumina NovaSeq 6000 system (Novogene Co., Ltd.).

first: Yimeng


title: Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis

status: Public on May 24 2023

city: Tromsø

first: Wei

last: Meng

address: MH bygget

department: Faculty of Health Sciences

institute: University of Tromsø

summary: Due to the lack of clinical, immunologic, genetic and laboratory markers to predict remission without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission, with active treatment-naïve ulcerative colitis and healthy control subjects underwent whole-transcriptome RNA-seq. Principal component analysis (PCA) and Cox proportional hazards regression analysis was applied to the remission data concerning duration and status of patients.  A randomly chosen remission sample set was used for validation of the applied methods and results. The analyses distinguished two different UC remission patient groups with respect to remission duration and outcome (relapse). Both groups showed that altered states of UC with quiescent microscopic disease activity still present. The patient group with the longest remission duration and no relapse revealed specific and increased expression of antiapoptotic factors belonging to the MTRNR2-like gene family and non-coding RNAs. In summary, the expression of anti-apoptotic factors and non-coding RNAs may contribute to personalized medicine approaches in UC by improving patient stratification for different treatment regimens.

overall_design:
Mucosal biopsies from patients in remission(RM and RL, n=19), test RM (Test, n=7), UC active (UC, n=14) and healthy control subjects (NN, n=16) underwent whole-transcriptome RNA-seq.

UC active is taken from GSE128682.

>>> Submitter states that raw data are unavailable due to patient privacy concerns <<<

first: Ruth

last: Paulssen

first: Christopher

last: Fenton

first: Kay-Martin

last: Johnsen


title: RNA Sequencing Analysis of Wild-type, Efferent Duct-Ligated, and W/Wv Caput Epididymal Transcriptomes

status: Public on May 23 2023

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

summary: Purpose: The goal of this study is to detect differentially expressed genes, between wild-type (WT) efferent duct ligation (EDL)-treated, and W/Wv caput epididymis by RNA sequencing  Methods: The EDL treatment of WT mice was performed from 10 weeks old and continued for 4 weeks until tissue sampling at 14 weeks old. Caput epididymal mRNA profiles of 14-week-old WT, EDL, and W/Wv mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.  Results: RNA-seq data identified differentially expressed transcripts.  Conclusions: Our results show that the expression of many genes was downregulated in EDL or W/Wv caput epididymis compared with WT one.

first: Masahito

last: Ikawa


title: Nonlinear DNA methylation trajectories in aging mice [RRBS]

status: Public on May 31 2023

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigated the methylation trajectories in DNA from 82 male mouse (C57BL/6J/Ukj) colons at five different time points (3, 9, 15, 24, 28 months). Our study indicates the existence of linear and nonlinear DNA methylation changes during aging. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 mo) and mid-to-late-life (15-24 mo) transitions, separating the rodents' life into three major stages. The results were validated with samples from an independent mouse cohort of 20 male C57BL6/J mice at four different ages (3, 7, 12, 27 months).

overall_design: Reduced representation bisulfite sequencing (RRBS) of 82 genomic DNA samples from male mouse (C57BL/6J/Ukj) colon at different ages: 3 (n = 16), 9 (n = 16), 15 (n = 16), 24 (n = 16), and 28 (n = 18) months. In the validation experiment RRBS was performed on 20 genomic DNA samples from male mouse (C57BL6/J) colon at different ages: 3 (n = 4), 7 (n = 5), 12 (n = 5), and 27 (n = 6) months.

first: Maja

last: Olecka

first: Alena

last: van Boemmel

first: Lena

last: Best

first: Madlen

last: Haase

first: Silke

last: Foerste

first: Björn

last: von Eyss

first: Marco

last: Groth

first: Sören

last: Franzenburg

first: Christoph

last: Kaleta

first: Christiane

last: Frahm

first: Steve

last: Hoffmann


title: Use of an ETEC proteome microarray to evaluate cross-reactivity of ETVAX® vaccine-induced IgG antibodies in Zambian children

city: Irvine

first: Arlo

middle: Zan

last: Randall

state: CA

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

summary: Enterotoxigenic E. coli (ETEC) is a major cause of moderate to severe diarrhoea in low-middle income countries (LMICs) and affects mostly children and travelers to endemic regions. ETEC are highly diverse pathovar with over 25 colonisation factors (fimbriae) described.  The development of a broadly protective vaccine to cover most of the ETEC variants is critical for disease control. This study evaluated whether vaccination with ETVAX®; the most clinically advanced ETEC vaccine candidate results in IgG responses that cross-react with other ETEC antigens/ colonisation factors not overexpressed in the vaccine. A proteome microarray was used to assess IgG responses before and after vaccination to gain insight in the antigenic composition of ETEC that children in Zambia are exposed to and to see whether ETVAX® provides a level of cross-protection against antigens not expressed in the vaccine. The study shows that ETVAX® containing CFA/1, elicits antibodies that cross-react with other class 5 fimbriae and has the potential to offer broad protection. We also see that other antigens apart from classical antigens are immunodominant and possibly play a role in ETEC pathogenesis and may need to be investigated for their role in protection

overall_design: 40 samples were evaluated from 20 participants of a single-site, double-blind, placebo-controlled, age-descending phase 1 trial investigating the safety, tolerability, and immunogenicity of an oral inactivated ETEC Vaccine (ETVAX®) adjuvanted with dmLT. 4 children were from the placebo group, received a 1/4 dose and 8 received a 1/8 dose of the adult vaccine dose. Blood samples were collected at baseline (pre-vaccination or D0 or visit 1 (V1)) and seven days after the third dose (D97 or visit 7 (V7)). We analysed 20 V1 samples and 20 V7 samples.

first: Cynthia

last: Mubanga

first: Michelo

last: Simuyandi

first: Kapambwe

last: Mwape

first: Kennedy

last: Chibesa

first: Caroline

last: Chisenga

first: Obvious

last: Chilya

first: Richard

last: Glashoff

first: Roma

last: Chilengi


title: Effect of SVA infection on circRNAs expression in PK-15 cells

status: Public on May 18 2023

city: Chongqing

first: Yanxi

last: Chen

address: 2 Tiansheng Street

department: College of Animal Medicine

institute: Southwest University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the changes in circRNAs expression after SVA infection in PK-15 cells, we established a model of SVA-infected PK-15 cells.

overall_design: Comparative gene expression profiling analysis of circRNA-seq data for PK-15/SVA cells and PK-15 cells.

first: Chen

last: Yanxi

first: Liu

last: Xiao

first: Wang


title: Gene expression analysis in islets from miR-203 TG mice

status: Public on May 19 2023

city: Nanjing

first: Yuqian

last: Yang

state: Jiangsu

address: 101 Longmian Avenue

department: Biochemistry and Molecular Biology

institute: Nanjing Medical University


title: Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of germ cell tumor related somati-type malignancies (STM), i. e. adenocarcinomas and rhabdomyosarcomas. As controls, yolk-sac tumors and teratoma without STM population were included.

overall_design: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA isolated from FFPE tissues of 5 STM-adenocarcinoma, 5 STM-rhabdomyosarcoma, 5 yolk-sac tumors, and 5 teratomas.


title: Transcriptional activity of an MPRA library containing sequences of genomic origin bound by the transcription factor CRX measured in retinas from mice carrying pathogenic CRX variants

status: Public on May 27 2023

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

summary: Dozens of mutations in the photoreceptor-specific transcription factor CRX are linked with different human blinding diseases that vary in their severity and age of onset. How these mutations in a single TF cause a range of pathological phenotypes is not understood. We deployed massively parallel reporter assays (MPRAs) in live mouse retina to directly measure changes to CRX cis-regulatory function caused by two disease-causing mutations, one in the DNA binding domain (p.R90W) and the other in the activation domain (p.E168d2).

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Two MPRA libraries were constructed containing 1,723 candidate cis-regulatory elment (CRE) sequences each 164 bp in length. The CREs were cloned upstream of one of two minimal promoters: rhodopsin (rho library) and hsp68 (hsp68 library). Each library was electroporated into mouse retinal explants from mice carrying each of six Crx genotypes: +/+, R90W/+, E168d2/+, R90W/R90W, E168d2/E168d2, -/-, with three biological replicates per combination. Additionally, each of the two input plasmid DNA libraries were sequenced.

first: James

last: Shepherdson

first: Ryan

last: Friedman

first: Yiqiao

last: Zheng

first: Chi

last: Sun

first: Inez

middle: Y

last: Oh

first: David

last: Granas

first: Barak

last: Cohen

first: Shiming


title: Interferon-gamma ameliorates experimental autoimmune encephalomyelitis by inducing homeostatic adaptation of microglia

status: Public on May 11 2023

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

summary: Compelling evidence has shown that interferon (IFN)-γ has dual effects in multiple sclerosis and in its animal model of experimental autoimmune encephalomyelitis (EAE), with results supporting both a pathogenic and beneficial function. However, the mechanisms whereby IFN-γ may promote neuroprotection in EAE and its effects on central nervous system (CNS)-resident cells have remained an enigma for more than 30 years. In this study, the impact of IFN-γ at the peak of EAE, its effects on CNS infiltrating myeloid cells (MC) and microglia (MG), and the underlying cellular and molecular mechanisms were investigated. IFN-γ administration resulted in disease amelioration and attenuation of neuroinflammation associated with significantly lower frequencies of CNS CD11b+ myeloid cells and less infiltration of inflammatory cells and demyelination. A significant reduction in activated MG and enhanced resting MG was determined by flow cytometry and immunohistrochemistry. Primary MC/MG cultures obtained from spinal cord of IFN-γ-treated EAE mice that were ex vivo re-stimulated with a low dose (1 ng/ml) of IFN-γ and neuroantigen promoted a significantly higher induction of CD4+ regulatory T (Treg) cells associated with increased transforming growth factor (TGF)-β secretion. Additionally, IFN-γ-treated primary MC/MG cultures produced significantly lower nitrite in response to LPS challenge than control MC/MG. IFN-γ-treated EAE mice had a significantly higher frequency of CX3CR1high MC/MG and expressed lower levels of program death ligand 1 (PD-L1) than PBS-treated mice. Most CX3CR1highPD-L1lowCD11b+Ly6G- cells expressed MG markers (Tmem119, Sall2, and P2ry12), indicating that they represented an enriched MG subset (CX3CR1highPD-L1low MG). Amelioration of clinical symptoms and induction of CX3CR1highPD-L1low MG by IFN-γ were dependent on STAT-1. RNA-seq analyses revealed that in vivo treatment with IFN-γ promoted the induction of homeostatic CX3CR1highPD-L1low MG, upregulating the expression of genes associated with tolerogenic and anti-inflammatory roles and down-regulating pro-inflammatory genes. These analyses highlight the master role that IFN-γ plays in regulating microglial activity and provide new insights into the cellular and molecular mechanisms involved in the therapeutic activity of IFN-γ in EAE.

overall_design: CD11b+Ly6G-CX3CR1highPD-L1lowcells obtained from SC of EAE mice treated with either IFN-γ or PBS

first: Juan

last: Tichauer

first: Gabriel

last: Arellano

first: Eric

last: Acuña

first: Luis

last: González

first: Nirmal

last: Kannaiyan

first: Paola

last: Mirgas

first: Concepción

last: Panadero

first: Jorge

last: Ibañez-Vega

first: Paula

middle: I

last: Burgos

first: Eileah

last: Loda

first: Stephen

last: Miller

first: Peter

last: Gebicke-Haerter

first: Rodrigo

last: Naves


title: Gene expression analysis in islets from miR-203 TG mice [scRNA-seq]

first: Yuqian

last: Yang

summary: To investigate the effect of miR-203 in type 2 diabetes, target genes of miR-203 need to be investigated. The β cell specific miR-203 transgene (miR-203 TG) mice was constructed, and scRNA-seq was then performed on mouse islets.

overall_design: We then performed gene expression profiling analysis using data obtained from scRNA-seq of islets from 8-week-old WT and TG mice.

first: Lu

last: He

first: Yunxia

last: Zhu

first: Xiao

last: Han


title: The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize (small RNA-Seq)

status: Public on May 10 2023

city: Oxford

first: Beibei

last: Liu

state: OH

address: Heather Ln. Apt.5

department: Biology Department

institute: Miami university (Ohio)

summary: To determine the causes of changes in methylation during hybridization, we investigated small RNAs, particularly 24 nt small interferring RNAs (siRNAs) at the differentially methylated regions. We compared the small RNA expression between two parents (B73 and Mo17), between parents and wild type F1 (WTF1), and between WTF1 and mop1 mutant F1 (mop1F1).

overall_design: Comparative small RNA expression analysis of small RNA sequencing data for for parents, WTF1, and mop1F1.

first: Miexia

last: Zhao


title: The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize (RNA-Seq)

summary: To investigate how differentially methylated regions affect the flanking gene expression, we compared the gene epression between two parents (B73 and Mo17), between parents and wild type F1 (WTF1), and between WTF1 and mop1 mutant F1 (mop1F1).

overall_design: Comparative gene expression analysis of RNA sequencing data for parents, WTF1, and mop1F1.


title: A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

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

overall_design: Refer to individual Series


title: The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize (WBGS)

summary: To understand the initiation of DNA methylation and its effects on gene expression, we performed high-throughput sequencing of DNA methylomes of F1 hybrids that were mutant for two genes, Mop1 (mediator of paramutation1) and Lbl1 (leafbladeless1), and their wild type F1 siblings as well as their parents. We first compared the methylation between the two parents (B73 and Mo17), and identified the differentially methylated regions (DMRs) between them. Next, we examined the methylation changes in wilde type F1 (WTF1) and mutant F1 (mop1F1 and lbl1F1) at these parental DMRs. Furthermore, to determine whether the methylation changes in the F1 through hybridization can me maintained to the next generation, we investigated the methylation levels of these DMRs in the BC1 generation.

overall_design: Comparative DNA methylation analysis of whole genome bisulfite sequencing (WGBS) data for parents (B73 and Mo17), wild type F1 (WTF1), mutant F1 (mop1F1 and lbl1F1), and BC1 individuals (WTBC1 and mop1-derived-BC1).