title: Mouse whole brain: Alteration of DNA methylation status caused by prenatal titanium dioxide nanoparticle exposure

city: Sanyo-onoda

first: Ken

last: Tachibana

state: Yamaguchi

address: 1-1-1 Daigaku-Dori

institute: Sanyo-Onoda City University

type: Methylation profiling by genome tiling array

summary: Reportedly, titanium dioxide nanoparticle exposure during pregnancy can affect the development of the central nervous system in mouse offspring; however, the underlying mechanism remains unknown. In the present study, we investigated the impact of prenatal dioxide nanoparticle exposure on global DNA methylation in the brains of neonatal mice. Pregnant C57BL/6J mice were intratracheally administered a dioxide nanoparticle suspension (100 ug/mouse) on gestational day 10.5, and brains were collected from male and female offspring at day 1 postpartum. After extraction of methylated DNA by immunoprecipitation, the DNA methylation profile was analyzed using a mouse CpG island microarray. Among genes in the CpG island microarray, DNA methylation was increased in 614 and 2924 genes and decreased in 6219 and 6463 genes in male and female offspring, respectively. Combined with mRNA microarray analysis, 88 and 89 genes were upregulated (≥ 1.5-fold) accompanied by demethylation of CpG islands, whereas 13 and 33 genes were downregulated (≤ 0.67-fold) accompanied by demethylation of CpG islands in male and female offspring mice, respectively. Gene Set Enrichment Analysis (GSEA) revealed that these genes were enriched in gene ontology terms related to the regulation of transcription factors, cell proliferation, and organism development. Additionally, MeSH terms related to stem cells and morphogenesis were enriched.

overall_design: Alteration of DNA methylation status caused by prenatal titanium dioxie nanoparticle exposure (GD14: 100 ug/mouse) in mouse brain was analyzed. Brains were collected from male and female offspring at day 1 postpartum and DNA methylation profiles were analyzed (Vehicle vs. titanium nanoparticle; both male and female).


title: Genomics analysis of hexanoic acid exposure in Drosophila species

status: Public on Oct 04 2021

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Ave.

department: Biology

country: USA

institute: Wesleyan University

type: Expression profiling by high throughput sequencing

summary: We analyze the gene expression response to hexanoic acid in Drosophila simulans, Drosophila melanogaster, and Drosophila sechellia

sample_organism:
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans

overall_design: Differential gene expression analysis of D. sechellia, D. simulans, and D. melanogaster flies exposed to control food and food supplemented with Hexanoic Acid (HA) using RNA-sequencing.

first: Zachary

last: Drum

first: Stephen

last: Lano

first: Sadie

last: Gregory

first: Serena

last: Shimshak

first: Mukshud

last: Ahamed

first: Will

last: Barr

first: Bethlehem

last: Bekele

first: Alison

last: Biester

first: Colleen

last: Castro

first: Lauren

last: Connolly

first: Nicole

last: Delguadio

first: William

last: Humphrey

first: Helen

last: Karimi

first: Sophie

last: Karolczak

first: Tay-Shaun

last: Lawrence

first: Andrew

last: McCracken

first: Noah

last: Miller-Medzon

first: Leah

last: Murphy

first: Cameron

last: Park

first: Sojeong

first: Rong

last: Qiu

first: Kevin

last: Serra

first: Gigi

last: Snyder

first: Alexa

last: Strauss

first: Spencer

last: Tang

first: Christina

last: Vyzas

middle: D


title: Mouse whole brain: Alteration of gene expression caused by prenatal titanium dioxide nanoparticle exposure

first: Ken

last: Tachibana

country: Japan

summary: Reportedly, titanium dioxide nanoparticle exposure during pregnancy can affect the development of the central nervous system in mouse offspring; however, the underlying mechanism remains unknown. We investigated the impact of prenatal dioxide nanoparticle exposure on mRNA expression patterns in the brains of neonatal mice. Pregnant C57BL/6J mice were intratracheally administered a dioxide nanoparticle suspension (100 ug/mouse) on gestational day 10.5, and brains were collected from male and female offspring at day 1 postpartum. Total RNA was obtained, and mRNA expression profiles were comprehensively assessed using microarray analysis. The results showed 88 and 89 genes were upregulated (≥ 1.5-fold) accompanied by demethylation of CpG islands, whereas 13 and 33 genes were downregulated (≤ 0.67-fold) accompanied by demethylation of CpG islands in male and female offspring mice, respectively. Gene Set Enrichment Analysis (GSEA) revealed that these genes were enriched in gene ontology terms related to the regulation of transcription factors, cell proliferation, and organism development. Additionally, MeSH terms related to stem cells and morphogenesis were enriched.

overall_design: Alteration of gene expression caused by prenatal titanium dioxie nanoparticle exposure (GD14: 100 ug/mouse) in mouse brain was analyzed. Brains were collected from male and female offspring at day 1 postpartum and mRNA expression profiles were analyzed (Vehicle vs. titanium nanoparticle; both male and female).


title: Single-cell RNAseq of the murine intestinal epithelium infected with rotavirus

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: To understand the impact of murine rotavirus infection on mouse intestinal epithelial tissue, we isolated total intestinal epithelium from uninfected and infected C57Bl6J mice and performed single-cell RNAseq.

overall_design: Three C57Bl6J mice were infected with murine rotavirus strain EC and compared to three uninfected C57Bl6J mice. The intestinal epithelium was isolated via FACs and profiled with single-cell RNAseq on the 10x Chromium platform.

first: Carolyn

last: Bomidi

first: Matthew

middle: J

last: Robertson

first: Hoa

last: Nguyen-Phuc

first: Cristian

last: Coarfa

middle: K

first: Sarah

middle: E

last: Blutt


title: Mouse whole brain: Molecular alterations caused by prenatal titanium dioxide nanoparticle exposure

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

overall_design: Refer to individual Series


title: Gene Expression and Histopathological Changes in the Placenta of the Serotonin Transporter (Slc6a4) Knockout Mouse Suggest a Role for Serotonin in Controlling Nutrient Acquisition

city: Columbia

first: Cheryl

middle: S

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling in 5-HT transporter SLC6A4 gene knockout 12.5 dpc mouse placenta. This study was to test the hypothesis that ablation of the Slc6a4 gene would result in morphological changes correlated with defined gene expression changes in the placenta. We found that Slc6a4 KO placentas had a much increased pTGC to spongiotrophoblast area ratio relative to WT placentas.  Slc6a4 KO placentas had significantly elevated expression of genes associated with intestinal functions such as nutrient sensing, uptake, and catabolism, and blood clotting. Integrative correlation analyses revealed that upregulation of many of these genes was correlated with the expansion of the pTGC layer. One other key gene in this module was dopa decarboxylase (Ddc), which catalyzes the conversion of L-5-hydroxytryptophan to 5-HT. Our studies suggest a new paradigm relating to how 5-HT operates in the placenta, namely as a factor regulating metabolic functions and blood clotting through autocrine actions. We further suggest that the pTGC are functional analogs of the enterochromaffin 5-HT-positive cells of the gut, which have roles in controlling similar activities within the intestinal mucosa. Our studies suggest a new paradigm in thinking about how 5-HT acts in the placenta, namely not so much as a classic neurotransmitter but as an endocrine factor regulating metabolic functions and blood clotting through autocrine actions.

overall_design: Placental mRNA profiles of 12.5 dpc wild type (WT) and Slc6a4 -/- mice

first: Jiude

last: Mao

first: Jessica

middle: A

last: Kinkade

first: Nathan

last: Bivens

first: R

middle: M

last: Roberts


title: Transcriptional regulation in primary mouse brain microvascular endothelial cells following apical or basolateral pharmacological treatment with S1P or S1P4 agonist in C57B/6J wildtype versus global S1P4 KO mice

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: The precise regulation of blood-brain-barrier (BBB) permeability for immune cells and blood-borne substances is essential to maintain brain homeostasis. Sphingosine-1-phosphate (S1P), a lipid signaling molecule enriched in plasma, is known to affect BBB permeability. Previous studies focussed on endothelial S1P receptors 1 and 2, reporting a barrier-protective effect of S1P1 and a barrier-disruptive effect of S1P2. Here we present novel data characterizing the expression, localization and function of the hitherto exclusively immunce cell-associated S1P receptor 4 (S1P4) on primary brain microvascular endothelial cells (BMECs). We detected a robust expression of S1P4 in homeostatic BMECs and pinpointed its localization to abluminal endothelial membranes by electron microscopy. Basolateral S1P treatment of BMECs led to increased permeability in vitro associated with S1P4 downregulation. Likewise, downregulation of S1P4 was observed in mouse brain microvessels after stroke, a neurological disease associated with BBB impairment. RNA sequencing analysis of BMECs suggested involvement of S1P4 in endothelial homeostasis, apicobasal polarity and barrier function. Using siRNA, pharmacological agonists and antagonists of S1P4 both in vitro and in vivo, we demonstrate a barrier-protective function of S1P4. We therefore suggest S1P4 as a novel target regulating BBB permeability and propose its therapeutic targeting in CNS diseases associated with BBB dysfunction.

overall_design: RNA sequencing analysis of MBMECs was performed 24h after pharmacological treatment with functionally barrier-opening (50nM S1P basal) or barrier-tightening (50nM S1P apical or 500nM S1P4 agonist apical and basal) agents or the respective vehicle control. n = 4 sets (replicates) of C57/B6 MBMECs, 12 mice/n. Global S1P4 KO MBMECs (4 replicates, 12mice/n) treated with vehicle control medium were included for comparison.

first: Lena

last: Hansen

first: Kavi

last: Devraj

first: Waltraud

last: Pfeilschifter


title: PLCG2 regulates endocannabinoid and eicosanoid networks in innate immune cells

city: La Jolla

first: Hui

last: Jing

state: CA

address: 10550 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

summary: Human genetic studies have pointed to a prominent role for innate immunity and lipid pathways in human immunological and neurodegenerative disorders. Our understanding of the composition and function of immunomodulatory lipid networks in innate immune cells, however, remains incomplete. Here, we show that phospholipase C gamma 2 (PLCγ2 or PLCG2) – mutations in which are associated with autoinflammatory disorders and Alzheimer’s disease – serves as a principal source of diacylglycerol (DAG) pools that are converted into a cascade of bioactive endocannabinoid (eCB) and eicosanoid lipids by DAG lipase (DAGL) and monoacylglycerol lipase (MGLL) enzymes in innate immune cells. We show that this lipid network is tonically stimulated by disease-relevant human mutations in PLCγ2, as well as Fc receptor activation in primary human and mouse macrophages. Genetic disruption of PLCγ2 in mouse microglia suppressed DAGL/MGLL-mediated eCB-eicosanoid crosstalk and also caused widespread transcriptional and proteomic changes, including the reorganization of immune-relevant lipid pathways reflected in reductions in DAGLB and elevations in PLA2G4A. Despite these changes, Plcg2-/- mice showed generally normal pro-inflammatory cytokine responses to lipopolysaccharide treatment, instead displaying a more restricted deficit in microglial activation that included impairments in prostaglandin production and CD68 expression. Our findings enhance the understanding of PLCγ2 function in innate immune cells, delineating a role in crosstalk with endocannabinoid/eicosanoid pathways and modulation of subsets of cellular responses to inflammatory stimuli.

overall_design: Transcriptome profiles of Plcg2+/+ and Plcg2-/- mouse neonatal microglia

first: Haoxin

last: Li

first: Benjamin

middle: F

last: Cravatt


title: Transcriptomic profiling of human senescent cells upon treatment with the senolytic agent procyanidin C1

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

country: China

institute: Chinese Academy of Sciences

summary: In the course of aging, the long term retention of senescent cells in vivo, a process mainly attributed to highly expressed BCL-family proteins, chronically damages tissues mainly through a senescence-associated secretory phenotype (SASP). It has been documented that accumulation of senescent cells accelerates aging and contributes to age-related diseases. Indeed, senescent cells can be removed by several strategies, thus preventing occurrence of chronic disorders and prolonging lifespan and healthspan. Senolytics, which eliminate senescent cells by pharmacological intervention, have recently emerged as a new line of therapeutic agents to ameliorate diverse age-related pathologies. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of life. We report the potential of procyanidin C1 (PCC1), an epicatechin trimer natural product derived from plant sources including grape, apple, and cocoa, in targeting senescent cells via induction of apoptosis. This study demonstrates the efficacy of PCC1 in minimizing the influence of senescent cells in tissue microenvironment and provides a strong rationale for its future use in aging control and geriatric medicine.

overall_design: Examination of in vitro efficacy of PCC1 in treating human senescent cells. This assay was performed beyond previous studies reporting their effects in treatment of disorders including but not limited to osteoporosis, osteoarthritis, atherosclerosis, cancer and neurodegenerative diseases including Alzheimer's and Parkinson's.

first: Qixia

last: Xu


title: Murine rotavirus infects and replicates in intestinal tuft cells

first: Mary

last: Estes

summary: RNAseq of coding and noncoding RNA isolated from intestinal tuft cells reveals murine rotavirus replication in intestinal tuft cells.

overall_design: Three C57Bl6J mice were infected with murine rotavirus strain EC and compared to three uninfected C57Bl6J mice. The intestinal tuft cells were isolated via FACs and profiled with RNAseq.

first: Carolyn

last: Bomidi

first: Matthew

last: Robertson

first: Hoa

last: Nguyen-Phuc


title: Transcriptome profiling of the effects of Aurora B mediated phosphoregulation of CNOT3 in differentiating mesendodermal cells

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Characterization of the transcriptome profile of CNOT3 phospho mutants of Aurora B target residues (T292/S294) in mesendoderm differentiated cells

overall_design: Transcriptome profiles of 4-day differentiated mesendodermal cells derived from wild-type E14 and Cnot3-T292A/S294A mutant ES cells

first: Moumita

last: Sarkar

first: Niall

last: Dillon

first: Yi-Fang

last: Wang


title: Global gene expression profiles of cellular response in human induced pluripotent stem cell-derived cardiomyocytes to CFZ treatment

city: Atlanta

first: Parvin

last: Forghani

state: GA

address: 2015 uppergate drive

department: Pediatric department

institute: Emory University

summary:
Purpose: Evaluate the molecular changes associated with Cfz -induced cardiotoxicity
Methods: RNA-Seq analysis was performed to analyze global transcriptome profiles of hiPSC-CMs treated with DMSO (Control group), 1 µM  Carfilzomib ( Cfz group). The Illumina TruSeq technology was used to prepare RNA-Seq libraries, and next-generation sequencing was done via an Illumina HiSeq 2000. RNA sequence reads were aligned to the human reference genome (GRCh38) using STAR v2.5. HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg's approach.
As detected by RNA-Seq, some differential genes regulated by Cfz were significantly involved in cardiac contraction and extracellular matrix (ECM).   Among the top 10 up-regulated genes post Cfz treatment,most of thoese genes was related to the heat shock protein expression( HSPA1B,HSPA6,,HSPH1, BAG3). And among the top 10 down-regulated genes post Cfz treatment, some correlated to contraction and Extra cellular matrix ( ITG11, SLC9A3, TNN1) .
Conclusion: Carfilzomib -induced alteration of hiPSC-CM transcriptomic profiles. Enhanced HSPs  and down regulate cardiac related contraction gene and extracellular matrix.

overall_design: RNA-Seq analysis was performed to compare global gene expression profiles of hiPSC-CMs treated with DMSO, 1 µM Cfz, in triplicate.

first: Chunhui


title: Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [M1_1]

status: Public on Oct 06 2021

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to M1 regions of human and mouse brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

overall_design: Apply snmC-seq2 to brain M1 regions to identify epigenomic landcape of the adult human and marmoset brains

first: Wei

last: Tian

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Anna

last: Bartlett

first: Fenna

last: Krienen

first: Rebecca

last: Hodge

first: Jacinta

last: Lucero

last: Nery

first: Angeline

last: Rivkin

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Huaming

last: Chen

first: Sheng-Yong

last: Niu

first: M

last: Behrens

first: Guoping

last: Feng

first: Ed

last: Lein


title: Metformin-treated hESC-derived pancreatic organoids

status: Public on Oct 03 2021

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

summary: The goal of this study is to investigate transcriptome profiles (RNA-seq) of human embryonic stem cell (hESC)-derived pancreatic organoids with or without metformin treatment at various concentrations.

overall_design: Treat hESC-derived pancreatic organoids without or with metformin treatment at 100μM.

first: Linh

middle: T

last: Nguyen

first: Shawn

last: Hoon


title: Comprehensive kinase activity assay of desmoplastic malignant mesothelioma

status: Public on Oct 01 2021

city: Tokyo

first: Rei

last: Noguchi

state: Tokyo

department: Division of Rare Cancer Research

institute: National Cancer Center Research Institute

summary: Desmoplastic malignant mesothelioma is a rare tumor. Due to the rarity, development of new treatment for desmoplastic malignant mesothelioma is difficult. To develop new treatment strategy using existing anti-cancer drugs, kinase activity profiling has not been thoroughly studied. We used PamChip array to identify the peptide profiles of desmoplastic malignant mesothelioma between the patient-derived cell line and the tumor tissue.

overall_design: cell lysate was collected from a patient-derived cell line named NCC-DMM1-C1 and its originated tumor tissue. Cell lysate was incubated on a PamChip array.

first: Tadashi

last: Kondo


title: Transcription Factor MEF2D is Required for the Maintenance of MLL-rearranged Acute Myeloid Leukemia [ChIP-Seq]

status: Public on Oct 02 2021

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) with MLL-rearrangement (MLL-r) comprises approximately 10% of all AML cases and portends poor outcomes. Much remains to be uncovered on how MLL-r AML drives leukemia development while preventing cells from normal myeloid differentiation. Here, we identified that transcription factor MEF2D is a highly expressed gene with a super-enhancer MLL-r AML. Knockout of MEF2D profoundly impaired leukemia growth, induced myeloid differentiation, and delayed oncogenic progression in vivo. Mechanistically, MEF2D loss led to robust activation of a CEBPE-centered myeloid differentiation program in AML cells. Chromatin profiling revealed that MEF2D binds to and suppresses the chromatin accessibility of CEBPE cis-regulatory regions. In human acute leukemia patient samples, MEF2D expression showed a strong negative correlation with the expression of CEBPE. Depletion of CEBPE partially rescued the cell growth defect and myeloid cell differentiation induced by the loss of MEF2D. Lastly, we show that MEF2D is positively regulated by HOXA9, and downregulation of MEF2D is an important mechanism for DOT1L inhibitor-induced anti-leukemia effects in MLL-r AML. Collectively, our findings suggest that MEF2D plays a critical role in human MLL-r AML and uncover the MEF2D-CEBPE axis as a crucial transcriptional mechanism regulating leukemia cell self-renewal and differentiation block in MLL-r AML.

overall_design: MEF2D ChIP analysis in MOLM-13 and MV4-11 AML cells

first: Lianzhong

last: Zhao


title: Progressive ER stress over time due to human insulin gene mutation contributes to pancreatic β-cell dysfunction, islet inflammation and compensatory responses

summary: Heterozygous human INS gene mutations are known to promote ER stress, leading to β-cell dysfunction and neonatal diabetes. Recent literature challenged the long-standing notion that neonatal diabetes occurs due to ER stress-induced β-cell apoptosis. Importantly, mechanisms of β-cell failure during the disease progression and why the other wild-type (WT) INS allele is unable to function still remain unclear. Here, our computational modelling studies, short-term and long-term expression studies in β-cells revealed the presence of ER stress, organelle changes and insulin processing defects, resulting in decreased insulin secretion but not insulin secretory capacity. By nine weeks of expression of mutant INS, dominant negative effects of mutant INS were evident and β-cell insulin secretory capacity declined. INS+/C109Y patient-derived β-like cells and single cell RNA-Sequencing analyses then revealed compensatory upregulation in genes involved in insulin secretion, processing and inflammatory response. Our results provide deeper insights into the mechanisms of β-cell failure during INS mutation-mediated diabetes disease progression. Decreasing CHOP-10, sXBP1 or inflammatory response could be avenues to restore the function of the remaining WT INS allele.

overall_design: To identify genome-wide transcriptomic perturbations caused by INS+/C109Y mutation, we performed single-cell RNA-Seq analyses on the hiPSC-derived β-like cells

first: Nur

last: Amirruddin

first: Yaw

last: Tan

first: Daphne

last: Gardner

first: Mong

middle: B

last: Yong

first: Chandra

last: Verma

first: Kok

middle: O

last: Lee


title: Transcriptomic analysis of E0771 tumors treated with FEC + oHSV-1 Vs PBS

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

summary:
E0771 tumors were implanted either subcutaneously on the left flank or orthotopically in the mammary fat pad and treated with either PBS or FEC + oHSV-1
Mice were sacrificed 5 days after the start of treatment and whole tumour digests were used for RNA extraction

overall_design: 5 mice treated with PBS, subcutaneous tumours; 10 mice treated with FEC + oHSV-1, subutaneous tumours; 5 mice treated with PBS, orthotopic tumours; 10 mice treated with FEC + oHSV-1, orthotopic tumours

first: Alyssa

last: Vito


title: De novo deletions and duplications at recombination hotspots in mouse germlines

city: New York

first: Agnieszka

last: Lukaszewicz

state: New York

address: 1275 York Avenue

department: Developmental Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here we uncover a new type of mutational event in which deletions form via joining of ends from two closely-spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.

overall_design: Amplicon deep sequencing was applied to detect deletions at a single mouse DSB hotspot on Chr1. Four overlapping amplicons across the hotspot were amplified for each genotype: Atm–/–, Atm+/–, Atm+/+ and Spo11–/–). Sixteen samples in total.

first: Scott

last: Keeney

first: Maria

last: Jasin


title: Transcription Factor MEF2D is Required for the Maintenance of MLL-rearranged Acute Myeloid Leukemia [RNA-Seq]

overall_design: RNA-seq analysis of guide RNA-expressing MOLM-13 cells at day 6 post-transduction.


title: Transcription Factor MEF2D is Required for the Maintenance of MLL-rearranged Acute Myeloid Leukemia [ATAC-Seq]

overall_design: ATAC-seq analysis of guide RNA-expressing MOLM-13 cells at day 6 post-transduction.


title: Longitudinal profiling of tumor specific CD8 T cells using single cell RNA-Seq in mouse lung adenocarcinoma

city: Cambridge

first: Rebecca

middle: H

last: Herbst

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

summary: T cell dysfunction is a critical obstacle to productive anti-tumor immunity. Previous work has demonstrated that a subset of dysfunctional CD8+ T cells expresses TCF-1, and that this population sustains the T cell response over time. However, the mechanisms that contribute to the generation and maintenance of TCF-1+ CD8+ T cells remain poorly understood. Here, using a model of lung adenocarcinoma, we demonstrate that TCF-1+ CD8+ T cells are found within both tumor and tumor draining LN (dLN), but phenotypically and functionally differ based on location. In tumors, TCF-1+ CD8+ T cells become dysfunctional with time, are heterogeneous, and decline over the course of progression, while TCF-1+ CD8+ T cells in the dLN remain stable. Blocking egress from the dLN decreased SlamF6+ TCF-1+ CD8+ T cells in tumors, demonstrating that the dLN is a critical reservoir of functional CD8+ T cells. Concomitant with the decline in CD8+ T cells in the tumor, migratory conventional dendritic cell type I (cDC1) numbers decreased in the dLN. Therapeutically, boosting cDC1 numbers and function using Flt3L/anti-CD40 antibody resulted in T cell proliferation within the dLN, an increased SlamF6+ TCF-1+ CD8+ T cells in tumors, and a decreased tumor burden. These data demonstrate the importance of migratory cDC1 cells in boosting TCF-1+ CD8+ T cells in the dLN, and provide rationale for targeting DCs in immunotherapy.

overall_design: 10X 5'  and SmartSeq2 single cell RNA-Seq and paired TCR sequencing was performed on sorted lung infiltrating H-2Kb/SIINFEKL specific and polyclonal CD8+ T cells from KrasG12D+/-  Trp53-/- lung adenocarcinoma bearing lungs. Using topic modeling, we identified multiple discrete cell states occupied by Tcf7+ H-2Kb/SIINFEKL specific CD8+ T cells that varied over tumor progression.

first: Aviv

last: Regev

first: Tyler

last: Jacks

first: Jason

last: Schenkel


title: The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA [RNA-seq]

city: Versailles

first: HAKIM

last: MIREAU

address: Route de Saint-Cyr

country: France

institute: INRAE

summary: The control of mRNA translation has been increasingly recognized as a key regulatory step for gene control but clear examples in eukaryotes are still scarce. Nucleo-cytoplasmic male sterilities (CMS) represent ideal genetic models to dissect genetic interactions between the mitochondria and the nucleus in plants. This trait is determined by specific mitochondrial genes and is associated with a pollen sterility phenotype that can be suppressed by nuclear genes known as restorer-of-fertility (Rf) genes. In the study, we focused on the Ogura CMS system in rapeseed and showed that the suppression to male sterility by the PPR-B fertility restorer (also called Rfo) occurs through a specific inhibition of the translation of the mitochondria-encoded cms-causing mRNA orf138. We also demonstrate that PPR-B binds within the coding sequence of orf138 and acts as a ribosome blocker to specifically impede translation elongation along the orf138 mRNA. Rfo is the first recognized fertility restorer shown to act this way. These observations will certainly facilitate the development of synthetic fertility restorers for CMS systems in which efficient natural Rfs are lacking.

overall_design: RNA profiles of mitochondrial genes in male-sterile (CMS) and restored (RS) rapaseed plants.

first: Hakim

last: Mireau

first: Chuande

last: Wang


title: The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA

overall_design: Ribosome footprint profiles of mitochondrial genes in male-sterile (CMS) and restored (RS) rapaseed plants.


title: RNASeq of bone marrow-derived macrophages treated with beta-glucan and lipopolysaccharide (LPS)

city: Nashville

first: Cody

middle: L

last: Stothers

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University

summary: We found that beta-glucan treatment induces early induction of transcripts associated with inflammation and metabolism. Several days after beta-glucan treatment, genes associated with differentation and housekeeping remain upregulated. LPS treatment induces a strong inflammatory response. Beta-glucan did not significantly alter the macrophage response to LPS.

overall_design: Bone marrow derived macrophages were harvested for RNA after 4hrs of beta-glucan treatment, 24hrs of beta-glucan treatment, and 3 days following the end of treatment (3dp). Additionally, macrophage RNA was harvested after 3dp beta-glucan treatment and restimulation with LPS for 6hrs.


title: RNA-seq analysis of TP309, rod1 and ROD1-OE leaves at tillering stage and inflorescence meristem at filling stage

city: 上海市

first: yang

last: he

state: 徐汇区

address: 上海市徐汇区枫林路300号植物生理生态研究所

institute: SIPPE

summary: We observed that  genes related to ROS homeostasis and cell wall reinforcement were enriched ,genes related to calcium binding and MADS-box genes were downregulated in rod1

overall_design: mRNA profiles of leaves and  inflorescence meristem were sequenced

first: Ming

last: Gao

first: Yang

last: He

first: Xin

last: Yin

first: Xiang

last: Zhong


title: WIND1 orchestrates wound-induced callus formation, vascular reconnection and defense response in Arabidopsis

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Wounding triggers de novo organogenesis, vascular reconnection and defense response but how wound stress evokes such a diverse array of physiological responses remains unknown. We previously identified an AP2/ERF transcription factor, WOUND INDUCED DEDIFFERENTIATION1 (WIND1), as a key regulator of wound-induced cellular reprogramming in Arabidopsis. To understand how WIND1 promotes downstream events, we performed time-course transcriptome analyses after WIND1 induction. We observed a significant overlap between WIND1-induced genes and genes implicated in cellular reprogramming, vascular formation and pathogen response. We demonstrated that WIND1 induces several reprogramming genes to promote callus formation at wound sites. We, in addition, showed that WIND1 promotes tracheary element formation, vascular reconnection and flagellin-triggered defense responses. These results indicate that WIND1 functions as a master regulator of wound-induced responses by promoting dynamic transcriptional alterations. This study provides deeper mechanistic insights into how plants control multiple physiological responses after wounding.

overall_design: WIND1-induced genes are monitored for 24 hours after induction in time-course manner.

first: Akira

last: Iwase

first: Yuki

last: Kondo

first: Anuphon

last: Laohavisit

first: Arika

last: Takebayashi

first: Momoko

last: Ikeuchi

first: Keita

last: Matsuoka

first: Masashi

last: Asahina

first: Ken

last: Shirasu

first: Hiroo

last: Fukuda

first: Keiko

last: Sugimoto


title: Transcriptome analysis of B cell populations in the peripheral blood of patients with multiple sclerosis

city: Kodaira

first: Kimitoshi

last: Kimura

address: 4-1-1 Ogawahigashi

department: Department of Immunology, National Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

summary: Transcriptome profiles of B cell populations in the circulation of patients with multiple sclerosis were obtained with nCounter system

overall_design: Four B cell populations were sorted from the circulation of three patients with multiple sclerosis. Characteristic gene expression profile was then explored for each B cell population.

first: Youwei

last: Lin

first: Takashi

last: Yamamura


title: Effect of Smox deletion and spermidine supplementation on colonic gene expression during carcinogenesis

first: Alain

middle: P

last: Gobert

address: 2215B Garland Ave

institute: VUMC

overall_design:
RNA sequencing by Illumina NovaSeq6000 was performed from colonic tissues of C57BL/6 WT and C57BL/6 Smox-/- mice ± AOM-DSS ± spermidine, after 56 days .
There was three mice per group

first: Keith

last: Wilson

first: Yvonne

last: Latour


title: Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology

first: Combiz

last: Khozoie

address: 726 Sir Michael Uren Hub

department: Brain Sciences

institute: Imperial College London

summary: To better define roles that microglia and astrocytes play in Alzheimer’s disease (AD), we used single-nuclei RNA-sequencing to comprehensively characterize transcriptomes in these glial nuclei isolated post mortem from non-diseased control and neuropathologically-defined AD brains.  Genes associated with AD risk were highly represented, especially in microglia. Transcriptome differences significantly correlated with immunohistochemical phospho-Tau (pTau) density included genetic risk genes for both microglia (APOE, BIN1, MS4A6A, PILRA) and astrocytes (APOE, CLU, MEF2C, IQCK).  Pathways associated with the top differentially expressed genes in microglia included those related to proteostasis and immune modulation while those for astrocytes also included proteostasis, as well as stress response and metal ion homeostasis.  Inferred regulons generated from co-expression networks implicated distinct transcriptional mechanisms associated with pTau for the two cell types.  Data-driven sub-clustering revealed additional glial cellular heterogeneity.   Our work provides a new resource, highlighting both potential causal mechanisms and protective glial responses in AD.

overall_design: Single-nuclei RNA-sequencing of microglia and astrocyte nuclei isolated post mortem from non-diseased control and neuropathologically-defined AD brains.

first: Amy

last: Smith

first: Karen

last: Davey

first: Stergios

last: Tsartsalis

first: Nurun

last: Fancy

first: See

last: Tang

first: Eirini

last: Liaptsi

first: Maria

last: Weinert

first: Aisling

last: McGarry

first: Robert

middle: C

last: Muirhead

first: Steve

last: Gentleman

first: David

last: Owen

first: Paul

last: Matthews


title: Expression profiling of multiple immune cells by high throughput sequencing

status: Public on Sep 30 2021

city: Suita

first: Kazuyo

last: Moro

state: Osaka

address: 2-2 Yamada-oka

department: Department of Microbiology and Immunology

institute: Osaka University

summary: ILC2s have the unique ability to produce cytokines such as constitutive production as well as rapid and abundant production during inflammation. We found that the unique type 2 cytokine prodution from ILC2s is regulated by post-transcriptional regulation. Here we identified the genes involved in the post-transcriptional regulation of type 2 cytokine production in ILC2s by comparing the gene expression between multiple immune cells.

overall_design: RNA-seq of multiple immune cells

first: Yuki

last: Hikichi

first: Yasutaka

last: Motomura


title: U2AF65Prp2 promotes intron definition by stabilizing U1 snRNP at the 5’ splice site

city: Barcelona

first: Jose

last: Ayte

address: Doctor Aiguader 88

country: Spain

institute: Universitat Pompeu Fabra

summary: Prp2 (U2AF65) is an essential splicing factor, that recognizes the poly-Py track near the 3' SS.  We have previously observed that when Prp2 is inactivated using a prp2 temperature-sensitive allele, while most of the pre-mRNA is not processed, some are normally spliced.  This observation even more noticeable during meiosis, since pre-mRNA regulation is executed at different levels (splicing, polyadenylation and stability). Using RNAseq, we have determined genome-wide the splicing efficiency of fission yeast cells as they progress into synchronous meiosis, in the presence or absence of functional Prp2.  To our surprise, the main characteristic that defines if any given intron requires Prp2 to be spliced depends on the last nucleotides of the preceding exon, next to the 5’ SS in the nucleotide that anneal with U1 RNA.  Thus, by simple genetic manipulation, we can modulate the dependency of any given intron on Prp2.  We propose that the role of Prp2 consist in the stabilization of a loop between the 5’SS and the 3’ SS, which also depends on the annealing strength between U1 and the 5’ SS.

overall_design: Splicing profile of two samples of cells entering into meiosis I, comparing the effect of temperature-inactivation of Prp2-1 (U2AF65)

first: Luca

last: Cozzuto


title: Transcriptomic profiling of Pityriasis Rubra Pilaris (PRP) and Psoriasis

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: The microarray experiment was employed to evaluate the gene expressions in skin lesions of PRP and psoriasis.

overall_design: To investigate the specific gene regulations, microarray profiling was performed on RNA extracted from paraffin embedded skin biopsy samples.

first: Johann

last: Gudjonsson


title: Transcriptional profiling of sequentially generated septal neuron fates

city: San Francisco

first: Corey

last: Harwell

address: 35 Medical Center way

department: Neurology

institute: University of California, San Francisco

summary: Single cell RNA-Seq analysis of the developing septum and MGE at embryonic stages, and septum at postnatal stages

overall_design: The entire embryonic septa and MGE/PoA complex of embryonic mice at embryonic days 11, 14 and 17, and the septa of mice at postnatal days 3, 10 and 30 were dissected out and submitted to single cell RNA sequencing, using the inDrops platform. CD-1 wildtype mice (Charles River strain code 022) were used.

first: Miguel

last: Turrero Garcia

first: Sinisa

last: Hrvatin

first: M

last: Nagy


title: SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity

city: Minato-ku

first: Kei

last: Sato

address: 4-6-1 Shiroganedai

institute: The Institute of Medical Science, The University of Tokyo

type: Genome variation profiling by high throughput sequencing

summary: During the current SARS-CoV-2 pandemic, a variety of mutations have been accumulated in the viral genome, and currently, four variants of concerns (VOCs) are considered as the hazardous SARS-CoV-2 variants to the human society. The newly emerging VOC, the B.1.617.2/Delta variant, closely associates with a huge COVID-19 surge in India in Spring 2021. However, its virological property remains unclear. Here, we show that the B.1.617.2/Delta variant is highly fusogenic, and notably, more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates the spike protein cleavage and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity than the parental virus. Our data suggest that the P681R mutation is a hallmark that characterizes the virological phenotype of the B.1.617.2/Delta variant and is closely associated with enhanced pathogenicity.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design:
To investigate the virological property of the B.1.617.2/Delta variant, the following recombinant viruses were generated by circular polymerase extension reaction (CPER) [Torii et al., Cell Rep., 2021; PMID: 33838744]: (i) WK-521 strain (GISAID ID: EPI_ISL_408667) with D614G mutation, (ii) WK-521 with D614G/P681R, (iii) GFP-inserted WK-521 with D614G, and (iv) GFP-inserted WK-521 with D614G/P681R. Regarding the recombinant viruses above and clinical isolates [a B.1.617.2/Delta isolate (EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (EPI_ISL_479681)], the viral supernatant stock (referred to as working virus) was prepared as follows: 100 μl of the seed virus was inoculated into VeroE6/TMPRSS2 cells (5,000,000 cells in a T-75 flask). At one hour after infection, the culture medium was replaced with Dulbecco’s modified Eagle’s medium (low glucose) (Wako, Cat# 041-29775) containing 2% FBS and 1% PS; at 2-3 days postinfection, the culture medium was harvested and centrifuged, and the supernatants were collected as the working virus. The genome sequences of the working viruses were verified using a viral RNA-sequencing analysis. Viral RNA was extracted using QIAamp viral RNA mini kit (Qiagen, Cat# 52906). The sequencing library for total RNA-sequencing was prepared using NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs, MA, Cat# E7530). Paired-end, 150-bp sequencing was performed using MiSeq (Illumina, San Diego, CA) with MiSeq Reagent Kit v3 (Illumina, Cat# MS-102-3001).
contributor: The Genotype to Phenotype Japan (G2P-Japan) Consortium


title: Transcriptomic and phytohormone profiling reveal early stage molecular variations upon co-application of abscisic or gibberellic acids with Fusarium graminearum-challenge of wheat

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

institute: National Research Council, Canada

summary: A comparative transcriptomic analysis of the responses arising 24 hours after infection of the susceptible T. aestivum variety ‘Fielder’, by Fg with co-application of either abscisic acid (ABA), gibberellic acid (GA) or the ABA-signaling inhibitor AS6, compared to stand-alone treatments is reported. Relevance of transcriptomic responses were assessed by differential expression feature evaluations (DEFE), highlighting that co-applied GA elicits a relatively strong opposing influence on Fg modulated genes, while co-applied ABA elicits similar responses to Fg. Co-applied AS6 elicited an opposing effect on gene regulation compared to co-applied ABA, and based on its lack of biological effect, was instrumental in reducing the identity of genes relevant to eliciting ABA and GA effects, to a subset of genes, largely defined within four DEFE patterns. A more targeted investigation of the impact of the co-applied conditions with respect to plant phytohormone biosynthesis and signaling pathways, correlated with select phytohormone profiles, confirmed activation of the ABA and GA pathways. Further analyses highlighted a novel interaction, potentially representing cross-talk, between co-applied ABA and the brassinosteroid signaling pathway. Additional responses within the classical defense hormone pathways as well as auxin and cytokinin pathways were found to correlate with expected defense responses. Togther these results yield insight into a range of mechanisms potentially underlying the observed contributions of ABA and GA to wheat susceptibility and resistance respectively to Fg, raising novel hypotheses for consideration in the development of FHB resistant wheat lines and agronomic practices in the longer term.

overall_design: In this paper, a comparative transcriptomic analysis of the responses arising 24 hours after infection of the susceptible T. aestivum variety ‘Fielder’, by Fg with co-application of either abscisic acid (ABA), gibberellic acid (GA) or the ABA-signaling inhibitor AS6, compared to stand-alone treatments is reported.

first: Michele

last: Loewen

first: Leann

last: Buhrow

first: Youlian

last: Pan


title: Expression data of mRNA from normal utricle and vestibular flat epithelium of adult mice

city: Beijing

first: Lu

last: He

address: No.95 Yongan Road

institute: Bejing Friendship Hospital, Capital Medical University

summary:
The vestibular sensory epithelium may degenerate into a layer of flat cells, known as flat epithelium, after a severe lesion, but the pathogenesis of vestibular flat epithelium remains unclear.
We used microarrays to detail the global programme of gene expression in normal utricle and vestibular flat epithelium and identified whether epithelial-mesenchymal transition participite in this process

overall_design: High dose of streptomycin was inoculated into the inner ear through the posterior semicircular canal to induce a severe lesion in the adult mouse utricle, normal utricle and vestibular flat epithelium samples were collected for RNA extraction and hybridization on Affymetrix mRNA arrays.

first: Guo-Peng

last: Wang

first: Jing-Ying

last: Guo

first: Zhong-Rui

last: Chen

first: Ke

first: Shu-Sheng

last: Gong


title: MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni

city: LONDON

first: Fauzy

last: Nasher

address: Keppel Street,

institute: London School of Hygiene and Tropical Medicine

summary: Methods: RNA-Seq was used to identify differentially expressed genes between wild type strains, ∆rrpA  and ∆rrpB mutants at mid-log (~6 hrs) of growth. 11168H wild type, 11168H∆rrpA, 11168H∆rrpB and 11168H∆rrpAB were plated out on BA plates and incubated at 37°C under microaerobic conditions for 6 hrs. RNA was extracted from the pelleted bacteria cells using PureLink™ RNA Mini Kit (Invitrogen), following manufactures protocol. RNA was isolated from five independent experiments performed on different days Ribosomal RNA was depleted using Ribominus (Invitrogen).Libraries were prepared using TruSeq® Stranded mRNA (Illumina).The paired-end reads were trimmed and filtered using Sickle v1.200  by using a sliding window approach and trimming the reads where the average base quality drops below 20. Only the reads that were above 10 bp length were kept after trimming. Bowtie2 was used to map the reads against the reference sequences; C. jejuni strains 11168H assembly GCA_900117385.1. This generated the mapping in SAM format which were converted to BAM format using Samtools  and were index sorted. We used gffread from cufflinks suite to convert annotations from GFF to GTF format. These were used in Bedtools (with multicov-bams option)with the mapped reads to generate transcript counts per samples. A shell utility by the authorswas then used to collate all these transcripts into a n=20 samples x p=1,628 transcripts for 11168H strain. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as meta data associated with the study (multifactorial design). We used DESeq DataSet from Matrix()function fromDESeq2  package with the adjusted p-value significance cut-off of 0.05 and log fold change cut-off of 1.5. This function uses negative binomial GLM to obtain maximum likelihood estimates for the transcripts log fold change between the two conditions.

overall_design: Transcriptome profiles of Campylobacter jejuni 11168H and its ∆rrpA, ∆rrpB and ∆rrpAB mutants.

first: Umer

middle: Z

last: Ijaz


first: Lydia

last: Freddolino

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

summary: There is increasing evidence that microbes maintain a structured chromosome, which in turn impacts gene expression. However tools to profile the genome landscape and binding of key architectural proteins have been limited. We recently discovered densely occupied, multi-kilobase regions in E. coli that are transcriptionally silent, similar to eukaryotic heterochromatin. These regions, termed EPODs, overlap metabolic pathways and parasitic elements such as prophages. Here, we investigate the contributions of nucleoid associated proteins (NAPs) to these domains by examining the impacts of deleting NAPs on EPODs genome-wide in E. coli and an evolutionarily distant species, Bacillus subtilis. We identify key NAPs contributing to the silencing of specific EPODs, where deletion of a particular NAPs opens a chromosomal region to RNA polymerase binding. In E. coli, we distinguish novel xenogeneic silencing NAPs, Fis and Hfq, that are essential for cell viability in the presence of domesticated prophages. Furthermore, we show that changes in EPODs facilitate an extra layer of transcriptional regulation to prepare cells for exposure to exotic carbon sources. Our findings demonstrate a new suite of mechanisms through which genomic architecture primes bacteria for changing metabolic environments and silences harmful genomic elements

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
IPOD-HR, ChIP-seq, RNA-seq of E. coli nucleoid associated protein deletions

Please note that the processed data for the RNA-seq samples have been replaced and the data processing description has been updated on 12/28/2021.

first: Haley

last: Amemiya

first: Thomas

middle: J

last: Goss

first: Taylor

last: Nye

first: Rebecca

last: Hurto

first: Lyle

last: Simmons

first: Peter


title: Cell type-specific chromatin accessibility in kidney.

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: We applied scATAC-seq to construct a cell type-specific epigenetic landscape of kidney at single-cell resolution.

overall_design: Single-cell ATAC-seq in human kidney

first: Qi

first: Yang

last: Zhang


title: SPEN is required for Xist upregulation during initiation of X chromosome inactivation

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

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

overall_design: Refer to individual Series


title: RNAseq of Runx1 ck/o B cells at the resting B cell stage and after 3 hours of activation with anti-IgM

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: We report the analysis by RNAseq of the changes in gene expression in mature B cells from mice that had the Runx1 gene conditionally knocked out at the transitional B cell stage.

overall_design: Examination of polyA+ mRNAs from resting B cells isolated from mouse spleen where Runx1 exon 4 was deleted at the transitional B cell stage due to the expression of Cre under the CD23 promoter. The RNAseq analysis was carried out on three replicates for each cell type (control CD23-iCre B cells and CD23-iCre/Runx1 ck/o=Runx1-KO B cells) and for each condition (resting B= 0hrs and 3hrs activation with anti-IgM+IL4). The Runx1 c-k/o / Cd23-Cre conditional knockout mice were generated by crossing the Runx1fl/fl mouse line (generously provided by Nancy Speck, University of Pennsylvania) with the Cd23-Cre transgenic mouse line (generously provided by Meinrad Busslinger, IMP Vienna).

first: Inesa

last: Thomsen

first: Niall

last: Dillon

first: Pierangela

last: Sabbattini

first: Yi


title: Genome surveillance through repression of intronless mobile elements by the HUSH complex

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

institute: AstraZeneca

summary: All life forms defend their genome against DNA invasion. Eukaryotic cells recognize incoming DNA and limit transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long interspersed element-1 retrotransposons (L1s) and retroviruses through histone H3 Lys9 trimethylation (H3K9me3). How HUSH recognizes and initiates silencing of these invading genetic elements is unknown. Here, we show that HUSH is able to recognize and transcriptionally repress a broad range of long, intronless transgenes. Intron insertion into HUSH-repressed transgenes counteracts repression, even in the absence of intron splicing. HUSH binds transcripts from the target locus, prior to and independent of H3K9me3 deposition, and target transcription is essential for both initiation and propagation of HUSH-mediated H3K9me3. Genomic data reveals how HUSH binds and represses a subset of endogenous intronless genes generated through retrotransposition of cellular mRNAs. Therefore, intronless cDNA, a hallmark of reverse transcription, provides a versatile means to distinguish invading retroelements from host genes and allows HUSH to protect the genome from ‘non-self’ DNA, despite no prior exposure to the invading element. Our findings reveal the existence of a genome surveillance system and explain how it provides immediate protection against newly acquired elements while avoiding inappropriate repression of host genes.

overall_design: UV-crosslinked RNA immunoprecipitation followed by next generation sequencing (UV-RIPseq) to identify RNA interactome of Periphilin. ChIPseq to identify methylation changes over lentiviral reporter and CRISPR/Cas9-modified endogenous locus.

first: Marta

last: Seczynska

first: Stuart

last: Bloor

last: Martinez Cuesta

first: Paul

last: Lehner


title: RUNX1 controls the rate of cell cycle entry during naive B cell activation by regulating expression of cell cycle and immunomodulatory genes in response to BCR stimulation


title: Hyperglycemia in Acute COVID-19 is Characterized by Adipose Tissue Dysfunction and Insulin Resistance

status: Public on Sep 29 2021

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: RNA sequencing was performed on Golden Syrian hamster fat tissue depots from hamsters inoculated with SARS-CoV-2 in PBS or PBS only

overall_design: RNA sequencing of Mock infected or SARS-CoV-2 treated hamsters treated

first: James

last: Lo

first: Robert

last: Schwartz


title: RNA-sequencing of mouse mammary tumor organoids that were modified to generate knockout lines for SOX4

city: Utrecht

first: Guy

last: Roukens

address: Uppsalalaan 8

institute: UMCU

summary: The transcription factor SOX4 is widely expressed during development and is essential to maintain progenitor pools in a variety of organs. In breast cancer SOX4 has been shown to be associated with poor survival and increased tumor size and metastasis formation. This has mostly been attributed to the ability of SOX4 to regulate Epithelial-to-Mesenchymal-Transition (EMT). However, SOX4 regulates target gene transcription in a plastic manner that is dependent on the cellular and epigenetic context. In this study we have investigated the loss of SOX4 in mammary tumor development utilizing organoids derived from a PyMT genetic mouse model. CRISPR-mediated loss of SOX4 led to a strong impairment in growth of primary mammary tumors and subsequent metastases through an EMT-independent mechanism. Instead, SOX4 is required for inhibiting differentiation by controlling genes that are highly activated in foetal mammary stem cells (fMaSC). These SOX4-dependent genes are associated with cell cycle progression, DNA biosynthesis, RNA processing and ribosome biogenesis suggesting that SOX4 controls active cycling of tumor cells. Analysis of genes co-expressed with SOX4 in the TCGA and METABRIC studies revealed that these cell cycle-related genes correlate with SOX4 expression in human tumors. Our study identifies a novel role for SOX4 in maintaining mammary tumors in an undifferentiated proliferative state.

overall_design: Organoids were derived from tumors from a MMTV-PyMT; MMTV-Cre; Ecadherin-mCFP genetically engineered mouse model. Control and SOX4KO organoids were generated using CRISPR/Cas9. We performed both bulk RNA-seq and single-cell RNA-seq to understand the consequences of loss of SOX4 in this breast cancer model.

last: Coffer


title: The Cholinergic Anti-Inflammatory Pathway Regulates Mammalian Heart Regeneration

status: Public on Sep 28 2021

city: La Jolla

first: Rebecca

middle: J.

last: Salamon

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

summary: Bulk RNA expression profiles were captured from hearts of alpha7 nicotinic acetylcholine receptor (Chrna7) knockout (KO) and wild type (WT) mice that underwent myocardial infarction (MI) or sham (SH) surgery at postnatal day 1 and full ventricle collection at 7 days post-surgery

overall_design: Heart ventricle mRNA profiles were generated from Chrna7 (Jax #003232) KO and WT neonatal mice by high throughput sequencing, in quadruplicates, on the Illumina HiSeq 4000.

first: R

first: M

last: McKeon

first: A

middle: I

last: Mahmoud


title: Genome-wide maps of transcription factor binding and histone modifications in splenic resting B cells isolated from mice

first: LMS

last: Bioinformatics Core

summary: Runx1 in resting B cells co-localises with the nucleosome remodeler subunit SRCAP and with the polycomb factor RING1B at promoter and enhancers of active and poised genes.

overall_design: Resting B cells were isolated from spleen of wild-type mice by using an EasySep Negative Selection- Mouse B Cell Isolation Kit (STEMCELL Technologies). The cells from replicates designated PS1,2,3,5,10,11,12 were formaldehyde-fixed and ChIP was carried out.

last: Wang

first: Mohammad

last: Karimi

first: Sanjay

last: Khadayate


title: RNA sequencing data from PNX0010 clear renal cell carcinoma cells overexpressing PARG

status: Public on Sep 27 2021

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

summary: ccRCC PNX0010 cell line with stable overexpression of PARG under Doxycycline induction was generated. Transcriptome analysis linked malignance reductuin phenotype with changes in gene expression levels for lipid metabolism, interferon signaling and angiogenesis pathways along with the changes in expression of key cancer-related genes.

overall_design: PNX0010 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml Doxycycline and RNA isolated.

first: Danping

last: Guo

first: Alexei

last: Tulin


title: Acsbg1 dependent mitochondrial fitness is a metabolic checkpoint for tissue Treg cell homeostasis

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

summary: Regulatory T (Treg) cells, which belong to the CD4 T cell subset, are critical for immunological tolerance and immune homeostasis. Using a combination of RNA-seq and proteome analyses, we found that Acsbg1, a member of ACSL, is selectively expressed in Treg cells. Furthermore, we found that gene loci of Acsbg1 was epigenetically regulated and opened up by Smad2/3 in Treg cells. Deletion of Smad2/3 decreased expression levels of Acsbg1 compared to control T reg cells.  We show that the genetic deletion and pharmacological inhibition of Acsbg1 causes not only mitochondrial dysfunction, but also dampens other metabolic pathways including glycolysis and the TCA-cycle. The extrinsic supplementation of sgAcsbg1 Treg cells with oleoyl-CoA restored the phenotype of the Treg metabolic signature. Furthermore, we also found evidence of this pathway in ST2+ effector Treg cells in the lung, which underlies the enhanced immunosuppressive capacity in the airway inflammation. This study provide a framework of Acsbg1 serving as a metabolic checkpoint governing Treg cell homeostasis and the resolution of lung inflammation.

overall_design:
Related to Fig 2, RNA-seq was performed to investigate lipid synthesis genes that are specifically upregulated in Treg cells.
Related to Fig 3, RNA-seq and ATAC-seq was performed to investigate the role of Smad2/3 on the regulation of Acsl6 gene expression.
Related to Fig 5, RNA-seq was performed to investigate the role of Acsbg1 on the gene expression profile of T reg cells.

first: Takahiro

last: Nakajima

first: Yusuke

last: Kawashima

first: Satoru

last: Yokoyama

first: Hikari

middle: K

last: Asou

first: Shigemi

last: Sasamoto

first: Koji

last: Hayashizaki

first: Yuki

last: Kinjo

first: Osamu

last: Ohara

first: Toshinori

last: Nakayama

last: Endo


title: Comparative analysis of blood-derived endothelial cells for designing next-generation personalized organ-on-chips

city: College Station

first: Tanmay

last: Mathur

state: TX

address: 101 Bizzell St

department: Biomedical Engineering

institute: Texas AM University

summary: Organ-on-chip technology has accelerated in vitro preclinical research of the vascular system, and a key strength of this platform is its promise to impact personalized medicine by providing a primary human cell-culture environment where endothelial cells are directly biopsied from individual tissue or differentiated through stem cell biotechniques.  But these methods are difficult to adopt in labs, and often result in impurity and heterogeneity of cells. This limits the power of organ-chips in making accurate physiological predictions. In this study, we report the use of blood-derived endothelial cells as alternatives to primary and iPSC-derived endothelial cells. Briefly, the genotype, phenotype and organ-chip functional characteristics of blood-derived outgrowth endothelial cells were compared against commercially available and most used primary endothelial cells and iPSC-derived endothelial cells. Through RNA sequencing we observe differences in gene expression profiles between different sources of endothelial cells, however blood-derived cells are relatively closer to primary cells than iPSC-derived suggesting that blood-derived endothelial cells may serve as an equally effective cell source for functional studies and organ-chips compared to primary cells or iPSC-derived cells.

overall_design: Study differences in transcriptional profiles of human umbilical vein endothelial cells, iPSC-derived endothelial cells and blood derived outgrowth endothelial cells

first: James

last: Tronolone

first: Abhishek

last: Jain


title: Expression data from mouse lung

city: Osaka

first: Takako

last: Fukuda

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chimical Co., Ltd

summary:
Female Crlj:CD1(ICR) mice were fed diets containing 0 (control),20, 500, 2500 and 5000 ppm permethrin for periods of 7 days.
We used microarrays to evaluate gene expression profiling in mouse lung at the early phase of treatment with permethrin.

overall_design: After treatment periods, lungs of 15 mice (3 mice in each group) were excised for RNA extraction and hybridization on Agilent microarrays.

first: Ayako


title: Differentiation of the high night temperature response in leaf segments of rice cultivars with contrasting tolerance

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Transcript and metabolite profiling were performed in leaf segments (sheath, base, middle, tip) of six rice cultivars with different sensitivity to high night temperatures (HNT). On the phenotypic level, leaves of HNT-sensitive rice cultivars showed clear stress symptoms by chlorosis and necrosis while almost no leaf phenotype different from the control was observed for the tolerant varieties. The aim of this study was to identify molecular key-player for HNT-sensitivity causing leaf senescence.

overall_design: Leaf sheath and segments of leaf blade (base, middle, tip) of six rice cultivars of the subspecies indica and japonica were analyzed. High night temperature (HNT) sensitivity was determined before and 3 cultivars of each class (tolerant, sensitive) were investigated under two different conditions (control and HNT treatment). In total, 48 samples were sequenced representing one cultivar for each condition and segment. Each sample was a pool of 5 individual replicates.

first: Stephanie

last: Schaarschmidt

first: Ulrike

last: Glaubitz


title: Expression data from Solanum lycopersicum after elicitor molecules treatment

city: Girona

first: Emilio

last: Montesinos

state: Girona

address: c/Pic de Peguera, 15. PCiT. Edif. Jaume Casademont, porta E, 4t pis

department: INTEA

institute: Universitat de Girona

summary:
After treatment with peptids, SA, JA and Et plants are primed due to the induction of plant immune system allowing to fight against plant pathogens.
We used microarray analysis to study the expression pattern of the diferents genes involved in plant defense mechanisms related to biotic and abiotic stresses

overall_design: The experimental design consisted of three biological replicates of 10 tomato plants (var. Rio Grande) per replicate and treatments consisted of peptide BP178 (125 µM), and flg15 (125 µM), SA (2.5 mM), JA (2.5 mM) and ethylene (reacting ethephon (1mM) with disodium hydrogen phosphate buffer (2.5mM)) and a water (NTC) non-treated control was used. We performed two experiments: Experiment 1 (NTC e1 vs BP178, SA, JA, Et); Experiment 2 (NTC e2 vs flg15). GeneChip™ Tomato Gene 1.0 ST Array (Affymetrix) was used for comparing transcriptomes from plants treated.

first: Laura


title: H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line [RNA-seq D4]

first: LMS

last: Bioinformatics Core

summary: To investigate the role of EZH2 in transcription regulation in mouse primordial germ cell like cells (PGCLCs), we isolated Ctrl and Ezh2 KO PGCLCs. Our data demonstrates that EZH2-mediated H3K27me3 is dispensible for transcription regulation in PGCLCs.

overall_design: Gene expression profiles of Ctrl and Ezh2 KO PGCLCs at PGCLC 4 days of induction.

first: Tien-Chi

last: Huang

first: Petra

last: Hajkova

first: YI-Fang

last: Wang


title: H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line [RNA-seq]

summary: To investigate the role of EZH2 in transcription regulation in mouse primordial germ cells, we isolated Ctrl and Ezh2 CKO male and female PGCs at E13.5. Our data demonstrates that EZH2-mediated H3K27me3 is required for regulating the expression of meiotic genes in the female germ cells. Furthermore, RNA-seq analysis shows that EZH2 is essential for transcriptional repression of retrotransposons.

overall_design: Expression profiles of Ctrl and Ezh2 CKO male and female mouse primordial germ cells at E13.5.


title: H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line [ChIP-seq]

summary: We used Ultra-Low native ChIP to interrogate the H3K27me3 and H3K9me3 chromatin states in primordial germ cells before and after gonadal reprogramming. Our data demonstrate that repressive heterochromatin is remodelled during epigenetic reprogramming.

overall_design: We mapped genome-wide distribution of H3K9me3 and H3K27me3 from E10.5 and E13.5 primordial germ cells using adapted ultra-low native ChIP (ULI-nChIP). This allowed us to investigate the chromatin dynamics during genome-wide DNA demethylation.


title: H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line


title: Next Generation Sequencing Quantitative Analysis of 0.5% BSA and IL10 treated Kasumi-1 cells' Transcriptomes

city: Tianjin

first: Yingxi

last: Xu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Examination the gene expression profile changes of Kasumi-1 cells treated with rhIL10.

overall_design: Kasumi-1 cells treated with rhIL-10(rhIL-10) or 0.5% BSA (Ctrl) for 72h

first: Min

first: Jianxiang


title: FGF19 as a Surgical Factor Contributing to the Metabolic Effects of Gastric Bypass Surgery

status: Public on Sep 25 2021

city: South San Francisco

first: Lei

last: Ling

state: CA

address: 333 Oyster Point Blvd

institute: NGM Biopharmaceuticals

summary:
Gastric bypass surgery has proven to be the most effective treatment in controlling hyperglycemia in severely obese patients with diabetes. Here we show that FGF19, a gut hormone, is rapidly induced by bypass surgery in rodents and humans.  Administration of FGF19 achieves remission of diabetes through mechanisms beyond weight loss in animal models of diabetes, supporting a role of FGF19 as part of hormonal changes that influence metabolism following surgery. Through an unbiased phenotypic screen in diabetic mice, we identified selective, safe and effective FGF19 analogues. Unexpectedly, FGF19 analogue failed to correct hyperglycemia in patients with type 2 diabetes. In contrast, administration of FGF19 analogue resulted in rapid, robust and sustained improvement in liver fat content and histology in patients with non-alcoholic steatohepatitis, faithfully replicating effect of the surgery. Thus, our work identifies a strategy of replacing gastric bypass surgery by equally effective, but less invasive, treatment for non-alcoholic steatohepatitis.
We used microarrays to detail the global programme of gene expression affected by gastric bypass surgery in rats.

overall_design: Rat ileum were selected for RNA extraction and hybridization on Affymetrix microarrays. RNA was isolated from ileum of Zucker fa/fa rats 2 weeks after duodenum-jejunum bypass or sham surgery. RNA integrity and purity were confirmed by Bioanalyzer with RIN numbers > 9.0. Affymetrix rat gene 1.0 ST whole-transcript arrays were used for hybridization.

first: Alex

last: DePaoli

first: Stephen

middle: A

last: Harrison

first: Mei

last: Zhou

first: Daniel

middle: D

last: Kaplan

last: Trotter

first: Angelo

last: Paredes

first: Steven

last: Hunt

first: Ted

last: Adams

first: Marc

last: Learned

first: Hui

last: Tian

last: Rossi


title: Loss of executioner caspases-3 and -7 in intestinal epithelial cells is dispensable but can be compensated allowing normal gut homeostasis

status: Public on Sep 22 2021

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

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

overall_design: Refer to individual Series


title: Reciprocal Transcription Factor Networks Govern Tissue-Resident ILC3 Subset Function and Identity

status: Public on Sep 23 2021

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Innate lymphoid cells (ILCs) play important roles in health and tissue homeostasis. While the transcriptional networks that drive their development have been defined, the transcriptional requirements that support the phenotypes and functions of mature tissue-resident populations remain poorly understood. Here we employed combinatorial inducible deletion of core transcription factors (TFs) to test how co-operative and antagonistic networks operate to control function and identity. Utilizing single cell sequencing and epigenetic profiling we dissect the complex interplay between ROR family member TFs and T-bet in determining the function and phenotype of ILC3 and NCR-lineage ILCs, defining the ontogeny and surface phenotype across a continuum of ILC3s and mature ILC1s in the small intestine, alongside the differential requirements for ROR family TFs in the maintenance of effector functions and phenotype in mature ILCs. Combined, our data demonstrates how TF networks integrate in vivo to sustain effector functions and restrict alternative differentiation programmes.

overall_design: Comparison of chromatin accessibility in small intestinal innate lymphoid cells expressing or lacking core lineage-defining transcription factors (TFs). Gene encoding core TFs are flanked with LoxP sites and can be deleted by the Cre recombinase (inducible action by administration of tamoxifen). The experiment contain biological replicates (2 or 3), each of them containing samples from 1 or 2/3 pooled mouse intestines.

first: David

last: Withers

first: Rémi

last: Fiancette

first: Claire

last: Willis


title: A Mutation in Transmembrane Protein 135 Impairs Lipid Metabolism in Mouse Eyecups

city: Madison

first: Akihiro

last: Ikeda

state: Wisconsin

address: 5322 Genetics Biotechnology Center, 425 Henry Mall

department: Medical Genetics

institute: University of Wisconsin-Madison

summary: Aging is a significant factor in the development of age-related diseases but the molecular underpinnings of how aging disrupts cellular homeostasis to cause retinal disease is unknown. Here, we further our studies on Transmembrane protein 135 (Tmem135), a gene involved in retinal aging, by examining the transcriptomic profiles of wildtype, heterozygous and homozygous Tmem135 mutant posterior eyecup samples through RNA sequencing (RNA-Seq). We found significant gene expression changes in both heterozygous and homozygous Tmem135 mutant mouse eyecups that correlates with visual function deficits. Further analysis revealed many genes involved in lipid metabolism are changed due to the Tmem135 mutation. We confirm these changes by finding increased lipid accumulation in mutant Tmem135 eyecup samples. Since mutant Tmem135 mice have similar ocular pathologies as human age-related macular degeneration (AMD) eyes, we compared our homozygous Tmem135 mutant eyecup RNA-Seq dataset with datasets of human AMD donor eyes. We find similar changes in genes involved in lipid metabolism between the homozygous Tmem135 mutant eyecups and AMD donor eyes. Our study suggests that the Tmem135 mutation affects lipid metabolism as similarly observed in human AMD eyes, thus Tmem135 mutant mice can serve as a good model for the role of dysregulated lipid metabolism in AMD.

overall_design: mRNA profiles of WT, Tmem135FUN025/+, and Tmem135FUN025/FUN025 posterior eyecups without the neural retina

first: Michael

last: Landowski

first: Vijesh

last: J. Bhute

first: Tetsuya

last: Takimoto


title: ARID3a is Required for Erythrocyte Lineage Differentiation of Hemin Stimulated Human K562 Cells

city: Norman

first: Carol

last: Webb

state: Oklahoma

address: Stephenson Parkway

department: Department of Medicine

institute: OUHSC

summary: Inhibition of ARID3a by shRNA in hemin-induced K562 cells results in significant decrease of erythroid specific lineage factors and alpha-globin genes.

overall_design:
Differential expression analysis of K562 cells treated with hemin and hemin + ARID3a shRNA.

For ATAC-seq samples, AL and BH represent the KO or "--" and BH and P represent wild type or "++" clones.

first: Josh

last: Garton


title: Identification of DNA Methylation Predicts Onset of PTSD and Depression Following Trauma

status: Public on Sep 21 2021

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary: We identified hyper- and hypo-methylated cytosine sites and genes genome-wide using bisulfite sequencing in comparison between PTSD and control group, and between Major Depressive Disorder (MDD) and control group,

overall_design: We performed differential methylation analysis: (1) PTSD and MDD; n = 12),  (2) MDD (patients with MDD only; n = 12), and (3) control (patients who did not have PTSD or MDD; n = 9).

first: S

first: J

last: Gill


title: Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary: This study determines the genome-wide binding profile of a V5-tagged KLF5 transription factor exogenously expressed in mouse embryonic stem cells.

overall_design: V5 ChIP-seq was performed in wild type mouse ES cells  overexpressing a V5-tagged KLF5 protein, and in wild-type D3 mouse ES cells as a  control. Normal IgGs pulldowns and input DNA were also sequenced as controls.

first: Claudia

last: Cattoglio

first: Martin

last: Kinisu

first: Lin

last: He


title: Spt4 helps RNAPII pass the +2 nucleosome barrier in vivo

city: Oxford

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

summary:
Aim and Methods: To understand the precise role of Spt4 in budding yeast, various high throughput sequencing techniques were used. Nucleosome positions were studied using MNase-seq in WT and spt4∆ cells. The position of RNAPII was examined using NET-seq in spt4∆ cells or cells in which Spt4 has been anchored away to the cytoplasm (Spt4 AA). RNAPII was also mapped in cells in which Spt5 has been anchored away to the cytoplasm (Spt5 AA). Steady-state transcript levels were assessed using RNA-seq in samples coupled with NET-seq. The position of the Spt4 on RNAPII was mapped at single nucleotide resolution using TEF-seq. With the same technique, the position of Spt5 on RNAPII was investigated in wild type (WT) and spt4 knock-out (spt4∆) cells. The position and levels of the pre-initiation complex were assessed using ChIP-seq on Sua7(TFIIB) in WT and spt4∆ cells.
Results: The interaction between the Spt4/5 complex and RNAPII periodically changes as RNAPII transitions through nucleosomes. The dynamic interaction of Spt5 with RNAPII is dependent on Spt4. In spt4∆ and Spt4 AA cells, RNAPII distribution is altered in a similar way compared to their respective controls. After transcribing into nucleosomes, RNAPII accumulates upstream of nucleosome dyads, especially around the +2 nucleosome. In Spt5 AA cells, the distribution and amount of RNAPII on genes are severely affected. Nucleosome positions are altered in spt4∆ cells. Although the position of the +1 nucleosome remains unchanged, nucleosome spacing from this point is increased, and the level of increase in nucleosome spacing correlates with the level of RNAPII accumulation.
Conclusion: This work suggests that Spt4 regulates nucleosome positioning by a mechanism related to transcription and promotes RNAPII movement through nucleosome barriers, especially the barrier set by the +2 nucleosome.

overall_design: MNase-seq in WT and spt4∆ in triplicates; Transcription elongation factor sequncing (TEF-seq) in WT and spt4∆ for Spt4 or Spt5;  Native elongation transcript sequencing (NET-seq) in WT, spt4∆, Spt4-AA, and Spt5-AA; RNA-seq in WT, spt4∆, Spt4-AA, and Spt5-AA; ChIP-seq in WT and spt4∆ for Sua7.

first: Ülkü

first: Harry

last: Fischl

first: Jane

last: Mellor


title: Platelet microRNA bioinformatics analysis in patients with hepatocellular carcinoma

city: Guangzhou

first: Beibei

last: Zhu

state: Guangdong

address: No. 613 W. Huangpu Avenue, Tianhe

department: Department of Infectious Diseases

institute: The First Affiliated Hospital of Jinan University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:To reveal platelet microRNAs（miRNAs） expression status and its potential clinical significance in patients with hepatocellular carcinoma(HCC) by bioinformatics analysis.
Method: 5 patients (4 male, 1 female) with hepatocellular carcinoma, and 5 healthy individuals(3 male，2 female) as control from June 2019 to November 2019 were taken part in this cohort. The leukocyte—depleted platelets were prepared from the anticoagulated whole blood samples. The platelet RNA were extracted to construct miRNA libraries by using conventional gradient centrifugation, MACS and instructions of miRNeasy Mini Kit, performed data analysis and bioinformatics analysis after sequencing.
Results: The DESeq2 package of R software was used to compare the gene expression level difference between the HCC group and the normal group. The cut-off criteria of differentially expressed miRNAs was |log2FC| >1 and p<0.05. Total 250 differentially expressed miRNAs were screened out, of which 111 miRNAs were down-regulated and 139 miRNAs were up-regulated. Gene Ontology(GO) analysis found that the differential miRNAs are involved in Positional Regulatory of Catabolic process, positional regulatory of cell catabolic process, negative regulation of phosphorylation, Wnt signaling pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that platelet miRNAs are involved in a number of signal pathways, including FoxO signaling pathway, ubiquitin mediated proteolysis, axon guidance, autophagy-animal, TGF-beta signaling pathway.
Conclusion:MiRNAs in platelets of patients with hepatocellular carcinoma were differentially expressed. Platelet miRNAs should be involved in the biological process of hepatocellular carcinoma, while more samples and molecular biological experiments are needed.

overall_design: 5 patients(4 males, 1 females) with hepatocellular carcinoma, and 5 healthy individuals(3 males，2 females) as control in this study

first: Shanshan

last: Gu

first: Hongke

last: Zhou

first: Youpeng

last: Chen


title: CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo

status: Public on Sep 20 2021

city: Stanford

first: Jin Billy

last: Li

state: CA California

address: 240 Pasteur Drive

department: Genetics Department

institute: Stanford University

summary: RNA base editing represents a promising alternative for genome editing. Recent approaches harness the endogenous RNA editing enzyme ADAR to circumvent problems related to the ectopic expression of an editing enzyme, but they suffer from sequence restriction, lack of efficiency, and bystander editing. Here, we present in‐silico optimized CLUSTER guide RNAs, which bind their target mRNAs in a multivalent fashion and thereby enable editing with unprecedented precision as shown by next generation sequencing. CLUSTER guide RNAs can be genetically encoded and manufactured into viruses to work in various cell lines. They achieve on‐target editing on endogenous transcripts like GUSB and NUP43 with yields up to 45% without bystander editing and have been shown to recruit endogenous ADAR in vivo. The CLUSTER approach tremendously enlarges the sequence space available for guide RNA design and opens new avenues for drug development in the field of RNA base editing.

overall_design: Identification of off-target editing events and gene expression changes in HEK293FT cell line transfected with guide RNA (gRNA) for RNA editing by RNA-Seq, 2 samples (Cluster gRNA and Leaper gRNA) , 1 control sample (NT gRNA), 2 biologically independent experiments for each sample, 6 samples in total

first: Philipp

last: Reautschnig

first: Nicolai

last: Wahn

first: Jacqueline

last: Wettengel

first: Annika

middle: E

last: Schulz

first: Ngadhnjim

last: Latifi

first: Paul

last: Vogel

first: Tae-Won

last: Kan

first: Laura

middle: S

last: Pfeiffer

first: Christine

last: Zarges

first: Ulrike

last: Naumann

first: Lars

last: Zender

first: Jin

first: Thorsten

last: Stafforst


title: Modeling Notch-induced tumor cell survival in the Drosophila ovary identifies cellular and transcriptional response to nuclear NICD accumulation

status: Public on Sep 19 2021

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

summary: Notch is a conserved developmental signaling pathway that is dysregulated in many cancer types, most often through constitutive activation. Tumor cells with nuclear accumulation of the active Notch receptor, NICD, generally exhibit enhanced survival while patients experience poorer outcomes. To understand the impact of NICD accumulation during tumorigenesis, we developed a tumor model using the Drosophila ovarian follicular epithelium. Using this system we demonstrated that NICD accumulation contributed to larger tumor growth, reduced apoptosis, increased nuclear size, and fewer incidents of DNA damage without altering ploidy. Using bulk RNA sequencing we identified the key Notch-induced targets involved in cell survival and DNA damage repair which were alternatively regulated prior to tumor formation. Finally, using single-cell RNA sequencing we demonstrated that genes contributing to many pathways are altered following tumor formation in a cell-type-specific manner. Ectopically expressing NICD produced dysregulated expression of genes involved in cell death regulation, immune and stress response, JAK/STAT signaling, cytoskeletal binding, adhesion, polarity, and growth regulation. This valuable tumor model for nuclear NICD accumulation in adult Drosophila follicle cells has allowed us to better understand the specific role of nuclear NICD accumulation in tumor cells in tumor cell survival and tumor progression.

overall_design: Whole-tissue RNA-Seq (2 replicates per genotype; 2 time-points - 24h and 96h) of tjTS>GFP (Control) and tjTS>lglRNAi, tjTS>NICD and tjTS>NICD+lglRNAi (Samples) and single-cell RNA-Seq (1 replicate; 1 time-point - 72h) of w1118 cells (Control) of the Drosophila ovary and tjTS>lglRNAi, tjTS>NICD and tjTS>NICD+lglRNAi cells (Samples) of the Drosophila ovary. Single-cell RNA-Seq: 10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry and Sequencing platform: Illumina NovaSeq 6000.

first: Deeptiman

last: Chatterjee


title: Identification and evolutionary comparison of circular RNAs in five mammalian species and three organs.

city: Lausanne

first: Franziska

last: Gruhl

address: University of Lausanne, Quartier Sorge

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary:
Circular RNAs (circRNAs) are found across eukaryotes and can function in post-transcriptional gene regulation. Their biogenesis through a circle-forming backsplicing reaction is facilitated by reverse-complementary repetitive sequences promoting pre-mRNA folding. Orthologous genes from which circRNAs arise overall, contain more strongly conserved splice sites and exons than other genes, yet it remains unclear to what extent this conservation reflects purifying selection acting on the circRNAs themselves.
Our analyses of circRNA repertoires across five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous genes from different species. Even the circRNAs from shared loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution – as a byproduct of splicing in orthologs prone to transposable element insertion. Overall, our findings argue against widespread functional circRNA conservation.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus
Monodelphis domestica

overall_design: Annotation and expression analyses of circRNAs using RNA-sequencing data in five mammalian species (opossum, mouse, rat, rhesus macaque, human) and three organs (liver, cerebellum, testis). Included are three biological replicates for each condition (conditions = species and tissues). All organisms used were male and wild type. Each replicate was splitted into two: the first sample was directly used for library preparation, the second one treated with RNase R prior library preparation to degrade linear RNAs, which subsequently enrichs circRNAs. Samples were sequenced using Illumina paired-end sequencing and circRNAs annotated and analysed for their evolutionary history.

first: Peggy

last: Janich

first: Henrik

last: Kaessmann

first: David

last: Gatfield


title: RNA-sequencing of ILC3 during murine EAE

status: Public on Sep 17 2021

city: New York

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: To determine the unique gene expression profile of central nervous system (CNS)-associated ILC3, we performed RNA-sequencing on sort-purified ILC3 from the CNS, cervical lymph nodes (cLN) and small intestine lamina propria (SI-LP) during EAE.

overall_design: ILC3s (Live, CD45+, CD3epsilon-, CD5-, CD8alpha -, NK1.1-, CD11b-, CD11c-, CD19-, CD127+, CD90.2+, ROR-gamma-t(GFP)+) (0.5-1 x 10^3 per tissue/mouse) were sort-purified using from Rorc-eGFP mice at day 15 active EAE (n = 4 mice, 4 samples each CNS/cLN, 2 samples SI-LP). Cells were sorted using FACSAria II cell sorter (BD Biosciences). Sorted cells were used to prepare RNA sequencing libraries by the Epigenomics Core at Weill Cornell Medicine, using the Clontech SMARTer UltraLow Input RNA Kit V4 (Clontech Laboratories). Sequencing was performed on an Illumina HiSeq 4000, yielding 50-bp single-end reads. Raw sequencing reads were demultiplexed with Illumina CASAVA (v.1.8.2). Adapters were trimmed from reads using FLEXBAR (v.2.4) and reads were aligned to the NCBI GRCm38/mm10 mouse genome using the STAR aligner (v.2.3.0) with default settings. Reads per gene were counted using Rsubread. For mouse cell-surface staining: CD45 (30-F11), CD3-epsilon (145-2C11), CD5 (53-7.3), CD8-alpha (53-6.7), NK1.1 (PK136), CD11b (M1/70), CD11c (N418), CD19 (eBio1D3), CD127 (A7R34), CD90.2 (Thy1.2) (30-H12).

first: John

last: Grigg

last: Sonnenberg


title: The butyrophilin 1a1 knock-out mouse revisited: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation

first: Thomas

middle: Joshua

last: Meyer

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary:
Purpose:  To assess global changes to the levels of mRNA and protein in butyrophilin-null mice (Btn1a1-/-), which were previously shown to be defective in regulated milk-lipid secretion in the lactating mammary gland.
Methods:  mRNA profiles of wild-type (WT) and Btn1a1-/-mice were generated by mRNA/cDNA library preparation (Illumina), qPCR quantitation, cluster generation and pair-end deep sequencing (Illumina HiSeq 4000 sequencer) using an Illumina HiSeq SBS kit.  Changes in mRNA levels (null/WT ≥ ± 2-fold; adjusted p ≤ 0.05) were assesed by GSEA and IPA analysis and compared with a proteomic analysis of the same sample set..
Results:  Samples had 95-167 million pass filter reads (92% above Q30).  Mapping of all samples was > 97% (mm10 reference genome).  Significant changes in mRNA amounts accounted for 1.4% of 11,834 transcipts (113 up and 53 down regulated).  Only 10 mRNA/protein pairs were significantly upregulated and one (Btn1a1) downregulated. Pathways and networks associated with inflammation, apoptosis and the cell cycle were upregulated and lipid synthesis and metabolism were downregulated.  Biochemical and histochemical analysis confirmed that lactation is maintained in null animals, in the face of significant apoptosis, by the continual regeneration of secretory epithelial cells. Cell death proceeded through several pathways including activation of caspases 8 and 3 and not by the lysosomal lysis pathway predominant in WT cells
Conclusions: Ablation of Btn1a1 has multiple effects on milk-secreting mammary cells, including disruption of lipid secretion, increased cell damage and death. Lactation is maintained by continuous regeneration of the epithelium.  Expression of functional Btn1a1 is essential for the maintainance of terminally differentiated mammary cells and optimal milk production throughout lactation.

overall_design: RNA-seq analysis of 12 mice (5 WT and 7 Btn1a1 KO).

first: Jaekwang

last: Jeong

first: Anil

last: Kadegowda

first: Lisa

first: Jerry

last: Dinan

first: Roberto

last: Weigert

first: Ian

last: Mather


title: The Functional Roles of RNAs Cargoes Released by Neutrophil-Derived Exosomes in Dermatomyositis

city: Changsha

first: Liya

last: LI

state: Hunan

address: Xiangya Road 87

department: Rheumatology and immunology

institute: Xiangya Hospital of Central South University

summary: Dermatomyositis (DM) is an idiopathic inflammatory myopathy characterized by cutaneous manifestations. We first identified the profiles of noncoding RNAs (lncRNAs and miRNAs) in peripheral neutrophil exosomes (EXOs) of DM patients and explored their potential functional roles. Bioinformatics analyses were performed with R packages. Real-time quantitative PCR was used to validate the altered RNAs in DM neutrophil EXO-stimulated human dermal microvascular endothelial cells (HDMECs) and human skeletal muscle myoblasts (HSkMCs). In DM neutrophil EXOs, 124 upregulated lncRNAs (with 1,392 target genes), 255 downregulated lncRNAs (with 1867 target genes), 17 upregulated miRNAs (with 2,908 target genes), and 15 downregulated miRNAs (with 2,176 target genes) were identified. GO analysis showed that the differentially expressed (DE) lncRNAs and DE miRNAs participated in interleukin-6 and interferon-beta production, skeletal muscle cell proliferation and development, and endothelial cell development and differentiation. KEGG analysis suggested that DE lncRNAs and DE miRNAs were enriched in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways. Many novel and valuable DE lncRNAs and DE miRNAs interacted and cotargeted in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways. Our study suggests that neutrophil EXOs participate in DM pathogenesis through lncRNAs and miRNAs in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways.

overall_design: lncRNA and miRNA profiles of neutrophil exosomes in DM patients and NC.

first: Honglin

last: Zhu

last: Li

first: Xiaoxia

last: Zuo

first: Di

last: Liu

first: Hui

last: Luo


title: Identification of five cytotoxicity-related genes involved in the progression of breast cancer

status: Public on Sep 15 2021

city: Fushan

first: Jianhua

last: Xu

address: No. 12, Jinsha Avenue, Shunde District, Foshan, Guangdong, P.R. China

institute: Department of Laboratory Medicine Shunde Hospital of Guangzhou University of Chinese Medicine

summary: Breast cancer is one of the deadly tumors in women, and its incidence continues to increase. This study aimed to identify novel therapeutic molecules using RNA sequencing (RNAseq) data of breast cancer from our hospitals.

overall_design: 30 pairs of normal and cancerous tissues from the same excision were collected from the Affiliated Cancer Hospital of Guangzhou Medical University, the Affiliated Cancer Hospital of Sun Yat-sen University and Guangzhou Army General Hospital. RNA sequencing was performed by Guangzhou Huayin Health medical Group. Original reads of RNA sequencing data were normalized as FPKM data.

first: Yan

last: Zhang

first: Xu

middle: X

last: Wei

first: Wei

last: Yang

first: Hong

last: Shen