title: Desmosomal protein degradation as underlying causes of arrhythmogenic cardiomyopathy [PKP2 c.1755delA/WT and WT]

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

country: Netherlands

institute: LUMC

summary: Arrhythmogenic cardiomyopathy (ACM) is an inherited progressive cardiomyopathy. The pathophysiological events are well understood, yet the underlying molecular mechanisms remain undefined. Here we use patient originated hiPSC-derived cardiomyocytes bearing a pathogenic PKP2 mutation (PKP2 c.2013delC/WT), a corresponding knock-in mouse model carrying the equivalent murine mutation (Pkp2 c.1755delA/WT), and human explanted ACM hearts, to identify disease driving mechanisms. Pkp2 c.1755delA/WT mice over time displayed signs of ACM as observed by cardiac dysfunction and pathological remodeling. At a molecular level these mice showed a reduction in desmosomal and adherens junction proteins as well as disarray of the intercalated discs in areas of active fibrotic remodeling. These findings were validated in the mutant hiPSC-derived cardiomyocytes as well as human explanted ACM hearts, indicating both the conservation and relevance of protein degradation in the pathogenesis of the disease. Led by proteomics data, we demonstrated that the ubiquitin-proteasome system was responsible for the observed desmosomal protein degradation. These findings show the importance of appropriate disease modeling and provide means for therapeutic intervention for the prevention of ACM disease progression.

overall_design: cardiac tissue mRNA profiles from PKP2 c.1755delA/WT and WT mice.

first: Hoyee

last: Tsui


title: Single-cell RNA sequencing Analysis of Treg cells from mouse B16 melanoma tumors

status: Public on Mar 23 2023

city: New York

first: Ning

last: Yang

state: NY

country: USA

institute: MSKCC

type: Expression profiling by high throughput sequencing

summary: Based on single-cell RNA sequencing technology, we studies gene expression profiles in Treg cells isolated from mouse tumors before and after rMVA therapy. We identified differential Treg populations from tumors before and after rMVA therapy. The difference of Treg clusters in tumors were also identified.

overall_design: Foxp3-GFP mice were intradermally implanted with B16 cells at 5x10^5 cells at the right side. After 7-10 days, tumors were dissected and digested into single cells. After staining with antibodies against CD45, CD3, CD4, GFP+ cells were sorted in BD FACSAria cell sorter and applied into Chromium Single Cell V(D)J Solution from 10x Genomics according to the manufacturer’s instructions. Cell-barcoded 5′ gene expression libraries were sequenced on an Illumina No-vaSeq6000 system.

first: Adrian

middle: Y

last: Tan

first: Liang

last: Deng


title: Desmosomal protein degradation as underlying causes of arrhythmogenic cardiomyopathy

overall_design: hiPSC-derived cardiomyocyte mRNA profiles for PKP2 c.2013delC/WT and Reverted cells.

middle: J


title: Expansion of tolerogenic dendritic cells in neonatal lungs programs lymph node maturation, but impairs T cell proliferation

status: Public on Mar 24 2023

city: Birmingham

first: Aaron

last: Silva Sanchez

state: AL

address: 1825 University Boulevard

department: Medicine

institute: The University of Alabama at Birmingham

summary: Multiple mechanisms restrain inflammation in neonates, most likely to prevent tissue damage caused by overly robust immune responses against newly encountered pathogens. Here, we identify a population of pulmonary dendritic cells (DCs) that express intermediate levels of CD103 (CD103int) and appear in the lungs and lung-draining lymph nodes of mice between birth and 2 weeks of age. CD103int DCs express XCR1 and CD205 and require expression of the transcription factor BATF3 for development, suggesting that they belong to the cDC1 lineage. In addition, CD103int DCs express CCR7 constitutively and spontaneously migrate to the lung-draining lymph node, where they promote stromal cell maturation and lymph node expansion. CD103int DCs mature independently of microbial exposure and TRIF- or MyD88-dependent signaling and are transcriptionally related to efferocytic and tolerogenic DCs as well as mature, regulatory DCs. Correlating with this, CD103int DCs show limited ability to stimulate proliferation and IFN-γ production by CD8+ T cells. Moreover, CD103int DCs acquire apoptotic cells efficiently, in a process that is dependent on the expression of the TAM receptor, Mertk, which drives their homeostatic maturation. The appearance of CD103int DCs coincides with a temporal wave of apoptosis in developing lungs and explains, in part, dampened pulmonary immunity in neonatal mice. Together, these data suggest a mechanism by which DCs sense apoptotic cells at sites of noninflammatory tissue remodeling, such as tumors or the developing lungs, and limit local T cell responses.

overall_design: 3 samples with 2 replicates each. Each sample is one of the conventional Dendritic cell subsets found in mice neonatal lung (as defined in thispublication): CD11b+ SIRPa+, CD103Hi XCR1+, CD103 int XCR1+

last: Silva-Sanchez

first: Selene

last: Meza-Perez

first: Sara

middle: L

last: Stone

first: Leopoldo

last: Flores-Romo

first: Alex

middle: F

last: Rosenber

first: Frances

middle: E

last: Lund

first: Troy

middle: D

last: Randall


title: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [ChIP-Seq]

city: new haven

first: Yuping

last: Zhou

state: CT

address: 310 cedar street

department: OB/GYN

institute: Yale

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identify an unexpected functional role for E3 in fetal reproductive system and brain. We further identify a novel mechanism of estrogen action, through recruitment of epigenetic modifiers to estrogen receptors and their target genes, which doesn’t correlated with the traditional view of estrogen potency.”

overall_design: We administered E3 to pregnant mice, exposing the fetus to E3 and identified an unexpected functional role for E3 and a novel mechanism of estrogen action.

first: Hugh

middle: S

last: Taylor


title: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [NimbleGen]

type: Methylation profiling by genome tiling array

summary: We identify an unexpected functional role for E3 in fetal reproductive system and brain. We further identify a novel mechanism of estrogen action, through recruitment of epigenetic modifiers to estrogen receptors and their target genes, which doesn’t correlated with the traditional view of estrogen potency.


title: RNA-seq profiles of 5 differentially RNAi sensitive wild C. elegans strains in control and embryonic RNAi conditions

city: Atlanta

first: Avery

middle: Davis

last: Bell

state: GA

address: North Avenue

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: This dataset addresses two phenomena affected by reference strain bias in model organism research, specifically in the nematode C. elegans. I) C. elegans is the leading system for research into RNA interference (RNAi); this research has been conducted exclusively in the reference strain. However, sensitivity to RNAi is remarkably diverse across wild-type strains. Here, we used RNA sequencing to evaluate the transcriptional response of the reference strain and four other strains to RNAi by transcriptionally profiling these strains in three conditions: exogenous RNAi targeting germline-expressed genes 1) par-1 and 2) pos-1, and 3) the control condition. II) Gene expression quantification in non-reference strains relies on successful alignment of DNA reads to the reference genome, but high sequence divergence can lead to mapping failure. Here, we used this RNA-seq dataset to characterize the extent to which poor DNA genome assembly limits expression quantification inferences.

overall_design: RNA-seq profiles of day 1 early adult C. elegans whole nematodes: 5 wild isolates (strains: reference strain N2, QX1211, CB4856, EG4348, JU1088) x 3 conditions (control, RNAi against par-1, RNAi against pos-1) x 3 biological replicates per condition (45 samples total)

first: Annalise

middle: B

last: Paaby

first: Han Ting

last: Chou


title: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [Affymetrix]


title: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

status: Public on Mar 22 2023

city: St. Louis

first: Yige

last: Wu

state: MO

address: 4520 McPherson Ave

department: Department of Medicine

institute: Washington University in St. Louis

summary: Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we have performed snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched bulk proteogenomics data. By identifying 20 tumor-specific markers through a multi-omics tiered approach, we reveal an association between higher ceruloplasmin (CP) expression and reduced survival. CP knockdown, combined with spatial transcriptomics, suggests a role for CP in regulating hyalinized stroma and tumor-stroma interactions in ccRCC. Intratumoral heterogeneity analysis portrays tumor cell-intrinsic inflammation and epithelial-mesenchymal transition (EMT) as two distinguishing features of tumor subpopulations. Finally, BAP1 mutations are associated with widespread reduction of chromatin accessibility, while PBRM1 mutations generally increase accessibility, with the former affecting five times more accessible peaks than the latter. These integrated analyses reveal the cellular architecture of ccRCC, providing insights into key markers and pathways in ccRCC tumorigenesis.

overall_design:
We performed snRNA-seq on 34 samples (25 patients) and matched snATAC-seq on 28 of these samples (24 patients) from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) ccRCC collection.

***RAW data will be deposited at dbGAP***

first: Li

last: Ding


title: Shared enhancer gene regulatory networks between wound and oncogenic programs [RNA]

city: Leuven

first: Stein

last: Aerts

state: Flemish-Brabant

address: Herestraat 49

department: Department of Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Wound response programs are often activated during neoplastic growth in tumors. In both systems, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to this response are the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different phenotypic responses is still unclear. Here, we aim to characterize the cellular states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system. We used single-cell multi-omics profiling to derive enhancer Gene Regulatory Networks (eGRNs) from chromatin accessibility, transcription factor binding motif and gene expression signals. We identify the eGRNs being activated following a transient wound induction, and compare them with the scRNA profiles obtained from a persistent induction of the rasv12 scrib-/- oncogenic driver. We detect a small cell population in the wound that activates a senescence program that is shared with cancer cells. This population is characterized by the C/EBP-like transcription factors Irbp18, Xrp1, slow-border and vrille. Our single-cell multiome and eGRNs resource offers a new perspective on gene regulation in the normal and wounded wing disc.

overall_design: Wild-type wing imaginal discs with induced Xrp1 expression were dissected and analysed using RNA-seq experiments

first: Swann

last: Floc'hlay

first: Mirka

last: Uhlirova

first: Anne-Kathrin

last: Classen


title: Methylation data to study immune response to SARS-CoV-2 virus infection in COVID-19 Health Action Response for Marines (CHARM) study

first: Stuart

last: Sealfon

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Methylation profiles from blood samples of participants in the COVID-19 Health Action Response for Marines (CHARM) study were generated to study innate immune responses to SARS-CoV-2 infection. We investigate (1) methylome changes after infection; (2) methylation site dynamics; (3) a methylation-based clock that enables accurate time since infection predictions following acute SARS-CoV-2 and (4) Immunological effects of methylation pattern and relations to other conditions.

overall_design: Methylation assay was performed on samples collected from 252 subjects at different time points as part of SARS-Cov-2 of initial outbreak and later surveillance on the Marine recruits. In total, there are 553 methylation samples in this submission.

first: Venugopalan

last: Nair

first: German

last: Nudelman

first: Weiguang

last: Mao

first: Andrew

middle: G

last: Letizia

middle: C


title: Transcriptomics reveals the effects of NTRK1 on endoplasmic reticulum stress response-associated genes in human neuronal cell lines

city: Wuhan

first: Bo

last: Jiao

state: Hubei Province

address: 1095 Jiefang Avenue

country: China

institute: Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology

summary: Background. NTRK1 gene, encoding TrkA, is essential for the nervous system and drives a variety of biological processes, including pain. Given the unsatisfied analgesic effects of some new drugs targeting NTRK1 in clinic, a deeper understanding for the mechanism of NTRK1 in neurons is crucial.  Methods. We assessed the transcriptional responses in SH-SY5Y cells with NTRK1 overexpression using bioinformatics analysis. GO and KEGG analyses were performed, PPI networks were constructed, and the functional modules and top 10 genes were screened. Subsequently, hub genes were validated using RT-qPCR.  Results. A total of 419 DEGs were identified, including 193 upregulated and 226 downregulated genes. GO showed that upregulated genes were mainly enriched in response to endoplasmic reticulum (ER) stress, protein folding in ER, etc., and downregulated genes were highly enriched in a series of cellular parts and cellular processes. KEGG showed DEGs were enriched in protein processing in ER and pathways associated with cell proliferation and migration. The finest module was dramatically enriched in the ER stress response-related biological process. The verified 7 hub genes consisted of 5 upregulated genes (COL1A1, P4HB, HSPA5, THBS1, and XBP1) and 2 downregulated genes (CCND1 and COL3A1), and almost all were correlated with response to ER stress.  Conclusion. Our data demonstrated that NTRK1 significantly influenced the gene transcription of ER stress response in SH-SY5Y cells. It indicated that ER stress response could contribute to various functions of NTRK1-dependent neurons, and therefore, ER stress response-associated genes need further study for neurological dysfunction implicated in NTRK1.

first: Mi

last: Zhang

first: Caixia

first: Xueqin

last: Cao

first: Baowen

last: Liu

first: Ningbo

last: Li

first: Jiaoli

last: Sun

first: Xianwei


title: DOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement

city: New Haven

first: Bluma

last: Lesch

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Unique chromatin remodeling factors orchestrate dramatic changes in nuclear morphology during differentiation of the mature sperm head. A critical step in this process is histone-to-protamine exchange, which must be executed correctly to avoid sperm DNA damage, embryonic lethality, and male sterility. Here, we define an essential role for the histone methyltransferase DOT1L in the histone-to-protamine transition. We show that DOT1L is abundantly expressed in meiotic and postmeiotic germ cells and that methylation of histone H3 lysine 79 (H3K79), the modification catalyzed by DOT1L, is enriched in developing spermatids in the initial stages of histone replacement. Elongating spermatids lacking DOT1L fail to fully replace histones and exhibit aberrant protamine recruitment, resulting in deformed sperm heads and male sterility. Loss of DOT1L results in transcriptional dysregulation coinciding with the onset of histone replacement and affecting genes required for histone-to-protamine exchange. DOT1L also deposits H3K79me2 and promotes accumulation of elongating RNA Polymerase II at the testis-specific bromodomain gene Brdt. Together, our results indicate that DOT1L is an important mediator of transcription during spermatid differentiation and an indispensable regulator of male fertility.

overall_design: single cell RNA-seq in control and Dot1L knockout testis

first: Aushaq

last: Malla

first: Shannon

middle: R

last: Rainsford

first: Zachary

last: Smith


title: The NELF pausing checkpoint mediates the functional divergence of Cdk9

city: Ithaca

first: Michael

last: DeBerardine

address: 426 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: Cdk9 is an essential transcriptional kinase that is conserved across distant eukaryotes, but we previously found that acute inhibition of Cdk9 causes different transcriptional phenotypes in NELF-containing higher eukaryotes (like mammals and Drosophila) vs. the NELF-lacking fission yeast S. pombe. NELF is known to participate in promoter-proximal pausing of RNA Polymerase II, and using NELF-depleted Drosophila cells,  we find that this NELF-mediated pause is necessary to prevent gene body entry by Pol II in the absence of Cdk9. Without NELF, the abnormal gene body entry that occurs following Cdk9 inhibition is strikingly similar to that seen in S. pombe, and in either case, these Pol II complexes have elongation defects and are unable to complete gene transcription. These results show that NELF enforces an early checkpoint for Cdk9 and efficiently shuts down gene transcription in its absence. We propose this would have been critical for the emergence of gene regulatory strategies acting via Cdk9 to modulate transcription of specific genes.

overall_design: Drosophila S2 cells were treated with dsRNA to knockdown either NELF-E or LacZ (an unexpressed control). Knockdowns were performed in 2 independent experiments (each with 2 biological replicates) in which cells were treated with Flavopiridol or DMSO (control) before harvesting for PRO-seq and RNA-seq. PRO-cap libraries are derived from a third independent experiment without replicates or drug treatments. In all cases, cells were combined with a small quantity of mouse embryonic fibroblasts as an exogenous spike-in control for normalization purposes.

first: Gregory

middle: T

last: Booth

first: Philip

middle: P

last: Versluis

first: John

last: Lis


title: Chromatin Profiling of SCaBER bladder cancer cell line

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of SCaBER cell line by ChIPseq for H3K27me3 and H3K27ac histone marks.

overall_design: Examination of 2 different histone modification in KK47 cell line

first: Hélène

last: Neyret-Kahn

last: Ye

first: François

last: Radvanyi

first: Irwin

last: Davidson

first: Isabelle

last: Bernard-Pierrot


title: Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing and increased daily irradiance

city: OLD BRIDGE

first: Benjamin

last: Diaz

state: New Jersey

address: K12B Pine Tree Boulevard

department: Department of Biochemistry and Microbiology

institute: Rutgers University

summary: Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle.  Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changing mixed layer depths remain unexplored.  Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing from 233 meters to 5 meters over the course of two days during the late spring in the Northwest Atlantic.  Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon ic pathways supportive of rapid cell growth.  In contrast, phytoplankton genera exhibited divergent transcriptional strategies for photosystem light harvesting complex genes during this transition. Active infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing.  A conceptual model is proposed to provide ecophysiological context for our findings, in which light limitation during deep mixing induces populations into a transcriptional state which maximizes interrupts the oscillating levels of transcripts related to photosynthesis, carbon storage, and carbon fixation found in shallow mixed layers with relatively higher growth rates.  We propose that upon sensing high light levels during mixed layer shallowing, phytoplankton resume diel oscillation of core sets of genes enabling photoprotection, biosynthesis and cell replication. Our findings highlight the shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom.

overall_design:
Comparative gene expression of phytoplankton comunities between different water depths corresponding to 40%,20% and 1% of surface PAR, and between the same relative irradiances in different mixed layer depths.  Incubations were performed on deck of the ship to simulate in situ light and temperature conditions of the North Atlantic.  The first incubation ("I") lasted for 3 days, while the next incubation lasted for 5 days.
Biological replicate numbers are not related to each other in terms of incubated and in situ samples - ie. 1_5_04_I_1 is not the incubated treatment of 1_5_04_B_1

first: Ben

first: Ehud

last: Zelzion

first: Kimberley

last: Halsey

last: Behrenfeld

first: Kay

last: Bidle

first: Peter

last: Gaube


title: Chromatin Profiling of SD48 bladder cancer cell line

summary: In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of SD48 cell line by ChIPseq for the following marks and transcription factor : H3K4me3, H3K9ac, H3K27me3, H3K9me3, H3K27ac, H3K4me1, CTCF and FOXA1.

overall_design: Examination of 6 different histone modifications, CTCF and FOXA1 in SD48 cell line


title: Chromatin Landscape of Normal Urothelial cells

summary: Describing the chromatin landscape of normal urothelial cells by ChIPseq analysis of 6 histones marks and 1 chromatin factor in 2 patient derived Normal Human Urothelial cells

overall_design: ChIPseq for 6 different histone modifications and one insulator factor in 2 patients derived NHU cells

first: Helene


title: Chromatin Profiling of 5637 bladder cancer cell line

summary: In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of 5637 cell line by ChIPseq for the following marks and transcription factor : H3K4me3, H3K9ac, H3K27me3, H3K9me3, H3K27ac, H3K4me1, CTCF and FOXA1.

overall_design: Examination of 6 different histone modifications, CTCF and FOXA1 in 5637 cell line


title: Chromatin Profiling of MGHU3 bladder cancer cell line

summary: In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of MGHU3 cell line by ChIPseq for H3K27me3 and H3K27ac histone marks.

overall_design: Examination of 2 different histone modification in MGHU3 cell line


title: IEC intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

summary:
Introduction: Intestinal epithelial cells (IECs) constitute a critical first line of defense against microbes by providing a physical barrier capable of producing antimicrobial peptides (AMPs) and cytokines. While IECs are known to respond to various microbial signals, the precise upstream cues regulating diverse IEC responses are not clear.
Method: Mouse intestinal crypts were isolated from colon tissue. Crypts were differentiated into 3D spheroids in matrigel by stimulating with LWRN media and growth factors. After differentiation colonoids were stimulated with IL-1b, IL-22, or IL-1b and IL-22 for 12 hours then RNA was isolated for RNA sequencing.
Conclusion: Transcriptional profiling of mColonoids reveals IL-1b synergizes with IL-22 to induced a unique gene profile

overall_design: mRNA profiles of mouse colonoids stimulated with IL-1b, IL-22 or IL-1b and IL-22 for 12 hours by Illumina sequencing in triplicate.

first: Garrett

last: Overcast

first: Hannah

last: Meibers


title: Transcriptome profiling of CML24-mediated Al resistance

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

summary: To understand the molecular network underlying the regulation of ALMT1 under Al stress by CML24, the transcriptional profile of wild type and cml24-2 mutant roots in the absence or presence of Al stress was examined using RNAseq.In roots of wild type, 1173 and 1493 genes were up- or down-regulated, respectively, by Al, while 919 and 1057 genes were up- or down-regulated, respectively, in roots of cml24-2 plants. Totally 382 and 176 genes were up- or down-regulated, respectively, at least 2-fold in the roots of the cml24-2 mutant compared with wild type plants in absence of Al. In presence of Al, a total of 412 genes were up-regulated and 178 genes were down-regulated at least 2-fold comparing the cml24-2 mutant with wild type plants.

overall_design: Total RNA obtained from control (non-treated roots) and Al-exposed roots. Six day old plants were treated with and without Al treatment for 6 h, then total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN). RNAseq analysis was performed by BGI Tech (Shenzhen, China) via BGISEQ-500 RNA-Seq platform.

first: Xue

last: Zhu

first: Zhimin

last: Bai


title: Chromatin Profiling of L1207 bladder cancer cell line

first: Tao

last: YE

summary: Tumor progression is related to both genetic and epigenetic alterations. Until relatively recently, epigenetic changes were thought to target single genes only but we show that in Bladder tumours, epigenetic changes can affect whole chromosomal regions, resulting in the silencing of all the genes within those regions. This phenomenon is probably very general, and has been described in bladder, colon, breast and prostate cancers.  In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of RT112 cell line by ChIPseq for the following marks : H3K4me3, H3K9ac, H3K27me3, H3K9me3, H3K27ac, H3K4me1, and CTCF.

overall_design: Examination of 6 different histone modifications and one insulator factor in L1207 cell line

first: Hélène

last: Neyret-Kahn


title: Profiling of bladder cancer

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

overall_design: Refer to individual Series


title: Chromatin Profiling of KK47 bladder cancer cell line

summary: In order to investigate epigenetic landscape and potential alterations in bladder, we established the chromatin profiling of KK47 cell line by ChIPseq for H3K27me3 and H3K27ac histone marks.

overall_design: Examination of 2 different histone modifications in KK47 cell line

last: Ye

first: François

last: Radvanyi

first: Irwin


title: Chromatin Profiling of RT112 bladder cancer cell line

overall_design: Examination of 6 different histone modifications and one insulator factor in RT112 cell line

last: Davidson


title: Gene expression of healthy airway epithelium and p.Sdel560 STAT3-epithelium (Job Syndrome patient) in homeostasis and after 1 hour infection with pseudomonas aeruginosa

status: Public on Mar 21 2023

city: Boston

first: Hongmei

last: Mou

state: MA

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

summary:
To explore the mechanism that underlies the lung infection susceptibility in job syndrome patients, we derived primary airway basal stem cells from a job syndrome patient which harbors a p.Sdel560-STAT3 mutation. After ALI differentiation, healthy airway epithelium and p.Sdel560 STAT3-epithelium were exposed to pseudomonas aeruginosa for 1 h. Then we collect the RNA to perform bulk-RNA sequencing.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy airway epithelium and p.Sdel560 STAT3-epithelium (Job Syndrome patient) in homeostasis and after 1 hour infection with pseudomonas aeruginosa.

first: Yihan

last: Zhang


title: ADAR1 biology can hinder effective antiviral RNA interference

first: Skyler

middle: Andrew

last: Uhl

state: New York

address: 1 Gustave L. levy Pl.

department: Microbiology

summary: Viruses constantly evolve and adapt to the antiviral defenses of their hosts. The biology of viral circumvention of these selective pressures can often be attributed to the acquisition of novel antagonistic gene products or by rapid genome change that prevents host recognition. To study viral evasion of RNA interference (RNAi)-based defenses, we established a robust antiviral system in mammalian cells using recombinant Sendai virus designed to be targeted by endogenous host microRNAs (miRNAs) with perfect complementarity. Using this system, we previously demonstrated the intrinsic ability of positive-strand RNA viruses to escape this selective pressure via homologous recombination, which was not observed in negative-strand RNA viruses. Here we show that given extensive time, escape of miRNA-targeted Sendai virus was enabled by host adenosine deaminase acting on RNA 1 (ADAR1). Independent of the viral transcript targeted, ADAR1 editing resulted in disruption of the miRNA-silencing motif, suggesting an intolerance for extensive RNA:RNA interactions necessary for antiviral RNAi. This was further supported in N. benthamiana, where exogenous expression of ADAR1 interfered with endogenous RNAi. Together, these results suggest that ADAR1 diminishes the effectiveness of RNAi and may explain why it is absent in species that utilize this antiviral defense system.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: RNA-sequencing of mammalian cells lines infected with recombinant Sendai viruses that have sequences with perfectly complemenatrity to host miRNAs added into the 3' UTR of the N gene or P gene to produce an artificial miRNA-based antiviral RNAi.  Cell lines, which include A549s, STAT1 KO A549s, STAT1/ADAR1 Double KO A549s, MEFs, and MDCKs were infected and RNA was collected at various timepoints post infection to assess host response and changes to viral genome. Samples where differential gene expression in host cells is assessed are in triplicate.

first: Benjamin

last: tenOever


title: Identification and characterization of alveolar and recruited lung macrophages during acute lung inflammation

city: Nashville

first: wei

last: han

address: 1161 21ST Ave S

department: pulmonary medicine

institute: vanderbilt university medical center

summary: To precisely identify mice resident alveolar macrophages (AMs) and bone marrow (BM)-derived macrophages, we developed a technique to separately label AMs and BM-derived macrophages with a fluorescent lipophilic dye followed by fluorescent-associated cell sorting (FACS). We utilized this approach to isolate BM-derived macrophages and AMs at different timepoints  after intratracheal (IT) instillation of E.coli lipopolysaccharide (LPS) and performed bulk RNAseq on these cell populations to characterize the individual phenotypes of resident AMs and BM-derived macrophages present in the lungs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BM-derived macrophages and resident AMs at day0, day1 day3,and day7 after IT LPS

first: Wei

last: Han

first: Harikrishna

last: Tanjore

first: Yang

last: Liu

first: Raphael

last: Hunt

first: Sergey

last: Gutor

first: Ana

last: Serezani

first: Timothy

last: Blackwell


title: Gene expression profiles of pre-basophils versus mature basophils stimulated with antigen/IgE- or IL-3-stimulation.

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

summary: Basophils are the least common granulocytes which represent less than 1% of peripheral blood leukocytes. Recent development of analytical tools for basophils enables us to understand their critical roles in allergic reactions and protection from parasitic infections. Nevertheless, the differentiation trajectory of basophils remains unclear. We have identified previously-unappreciated pre-basophil subpopulation which encompasses previously-defined basophil precursors (BaPs) in a series of experiments including scRNA-seq analysis (deposited to GSE206589). In this study, we explored gene expression profiles of pre-basophils and mature basophils activated by antigen/IgE-stimulation or IL-3-stimulation. We have revealed that IL-3 activated pre-basophils displayed distinct gene expression profiles from antigen/IgE- or IL-3-stimulated mature basophils, suggesting the unuque property of pre-basophils.

overall_design: Mice were intravenously sensitized with TNP-specific IgE 1 day prior to the experiment.  CD34-CLEC12Ahi pre-basophils and CD34-CLEC12Alo mature basophils isolated from the bone marrow of TNP-IgE sensitized mice were separately cultured ex vivo in the presence of OVA (Control), TNP-conjugated OVA (TNP-OVA), or IL-3 for 4h and were subjected to bulk RNA-Seq analysis.

first: Junya

last: Ito

first: Jun

last: Nakabayashi

first: Shichino

last: Shigeyuki

first: Hajime

last: Karasuyama


title: Remodeling oncogenic transcriptomes by small molecules targeting NONO

city: La Jolla

first: Garrett

middle: Lee

last: Lindsey

state: CA

address: 10650 N Torrey Pines Rd

department: Chemistry

institute: Scripps Research


title: Transcriptome changes in 22Rv1 cells with a double knockout or over expression of C145S, Empty vector, or Wild type NONO.

summary: RNA-Sequencing to determine transcriptome changes in 22Rv1 cells after knockdown of PSPC1 and SFPQ

overall_design: sgControl or sgNONO 22Rv1 cells were treated in biological triplicate with sgCtrl ,sgPSPC1, or sgNONO for 72 hours prior to RNA-sequencing. 22Rv1 cells that were overexpressing NONO C145S, Empty vector, or Wild type NONO treated with  DMSO (0.04%) or SKBG-1 (R) or SKBG-1 (S) (20µM for 4 hours prior to RNA-sequencing.

first: Stefan

last: Kathman

last: Cravatt


title: Gene expression profiles of IL-3 stimulated bone marrow-derived basophils (BMBAs).

summary: In this study, we explored gene expression profiles of bone marrow-derived basophils stimulated with either IL-3 or control PBS.

overall_design: Bone marrow-derived basophils were stimulated with IL-3 or control PBS for 6hrs, and were subjected to bulk RNA-seq analysis.

first: Shigeyuki

last: Shichino


title: Neuronal identity defines a-synuclein and tau toxicity

first: Patrik

last: Verstreken

summary: Pathogenic a-synuclein and tau are critical drivers of neurodegeneration and their mutations cause neuronal loss in patients. Whether the underlying preferential neuronal vulnerability is a cell-type intrinsic property or a consequence of increased expression levels remains elusive. Here, we explore cell-type specific a-synuclein and tau expression in human brain datasets and use deep phenotyping as well as brain- wide single-cell RNA sequencing of >200 live neuron types in fruit flies to ask which cellular environments react most to a-synuclein or tau toxicity. We detect phenotypic and transcriptomic evidence of differential neuronal vulnerability independent of a-synuclein or tau expression levels. Comparing vulnerable with resilient neurons in Drosophila enabled us to predict numerous human neuron subtypes with increased intrinsic susceptibility to pathogenic a-synuclein or tau. By uncovering synapse and Ca2+ homeostasis related genes as tau toxicity modifiers our work paves the way to leverage neuronal identity to uncover modifiers of neurodegeneration-associated toxic proteins.

overall_design: Drosophila brains at 5, 25 and 45 days were dissected, dissociated and scRNAseq performed with 10x v3.1 chemistry; GFP+ C2_3 neurons were FAC-sorted and 400 cells/sample were processed with an adapted Smart-seq3 protocol.

first: Roman

last: Praschberger

first: Suresh

last: Poovathingal


title: Gene expression profiles of immature versus mature bone marrow-derived basophils (BMBAs) elicited by either IL-3 or TSLP.

summary: In this study, we explored gene expression profiles of mature and immature basophils from either IL-3-elicited or TSLP-elicited BMBAs. We revealed that TSLP-elicited mature basophils displayed gene expression profile similar to that of IL-3-elicited mature rather than immature basophils.

overall_design: We cultured bone marrow cells in thepresence of IL-3 or TSLP for 7 days. We then isolated immature and mature basophils from either IL-3-cultured or TSLP-cultured bone marrow cells.


title: Mesenchymal loss of p53 alters stem cell capacity and models human soft tissue sarcoma traits [scRNA-seq]

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

summary: Soft tissue sarcomas (STSs) are a heterogeneous group of tumors that originate from mesenchymal cells. p53 is frequently mutated in human STS. In this study, we found that the loss of p53 in mesenchymal stem cells (MSCs) mainly causes adult undifferentiated soft tissue sarcoma (USTS). MSCs lacking p53 show changes in stem cell properties, including differentiation, cell cycle progression, and metabolism. The transcriptomic changes and genetic mutations in murine p53-deficient USTS mimic those seen in human STS. Furthermore, single-cell RNA sequencing revealed that MSCs undergo transcriptomic alterations with aging—a risk factor for certain types of USTS—and that p53 signaling decreases simultaneously. Moreover, we found that human STS can be transcriptomically classified into six clusters with different prognoses, different from the current histopathological classification. This study paves the way for understanding MSC-mediated tumorigenesis and provides an efficient mouse model for sarcoma studies.

overall_design: Bone marrow mesenchymal stem cells were collected from either young (9 weeks) or old (24 months) mice and single cell RNA-seq was performed using the Fluidigm C1 system.

first: Yuriko

last: Sorimachi

first: Hiroshi

last: Kobayashi

first: Yusuke

last: Shiozawa

first: Ryuichiro

last: Nakato

first: Katsuhiko

last: Shirahige


title: Context-dependent activation of STING-interferon signaling by CD11b agonists enhances anti-tumor immunity

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

summary: Chronic activation of inflammatory pathways and suppressed interferon are hallmarks of immunosuppressive tumors. Previous studies have shown that CD11b integrin agonists could enhance anti-tumor immunity through myeloid reprograming, but the underlying mechanisms remain unclear. Herein we find that CD11b agonists alter tumor-associated macrophage (TAM) phenotypes by repressing NF-κB signaling and activating interferon gene expression simultaneously. Repression of NF-κB signaling involves degradation of p65 protein and is context independent. In contrast, CD11b agonism induces STING/STAT1 pathway-mediated interferon gene expression through FAK-mediated mitochondrial dysfunction, with the magnitude of induction dependent on the tumor microenvironment and amplified by cytotoxic therapies. Using tissues from phase I clinical studies, we demonstrate that GB1275 treatment activates STING and STAT1 signaling in TAMs in human tumors. These findings suggest potential mechanism-based therapeutic strategies for CD11b agonists and identify patient populations more likely to benefit.

overall_design: Immune cells of subcutaneous PDAC Tumor tissue from C57BL/6 mice were isolated by Fluorescence-activated cell sorting (FACS) according to CD45+ staining and analyzed using scRNAseq.

first: Xiuting

last: Liu

first: John

last: Baer


title: Transcriptome analysis of interferon receptor locus dosage correction in a mouse model of Down syndrome

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus


title: Single cell transcriptomics resolves basophil differentiation trajectory and identifies pre-basophils

first: Kensuke

last: Miyake


title: Single-cell RNA-sequence of basophils under homeostatic conditions

summary: Basophils are the least common granulocytes which represent less than 1% of peripheral blood leukocytes. Recent development of analytical tools for basophils has enabled us to understand their critical roles in allergic reactions and protection from parasitic infections. Nevertheless, the differentiation trajectory of basophils remain unclear. To explore differentiation trajectory of basophils, we conducted highly sensitive single cell RNA sequencing (scRNA-seq) of bone marrow-derived basophils (BMBAs) and basophils under homeostatic conditions. As a result, we identified previously-unappreciated pre-basophils which are located down-stream of bi-potential basophil and mast cell common precursors and upstream of mature basophils along the ontogeny of  basophlis.

overall_design: Basophils isolated from the bone marrow and spleen of the Mcpt8-GFP Tg mice and bone marrow cells cultured with IL-3 for 3 or 7 days were subjected to scRNA-seq.

first: Junya

last: Ito

first: Jun

last: Nakabayashi

first: Hajime

last: Karasuyama


title: A myogenin+/CD74+ adult muscle stem cell population during regeneration of skeletal muscle lacking miR-501

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Adult muscle stem cells show a high transcriptional and clonal heterogeneity during ageing. Whether microRNAs contribute to this diversity is not known. Here we use tissue-specific genetic deletion of microRNA (miR)-501 that is highly enriched in activated myogenic progenitor cells to address this question. Single-cell sequencing revealed a novel subpopulation of committed myogenic progenitor cells in miR-501 knockout mice that express high levels of terminal differentiation markers and inflammatory genes such as CD74. Our data show that stem cell heterogeneity in skeletal muscle during ageing is under miRNA control.

overall_design: We performed genome-wide identification of differentially expressed genes upon genetic deletion of miR-501. For each run, 3 Pax7Cre and 3 Pax7CremiR-501fl/Y (miR-501KO) mice were subjected to cardiotoxin-induced muscle regeneration. On day 6, the skeletal muscle resident stem cells called myogenic progenitors were FACS-sorted and immediately processed for single-cell sequencing. For data analysis, two independent experiments were merged, creating a dataset of 6 miR-501KO mice vs. 6 control littermates.

first: Alexandra

last: Fahrner

first: Edlira

last: Luca

first: Jan

last: Krützfeldt


title: Hematopoietic Stem Cells Preferentially Traffic Misfolded Proteins to Aggresomes and Depend on Aggrephagy to Maintain Protein Homeostasis

first: Robert

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

institute: UCSD

summary: Hematopoietic stem cells (HSCs) regenerate blood cells throughout life. To preserve their fitness, HSCs are particularly dependent on maintaining protein homeostasis (proteostasis). However, how HSCs purge misfolded proteins is unknown. Here we show that in contrast to most cells that primarily utilize the proteasome to degrade misfolded proteins, HSCs preferentially traffic misfolded proteins to aggresomes in a Bag3-dependent manner, and depend on aggrephagy, a selective form of autophagy, to maintain proteostasis in vivo. When autophagy is disabled, HSCs compensate by increasing proteasome activity, but proteostasis is ultimately disrupted as protein aggregates accumulate and HSC function is impaired. Bag3-deficiency blunts aggresome formation in HSCs, resulting in protein aggregate accumulation, myeloid-biased differentiation, and diminished self-renewal activity. Furthermore, HSC aging is associated with a severe loss of aggresomes and reduced autophagic flux. Protein degradation pathways are thus specifically configured in young adult HSCs to preserve proteostasis and fitness, but become dysregulated during aging.

overall_design: 7 experimental conditions, 3 replicates per condition.

first: Bernadette

middle: A

last: Chua

first: Connor

last: Lennan

first: Mary Jean

last: Sunshine

first: Daniela

last: Dreifke

first: Ashu

last: Chawla

first: Eric

last: Bennett


title: Gene expression profiles of basophil progenitors, CD34- pre-basophils and mature basophils

summary: In this study, we explored gene expression profiles of CD34-CLEC12Ahi pre-basophils isolated from the bone marrow as well as CD34-CLEC12Alo mature basophils from the bone marrow and CD34+ basophil progenitors. We revealed that the gene expression of mature basophils isolated from the bone marrow and spleen resembled each other whereas pre-basophils and mature basophils showed distinct gene expression profiles.

overall_design: We isolated CD34-CLEC12AhiCD9lo pre-basophils from the bone marrow as well as CD34-CLEC12AloCD9hi mature basophils from the bone marrow and spleen separately and compared their gene expression profiles using bulk RNA-seq analysis. As reference, we also included sort-purified CD200R3+cKit-CLEC12AhiCD34+ bone marrow cells that correspond to uni-potent basophil progenitors (BaPs).

first: Shigeyuki

last: Shichino


title: RNA-seq analysis of shCTR and shSF3B1 NHD13-derived HSPC (cKIT+) cells

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDS), clonal hematopoietic disorders with variable risk of leukemic transformation. Although the tumorigenic effects of SF3B1 mutations have been defined, the role of “non-mutated” SF3B1 in cancer remains largely unresolved. Here we identify a conserved epitranscriptomic program that steers SF3B1 translation to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals a remarkable SF3B1 protein increase. Selective inhibition of SF3B1 upregulation accelerates MDS-to-leukemia progression in vivo. Mechanistically, ALKBH5-driven m6A demethylation within the SF3B1 5’ UTR fine-tunes SF3B1 translation to direct splicing of central DNA repair and epigenetic regulators during transformation. Loss of 5’ UTR m6A increases SF3B1 abundance, genome stability and delays leukemia progression in vivo, supporting integrative analysis of SF3B1 molecular signatures in humans that may predict tumor mutational burden and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.

overall_design: 2 sets of samples including shCTR and shSF3B1 were included in the study. Each sample was prepared in the biologically indpendent, matched triplicates.

first: Maciej

last: Ciesla

last: Thi Ngoc

first: Cristian

last: Bellodi


title: Single-cell RNA-sequence of basophils during second Nippostrongylus brasiliensis (Nb) infection

first: Kensuke

last: Miyake

summary: To explore gene expression profiles of basophils during the second Nb infection, basophils were isolated from the bone marrow, spleen and skin inoculation site and subjected to scRNA-seq analysis

overall_design: C57BL/6J WT mice were infected twice with Nb. Basophils isolated from the bone marrow, spleen, and the skin inoculation site were subjected to scRNA-seq analysis.

first: Junya

last: Ito

first: Jun

last: Nakabayashi

first: Kenji

last: Ishiwata

last: Karasuyama


title: m6A-driven translation control of SF3B1 steers splicing to direct genome integrity and leukemogenesis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Tumour immune rejection triggered by activation of a2-adrenergic receptors (scRNA-Seq)

status: Public on Mar 20 2023

city: Brussels

first: Benoit

last: Van den Eynde

state: Please Select

address: Avenue Hippocrate, 75 - Bte B1.74.10

institute: de Duve Institute

summary: Single-cell analysis of MC-38 OVA and TC-1 mice treated with clonidine and indicates changes in macrophages.

overall_design: 10X sequencing of pooled MC38-OVA and TC-1 mice before and after clonidine treatment.

first: Jingjing

last: Zhu

first: Stefan

last: Naulaerts

first: Loubna

last: Boudhan

first: Manon

last: Martin

first: Laurent

last: Gatto

first: Benoît


title: Transcriptome changes in 22Rv1 and MCF7 cells after treatment with NONO ligands and controls

first: Garrett

last: Lindsey

summary: RNA-Sequencing to determine transcriptome changes in 22Rv1 and MCF7 cells after treatment with NONO ligands and controls. NONO KO (sgNONO) or control (sgControl) cells were treated.

overall_design: sgControl or sgNONO 22Rv1 or MCF7 cells were treated in biological triplicate with DMSO (0.04%) or SKBG-1 (R) or SKBG-1 (S) (20µM and 5µM in 22Rv1 and MCF7 cells, respectively) for 4 hours prior to RNA-sequencing.

last: Kathman

first: Benjamin

last: Cravatt


title: Alterations in Germinal Center Formation and B Cell Activation during Severe Orientia tsutsugamushi Infection in Mice [Nanostring]

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: We performed NanoString analysis on total RNA extracted from spleens of mice infected with Orientia tsutsugamushi to investigate the transcriptomic signature of these cells throughout infection.

overall_design: Mouse spleen samples were collected from mock (D0) and D8 infected mice, and stored in RNALater (Ambion, Austin, TX) until extraction was performed. Total RNA was extracted by using the RNeasy Mini kit (Qiagen), and total RNA samples (3 mice/group, 200 ng/sample in ribonuclease-free water) were processed at the Baylor College of Medicine Genomic and RNA Expression Profiling Core (Houston, TX). We utilized the comercially available Mouse Immunology Panel NanoString kit. Gene expression profiling was performed by using the nCounter platform and the Mouse Immunology Panel NanoString kit, which comprised 561 genes and 14 housekeeping genes (NanoString Technologies, Seattle, WA). Raw data were then normalized and analyzed by ROSALIND (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc (San Diego, CA).

first: Casey

last: Gonzales

first: Yuejin

last: Liang


title: Tumour immune rejection triggered by activation of a2-adrenergic receptors

summary: High-throughput bulk transcriptome sequencing reveals an increase in immune response, cytokine response and cell communication after clonidine treatment.

overall_design: RNASeq sequencing of bulk tumor tissue from wildtype or Adra2a KO mice treated with PBS or Clonidine


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult mouse brain tissue

first: Matthew

last: Galbraith

summary: Analysis of steady-state mRNA levels in adult mouse brain tissue at 17-35 weeks  from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type (n=6), Dp16 (n=5), and Dp16^2xIFNRs (n=7).

first: Katherine

last: Waugh

first: Kelly

last: Sullivan

first: Joaquin

middle: M

last: Espinosa


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from embryonic mouse facial mesenchyme tissue

summary: Analysis of steady-state mRNA levels in embryonic mouse facial mesenchyme tissue at E10.5  from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type (n=3), Dp16 (n=3), and Dp16^2xIFNRs (n=3).


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from embryonic E12.5 mouse heart tissue

summary: Analysis of steady-state mRNA levels in embryonic mouse heart tissue at E12.5 from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type (n=6), Dp16 (n=6), and Dp16^2xIFNRs (n=6).


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from embryonic E18.5 mouse heart tissue

summary: Analysis of steady-state mRNA levels in embryonic mouse heart tissue at E18.5 from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/


title: Gene expression of normal airway epithelium and squamous in homeostasis.

first: Hongmei

last: Mou

summary: Bulk RNA sequencing analysis was performed to investigate transcriptional profiles in normal airway epithelium and squamous.

overall_design: For squamous cells differentiation, we treat the basal cells with 2 uM CHIR99021  during ALI differentiation and valiated with KRT13 staining. Then we collect the RNA to perform bulk-RNA sequencing.

first: Yihan

last: Zhang


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult mouse mesenteric lymph nodes

summary: Analysis of steady-state mRNA levels in adult mouse mesenteric lymph nodes at week 17-18 from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type (n=5), Dp16 (n=6), and Dp16^2xIFNRs (n=6).


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult mouse heart tissue

summary: Analysis of steady-state mRNA levels in adult mouse heart tissue at week 17-18 from wild-type C57BL/6, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type (n=5), Dp16 (n=6), and Dp16^2xIFNRs (n=5).


title: Liver-Specific Overexpression of HKDC1 Increases Hepatocyte Size and Proliferative Capacity

city: Chicago

first: Md. Wasim

last: Khan

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

summary: A primary role of the liver is to regulate whole body glucose homeostasis. Glucokinase (GCK) is the main hexokinase (HK) expressed in hepatocytes and functions to phosphorylate the glucose that enters via GLUT transporters to become glucose-6-phosphate (G6P), which subsequently commits glucose to enter downstream anabolic and catabolic pathways. In the recent years, Hexokinase Domain-Containing-1 (HKDC1), a novel 5th HK, has been characterized by our group and others. Its expression profile varies but has been identified to have low basal expression in normal liver but increases during states of stress including pregnancy, nonalcoholic fatty liver disease (NAFLD), and liver cancer. Here, we have developed a stable overexpression model of hepatic HKDC1 in mice to examine its effect on metabolic regulation. We found that HKDC1 overexpression, over time, causes impaired glucose homeostasis in male mice and shifts glucose metabolism towards anabolic pathways with an increase in nucleotide synthesis.  Furthermore, we observed these mice to have larger liver sizes due to greater hepatocyte proliferative potential and cell size, which in part, is mediated via Yes-associated protein (YAP) signaling

overall_design: mRNA samples from liver and subcuatneous fats tissue  either expressing a Null AAV (Null) or overexpressing HKDC1 (FL) was extracted for RNA-seq.

first: Brian

last: Layden


title: RNA-seq analysis in fibroblast IMR90 CTRL/MYC/MYC+SF3B1 KD

first: Phuong

last: Cao Thi Ngoc

overall_design: 3 sets of samples including control (CTRL) or MYC overexpressing cells with short hairpin control (MYC) or short hairpin targeting SF3B1 (MYC+SF3B1 KD) were included in the study. Each sample was prepared in the biologically independent, matched triplicates.

first: Maciej

last: Ciesla

last: Thi Ngoc

first: Cristian

last: Bellodi


title: E2F regulation of Phosphoglycerate kinase (Pgk) gene is functionally important in Drosophila development

first: Maria

middle: Paula

last: Zappia

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

summary: Our study focuses on understanding the changes in chromatin accessibility in the Pgk-DeltaE2F mutant that takes place during flight muscles development in Drosophila. E2F binding sites were mutated upstream Pgk gene. E2F/Dp/Rbf were no longer recruited to this regulatory region. As a result of this, the expression of Pgk mRNA was downregulated, which led to reduced levels in many metabolites that are glycolytic and TCA intermediates. Using ATAC-seq we determined that there was a global reduction in chromatin accessibility in the mutant compared to control, and it was accompagnied by a widespread reduction in gene expression, including metabolic genes. In addition we identified a broad range of phenotypes when analyzing the functional relevance of E2F regulation on Pgk gene. These phenotypes range from low ATP content, abnormal mitochondrial morphology, shortened life span to embrionic lethality. Furthermore, defects in high-energy consuming organs, such as ovaries and muscles, were found. In sum, our results illustrate the pleiotropic effects on metabolism, gene expression and development in the Pgk-deltaE2F animals, which underlies the importance of E2F regulation on a single E2F target, Pgk.

overall_design: ATAC-Seq on nuclei extracted from thoracic muscles enriched for flight muscles staged at pharate (96h APF). The Pgk.deltaE2F mutant was compared to control. A total of 2 replicates per genotype were processed.

first: Maxim

middle: V

last: Frolov

first: Abul

last: Islam


title: Genome-wide DNA methylation profiling in tongue squamous cell carcinoma

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

summary: DNA methylation is one of the most studied epigenetic alterations in cancer. Genome-wide DNA methylation profiling was conducted in 6 oral tongue squamous cell carcinomas and matched normal tissues. In the present study, the Illumina Infinium HumanMethylationEPIC BeadChip (EPIC array) was used to characterize the DNA methylation pattern across approximately 850,000 CpG dinucleotide methylation loci using DNA isolated of formalin-fixed and paraffin-embedded tissue sections.

overall_design: Total genomic DNA from formalin-fixed paraffin-embedded (FFPE) tissue sections of oral tongue squamous cell carcinoma (OTSCC) and normal tongue tissue were processed on the Infinium MethylationEPIC array (850K). Samples that passed the quality controls using GenomeStudio and BeadArray Controls Reporter (Illumina), were analyzed to asses their DNA methylation profile.

first: María Mercedes

last: Suárez-Cunqueiro


title: Single-nuclei transcriptome sequencing of 5xFAD mouse brain hemisphere with myelin dysfunction

city: Göttingen

first: Ting

last: Sun

state: Germany (DEU)

address: Hermann-Rein-Straße 3

department: Neurogenetics

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciencesi

summary: The aim of the dataset is to identify cell heterogeneity changes under myelin abnormalities. Alzheimer’s disease (AD) is the most common form of dementia and neurodegenerative disease with increasing prevalence due to longer lifespan in the human population. Why aging constitutes the greatest risk factor for development of AD, however, remains poorly understood. Aging markedly affects oligodendrocytes and the structural integrity of their myelin sheaths which also causes secondary tissue inflammation. We propose a mechanistic link between aging-associated myelin dysfunction and the deposition of Amyloid-ß (Aß) as primary neuropathological hallmark of early AD and hypothesized that breakdown of myelin - especially in cortical regions – is an upstream driver of amyloid deposition in AD. Here, we show that in transgenic mouse models of AD, genetically induced myelin defects by Cnp or Plp1 depletion, as well as direct demyelination are potent drivers of amyloid deposition in vivo as shown by light sheet microscopy imaging. At transcriptomic level, bulk and single-cell RNA sequencing revealed successfully induced disease-associated-microglia (DAM)-like phenotypes in Cnp-/- animals. These activated microglia, however, are primarily engaged with myelin seemingly preventing the protective reactions of the microglia pool to Aß plaques. Our work, therefore, identifies myelin aging as a previously overlooked risk factor for AD and makes the case for myelin health-directed therapies in AD.

overall_design: Brain hemispheres were dissected from 6-month-old animals and subjected to single-nuclei RNA sequencing using 10x genomics Chromium 3’ assay. In total 4 genotypes were included for the experiment (WT, Cnp-/-, 5xFAD, Cnp-/-x5xFAD), each genotype has n=2 replicates.

first: Constanze

last: Depp

first: Klaus-Armin

last: Nave


title: Gene expression data from normal human atrial cardiac fibroblasts, normal human ventricular cardiac fibroblasts, normal human dermal fibroblasts, human bone marrow-derived mesenchymal stem cells and human iPS cell-derived fibroblasts.

city: Shinjuku, Tokyo

first: Shinako

last: Masuda

address: 8-1 Kawada-cho

department: Institute of Advanced Biomedical Engineering and Science

institute: Tokyo Women's Medical University

summary: Comparison of gene expression profiles in three samples of normal human atrial cardiac fibroblasts, normal human ventricular cardiac fibroblasts, normal human dermal fibroblasts, human bone marrow-derived mesenchymal stem cells and human iPS cell-derived fibroblasts using microarray analysis.

overall_design: To compare cell-type specific gene expression, cells were cultured under basal conditions and used for Agilent one color microarray.

first: Katsuhisa

last: Matsuura


title: Quantitative analysis of tet inducible SOX18 during hematopoietic differentiation and Natural killer cell differentiation

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

summary: Using inducible SOX18 human PSCs, we found overexpression of SOX18 showed change of transcriptional program at D8 especially T cell receptor and Toll like receptor signaling pathways. So this suggests SOX18 has an effect on lymphoid differentiation program. Specifically overexpressed SOX18  enhance NK cell production, and related to metabolism pathway. This finding that SOX18 promotes development of progenitors with superior NK cell potenital will advance our understanding of molecualr network regulating specification on lymphoid cells and can help to improve the scalability of NK CELL production form hPSCs form immunotherapies.

overall_design: mRNA profiling of 18 samples for 5 different populations obtained from hematopoietic differentiation cultures of hESCs with doxycyclin (DOX)-inducible SOX18 expression. Samples obtained form HE isolated on day 4 (D4) of diiferentiation following D2 through D4 DOX treatment, hematopoiteic progenitors isolated on D8 of differntiation following D2-8 DOX treatment, and NK cell generated after 3 weeks of cultures of hematopoietic progenitors following DOX2-8 treatment. Cultures without DOX treatment were used as a control.

first: Ho

last: Jung

first: Peng

last: Liu

first: Sean

last: McIlwain

middle: I


title: Genome-wide analysis of ARNT/HIF binding sites in BeWo cells cultured under low oxygen

city: London

first: Stephen

middle: James

last: Renaud

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

summary: In this study, we provide new insight into the role of the hypoxia-inducible factor (HIF) complex in the inhibition of syncytiotrophoblast formation under low oxygen. Through a genome-wide analysis of binding sites for the aryl hydrocarbon nuclear receptor translocator (ARNT; a key component of HIF), we identified the downstream targets of ARNT/HIF that potentially mediate its repressive effect on syncytialization.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-Seq) for ARNT binding sites

first: Adam

last: Jaremek

first: Mariyan

middle: J

last: Jeyarajah

first: Gargi

last: Jaju Bhattad


title: Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA-seq]

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis.

overall_design: Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but where and how HSPC heterogeneity occurs remain unclear. Here, we performed scRNA-seq and scATAC-seq with zebrafish 36 hpf VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish, we performed STRT-seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency, we performed scRNA-seq with the sorted ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC, we examined genome-wide spi2 binding by cut-tag assay in fli1a-flag-spi2-EGFP+ cells sorted from trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.

first: Jun

last: Xia

first: Mengyao


title: Transcriptome analysis of wild-type and mir-125b-2 maternal knock-out mice whole brain by Next Generation Sequencing

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm. 1547, 15F., No. 1, Sec. 1, Ren'ai Rd., Zhongzheng Dist

country: Taiwan

institute: National Taiwan University College of Medicine

summary: Genomic imprinting, a special case of epigenetic mechanisms, predominantly occurs in placenta and brain. Few imprinted microRNAs were identified in brain and their functional roles in brain were not well-investigated. Here we identified Mir125b-2 was maternally, but not paternally, expressed in mouse brain in a brain-region-specific manner. Mir125b-2 is predominantly expressed in mouse brain during neonatal stage and Mir125b-2 homozygous knockout (KO) mice displayed decreased brain weight.

overall_design: We analyzed the gene expression pattern of whole brain of wildtype and mir-125b-2 maternal knockout mice at post-natal day 0.

first: Xuhui

last: Cao

first: Chih-Yu

last: Lee


title: Arg1+ microglia are critical for shaping cognition in female mice

city: Stockholm

first: Vassilis

last: Stratoulias

address: Nobels Väg 13

department: Institute of Environmental Medicine

institute: Karolinska Institutet

summary: Here, we describe a microglial subtype characterized by the expression of the enzyme Arginase-1, i.e. Arg1 +microglia.

overall_design: Comparison of ARG1-YFP-positive vs ARG1-YFP-negative microglia, isolated from P13 YARG female and male mice

first: Fredrik

last: Fagerström-Billai

first: David

last: Brodin

first: Bertrand

last: Joseph


title: RNA-seq analysis in SF3B1 5’UTR WT and A88G MOLM-13 cells

first: Phuong

last: Cao Thi Ngoc

summary: SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDS), clonal hematopoietic disorders with variable risk of leukemic transformation. Although the tumorigenic effects of SF3B1 mutations have been defined, the role of “non-mutated” SF3B1 in cancer remains largely unresolved. Here we identify a conserved epitranscriptomic program that steers SF3B1 translation to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals a remarkable SF3B1 protein increase. Selective inhibition of SF3B1 upregulation accelerates MDS-to-leukemia progression in vivo. Mechanistically, ALKBH5-driven m6A demethylation within the SF3B1 5’ UTR fine-tunes SF3B1 translation to direct splicing of central DNA repair and epigenetic regulators during transformation. Loss of 5’ UTR m6A increases SF3B1 abundance, genome stability and delays leukemia progression in vivo, supporting integrative analysis of SF3B1 molecular signatures in humans that may predict tumor mutational burden and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.

overall_design: 2 sets of samples including wild-type (WT) and CRISPR/CAS9 edited SF3B1 5'UTR A88 (A88G) were included in the study. Each sample was prepared in the biologically independent, matched quadruplicates.

first: Maciej

last: Ciesla

last: Thi Ngoc

first: Cristian

last: Bellodi


title: Transcriptome profiling of mouse brain microglia in Cnp null mice with 5xFAD background

first: Ting

last: Sun

summary: Alzheimer’s disease (AD) is the most common form of dementia and neurodegenerative disease with increasing prevalence due to longer lifespan in the human population. Why aging constitutes the greatest risk factor for development of AD, however, remains poorly understood. Aging markedly affects oligodendrocytes and the structural integrity of their myelin sheaths which also causes secondary tissue inflammation. We propose a mechanistic link between aging-associated myelin dysfunction and the deposition of Amyloid-ß (Aß) as primary neuropathological hallmark of early AD and hypothesized that breakdown of myelin - especially in cortical regions – is an upstream driver of amyloid deposition in AD. Here, we show that in transgenic mouse models of AD, genetically induced myelin defects by Cnp or Plp1 depletion, as well as direct demyelination are potent drivers of amyloid deposition in vivo as shown by light sheet microscopy imaging. At transcriptomic level, bulk and single-cell RNA sequencing revealed successfully induced disease-associated-microglia (DAM)-like phenotypes in Cnp-/- animals. These activated microglia, however, are primarily engaged with myelin seemingly preventing the protective reactions of the microglia pool to Aß plaques. Our work, therefore, identifies myelin aging as a previously overlooked risk factor for AD and makes the case for myelin health-directed therapies in AD.

overall_design: Microglia cells from 6-month-old mouse brain hemispheres were isolated using the MACS sorting system and subjected to 50 bp single-end mRNA sequencing. Each genotype has n=4 replicates, in total 4 genotypes were included for experiment (WT, Cnp-/-, 5xFAD, Cnp-/-x5xFAD).

first: Constanze

last: Depp

first: Klaus-Armin

last: Nave


title: Ageing-associated myelin dysfunction drives amyloid deposition in mouse models of Alzheimer's disease

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

overall_design: Refer to individual Series


title: Single-nuclei transcriptome sequencing of mouse grey and white matter under myelin abnormalities

overall_design: Cortex and corpus callosum were dissected from every two animals (3-month-old) and pooled into one sample for single-nuclei RNA sequencing using 10x genomics Chromium 3’ assay. Each genotype has 2 replicates (in total n=4 animals).


title: The study of SOX2 deposition in asynchronous and mitotic E14TG2a cells

status: Public on Mar 19 2023

city: Memphis

first: Zhexin

last: Zhu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: We executed ChIPseq for SOX2 a different mouse strain E14TG2a.

overall_design: Examination of SOX2 binding in a different mouse strain to preclude the strain specificity.

first: ZHEXIN

last: ZHU

first: XIAOLONG

last: CHEN


title: Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mouse embryonic body

summary: To evaluate the differential potential affected by SMARCE1 -MD/MD(R42A) , we performed RNA-sequencing (RNA-seq) of Smarce1-MD and control Smarce1-MD (R42A) embrynoic body.


title: The study of chromatin occupancy other mitotically bound factors upon the mitotic depletion of SMARCE1 in mouse ES cells.

summary: We executed CUT&RUN-seq for SOX2, ESRRB, and EZH2 upon the mitotic depletion of SMARCE1 in mouse ES cells.

overall_design: Examination of SOX2, ESRRB and EZH2 binding in DMSO or 5-Ph-IAA treated Smarce1-AID cells at 30 minutes after mitotic release.


title: The study of SOX2 deposition in asynchronous and mitotic E14TG2a mouse ES cells.

summary: We executed CUT&RUN-seq for SOX2 a different mouse strain E14TG2a


title: Transcription profiling of Smarce1- AID mESCs , cultured the cells with IAA treatment from 0min to 7 days.

summary: To evaluate the effects of degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of two Smarce1-AID mESCs. We found that transcription of the core pluripotency regulatory network was disrupted starting from 240min and there is an accumulation till day 7 .

overall_design: We performed RNA-seq in two Smarce1-AID clones mESCs in time course manner.


title: The study of SMARCE1 and SOX2 deposition in DMSO or BRM014 treated Smarce1-MD(R42A) and Smarce1-MD cells at 90 min after releasing from mitosis.

summary: We executed CUT&RUN-seq for SMARCE1 and SOX2 in BRG1 inhibitor BRM014 treated ,in MD or MD mutatnt mouse embryonic stem cells at 90 min from mitotic release.

overall_design: Examination of SOX2 and BAF57 binding in DMSO or BRM014 treated Smarce1-MD(R42A) and Smarce1-MD cells at 90 min after releasing from mitosis.


title: The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis II

summary: We conduct ATAC-seq in SMARCE1 MD/MD(R42A) after mitotic release 90 min in either DMSO treated or BRG1 inhibitor BRM014 treated conditions

overall_design: Examination of chromatin accessibility in mitotically degraded SMARCE1  and control on either DMSO or BRG1 inhibitor BRM014 treated ES cells.


title: Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila

city: Chapel Hill

first: Bo

last: Li

state: North Carolina

address: Genome Sciences Building 3244, 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

summary: Quorum sensing is a communication strategy that bacteria use to collectively alter gene expression in response to cell density. Pathogens use quorum sensing systems to control activities vital to infection, such as the production of virulence factors and biofilm formation. The Pseudomonas virulence factor (pvf) gene cluster encodes a quorum sensing system (Pvf) that is present in over 500 strains of proteobacteria, including strains that infect a variety of plant and human hosts. We have shown that the Pvf quorum sensing system regulates the production of secreted proteins and small molecules in the insect pathogen Pseudomonas entomophila L48. Here, we identified genes that are likely regulated by Pvf using the model strain P. entomophila L48 which does not contain other known quorum sensing systems. Pvf regulated genes were identified through comparing the transcriptomes of wildtype P. entomophila and a pvf deletion mutant (ΔpvfA-D). We found that deletion of pvfA-D affected the expression of approximately 300 genes involved in virulence, the type VI secretion system, siderophore transport, and branched chain amino acid biosynthesis. Additionally, we identified seven putative biosynthetic gene clusters whose expression are reduced in ΔpvfA-D. Our results indicate that Pvf controls multiple virulence mechanisms in P. entomophila L48. Characterizing genes regulated by Pvf will aid understanding of host-pathogen interactions and development of anti-virulence strategies against P. entomophila and other pvf-containing strains.

overall_design: Here, we analyze the P. entomophila L48 transcriptome using RNA sequencing and identified genes that are likely regulated by Pvf through differential expression between wildtype and a pvf deletion mutant (ΔpvfA-D).

first: Katie

last: Acken


title: Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mESCs with BMP4 rescue.

summary: To evaluate the effects of mitotic degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of four independent subclones each of Smarce1-MD and control Smarce1-MD (R42A) mESCs. We found that transcription of the core pluripotency regulatory network was not disrupted. In contrast, GO analysis showed that neural differentiation-associated terms were enriched among genes upregulated in Smarce1-MD mESCs.   To better understand the difference in neural fates in the neural induction experiments, we performed differential gene expression analysis and gene set enrichment analysis (GSEA) studies. Mitotic degradation of SMARCE1 resulted in higher expression of GABA receptors and hyper-activation of synaptic signaling on neural induction, indicating the aberrant neural cell fate commitment compared to SMARCE1-MD (R42A) cultures. And then we add back BMP4 to partically rescue the phenotype and very small amount of BMP4 will rescue the phenotype.

overall_design: We performed RNA-seq in Smarce1- MD (R42A) and Smarce1- MD mESCs with different concentration of BMP4 rescue.


title: The study of histone modifications and SOX2 occupancy in asynchronous and mitotic mESCs.

summary: We performed ChIP-seq for H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K36me3, H3K9me3, and H4K20me3 to characterize chromatin states and investigated SOX2 deposition in asynchronous and mitotic cells.

overall_design: Examination of H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K36me3, H3K9me3, and H4K20me3 deposition in asynchronous and mitotic mESCs. Examination of SOX2 binding in in asynchronous and mitotic mESCs.

last: Chen


title: The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis

summary: We executed CUT&RUN-seq for SWI/SNF components ARID1A, BRD9, SMARCA4, SMARCB1, SMARCE1, as well as ESRRB, SOX2, and EZH2 in asynchronous and mitotic cells and reported that, in asynchronous cells, ARID1A localized primarily at enhancer regions and EZH2 preferentially deposited at bivalent promoters and silent enhancer domains. The remaining factors were enriched at both TSS/promoters and to varying degrees at active enhancers. Unexpectedly, in mitosis, the chromatin regulatory factors almost all tethered at proximal gene regions with very little binding at enhancers. While the SWI/SNF subunits were bound principally at promoters, EZH2, the catalytic subunit of Polycomb Repressive Complex 2 was bound at both promoters and silent enhancers in mitotic cells. Moreover, we reported that upon the degradation of SMARCE1 in mitosis, the occupancy of SOX2, ESRRB, and EZH2 on mitotic chromatin was disrupted.

overall_design: Examination of ARID1A, BRD9, SMARCA4, SMARCB1, SMARCE1, as well as ESRRB, SOX2, and EZH2 deposition in asynchronous and mitotic cells. Examination of SOX2, ESRRB, and EZH2 occupancy in mitotically degraded SMARCE1 cells and control cells.


title: Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mESCs, and their derived cell cultures at day 06 after neural induction.

summary: To evaluate the effects of mitotic degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of four independent subclones each of Smarce1-MD and control Smarce1-MD (R42A) mESCs. We found that transcription of the core pluripotency regulatory network was not disrupted. In contrast, GO analysis showed that neural differentiation-associated terms were enriched among genes upregulated in Smarce1-MD mESCs.   To better understand the difference in neural fates in the neural induction experiments, we performed differential gene expression analysis and gene set enrichment analysis (GSEA) studies. Mitotic degradation of SMARCE1 resulted in higher expression of GABA receptors and hyper-activation of synaptic signaling on neural induction, indicating the aberrant neural cell fate commitment compared to SMARCE1-MD (R42A) cultures.

overall_design: We performed RNA-seq in Smarce1- MD (R42A) and Smarce1- MD mESCs. We also performed RNA-seq in Smarce1- MD (R42A) and Smarce1- MD derived cultured upon direct neural induction.


title: Transcriptional profiling of Brucella-infected brains

status: Public on Mar 17 2023

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

summary: In order to uncover transcriptional changes occurring in Brucella- infected mouse brains that might lead to neurologic complications, we infected susceptible mice intranasally with Brucella and harvested their brains.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of mock- and Brucella-infected brains.

first: Charles

last: Moley


title: Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency

status: Public on Mar 18 2023

city: Salt Lake City

first: Tejia

last: Zhang

state: UT

address: 30 South 2000 East

department: Pharmacology and Toxicology

institute: University of Utah

summary: Combined Saposin Deficiency is a lysosomal storage disease with multiple-organ pathologies that often involve neurodegeneration and early mortality.  To investigate the mechanisms driving saposin loss-associated demyelination, the brains of psap-/- zebrafish and wildtype siblings were analyzed via RNA-seq.

overall_design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR-Cas9 targeting the prosaposin (psap) gene, which codes for saposins A-D.  Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing, and fish carrying the mutations of interest were propagated to homozygosity.  RNA was isolated from the brains of four months-post-fertilization psap-/- zebrafish and wildtype siblings.

first: Chris

last: Stubben

first: Randall

last: Peterson


title: NADcapPro Seq and CircNAD –Methods for Accurate Profiling of NAD and Non-Canonical RNA Caps in Eukaryotes

city: Piscataway

first: Megerditch

last: Kiledjian

address: 604 Allison Road

institute: Rutgers University

summary: Accurate identification of NAD-capped RNAs is essential for understanding their biological function. Previous transcriptome-wide methods used to profile NAD-capped RNAs contain inherent limitations of having hindered the accurate identification of NAD caps from eukaryotic RNAs. Herein we introduced two novel orthogonal methods to precisely identify NAD-capped RNAs. One is D-SPAAC, a copper-free click-chemistry-based approach, and the second is an intramolecular ligation-based circNAD to resolve implicit limitations of the previous methods, which enabled us to unravel unforeseen features of NAD RNAs in budding yeast. Contrary to previous reports, we find that 1) cellular NAD RNAs can be full-length and polyadenylated transcripts, 2) transcription start sites for NAD-capped and canonical m7G-capped RNAs are different, and 3) NAD caps can be added post-transcriptionally. Moreover, we uncovered a dichotomy of NAD RNAs in translation where NAD RNAs are detected with mitochondrial ribosomes but not cytoplasmic ribosomes indicating their propensity to be translated in mitochondria.

overall_design: NADcapPro Seq, a copper-free click-chemistry-based approach to profile NAD capped RNAs in budding yeast

first: Sunny

last: Sharma

first: Jun

last: Yang

first: John

last: Favate

first: Premal

last: Shah


title: The study of nascent RNA transcripts in asynchronous cells and cells released from mitosis at the indicated timepoints between Smarce1- MD (R42A) and Smarce1- MD mESCs.

summary: SMARCE1 binding on mitotic chromatin is required for the timely reinitiation of expression of SMARCE1-bookmarked genes and maintaining identity memory in cell division.

overall_design: To examine the effect of mitosis-specific degradation of SMARCE1 on transcription reactivation following exit from mitosis, we used 5- ethynyluridine (EU) to pulse-label nascent transcripts in Smarce1-MD (R42A) (clone#A04, #A10) and Smarce1-MD (clone#MD09, #MD30) mESCs. Pulse-labeled transcripts were analyzed at 0, 45, 90, 180, and 240 min after nocodazole washout as well as in asynchronous cells.


title: Identification of MATR3 RNA-interactors in WT and Charme KO condtion during cardiac development [CLIP-seq]

city: Rome

first: Monica

last: Ballarino

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: MATR3 CLIP-seq analysis on embryonal (E15) murine hearts was performed to identify the protein RNA-interactors during murine cardiac development and to characterize the differential binding of the protein in conditon of KO of the lncRNA Charme.

overall_design: Cross-linking immunoprecipitation (CLIP-seq) for MATR3 in E15 hearts of WT  and Charme KO condition mice

first: Adriano

last: Setti


title: Explore the role of RHAMM in invasion/metastasis of breast cancer

city: Minneapolis

first: Andrew

last: Nelson

state: Minnesota

address: 420 Delaware St SE

institute: University of Minnesota

summary: To understand the mechanism of breast cancer invasion and metastasis, we collected tumor tissue from a cohort of 120 breast cancer patients and performed a Nanostring gene profiling assay (26 cases were removed from further analysis during quality control). Differential gene expression (DGE) analysis was done by comparing patients with/without lymph node metastasis lymph nodes. To explore the role of RHAMM in breast cancer invasion and metastasis, we created an RHAMM Related Signature (RRS) by intersecting the top 50 genes with another DGE list generated from a murine model wherein overexpression of an oncogenic RHAMM isoform increased cell motility in vivo tumor engraftment, and metastasis to identify RHAMM-related transcriptome changes specifically.

overall_design: We designed a custom Nanostring nCounter assay for quantitative assessment of expression of 356 genes consisting of TME interactions, inflammatory signaling, steroid receptor and growth factor signaling, cell cycle, apoptosis, and DNA repair, plus PAM50 classifier genes. A total of 26 cases were excluded for data analysis during quality control step.

first: Todd

last: Knutson

first: Yuyu

last: He


title: Multi-dimensional conservation analysis reveals transcriptional codes ruling the expression of conserved long noncoding RNAs

city: Singapore

first: Lei

last: Sun

address: 8 College Road Singapore

department: Cardiovascular & Metabolic Disorders Program

country: Singapore

institute: DUKE-NUS Medical School

summary: Although long non-coding RNAs (lncRNAs) encounter weaker evolutionary constraints and exhibit lower sequences conservation than coding genes, lncRNAs can conserve their features at different aspects. Here, we employed multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1731 conserved lncRNAs with 427 ultraconserved ones meeting multiple criteria. The conserved lncRNAs, in comparison with non-conserved ones, in generally have longer gene bodies, higher numbers of exons and transcripts, closer connections with human diseases, and are more abundant and widespread across different tissues. The transcriptional factor profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger impacts on their expression than non-conserved lncRNAs’ expression. Thus, our study has revealed a new set of transcriptional “codes” that rules the expression of the conserved lncRNAs.

overall_design: Examination of lncRNA's expression change in 293T cells

first: Dan

last: Xu


title: hMeDIP-Seq of Tet2 overexpressing hippocampal neurons

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

type: Methylation profiling by high throughput sequencing

summary: Tet2 regulates gene expression by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine. Profiling the genomic locations of 5-hydroxymethylcytosine after Tet2 manipulation can inform us of the targets of Tet2 regulation. We profiled hydroxymethylcytosine in Tet2 ovexpressing neurons to determine the targets of Tet2 in neurons.

overall_design: hMeDIP-Seq of Tet2 overexpressing or GFP hippocampal neurons

first: Karishma

last: Pratt

first: Saul

last: Villeda


title: Constitutive active STING signaling in MC38 tumor cells

city: München

first: Jürgen

last: Ruland

address: Einsteinstraße 25

institute: Technical University of Munich

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

overall_design: Refer to individual Series


title: Constitutive active STING signaling in MC38 tumor cells [RNA-Seq]

summary: Parental MC38 tumor cells were transduced with the STING-N153S mutant and RNA-seq for differential gene expression analysis was performed

overall_design: Gene expression analysis of RNA-seq data from parental versus STING-N153S mutant MC38 tumor cells

first: Larsen

last: Vornholz

first: Daniel

last: Strobl


title: High-throughput Functional Analysis of Autism Genes in Zebrafish Identifies Convergence in Dopaminergic and Neuroimmune Pathways

city: New Haven

first: Hellen

last: Weinschutz Mendes

state: Connecticut

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

summary: Investigation of convergence and divergence of different Autism Risk genes at the molecular level, in the brain of zebrafish ASD mutants at 6 days-post-fertilizitation (dpf)

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of the high-confidence Autism Risk Genes: scn1lab and dyrk1a.

first: Uma

last: Neelakantan

first: Yunqing

last: Liu

first: Sarah

middle: E

last: Fitzpatrick

first: Tianying

last: Chen

first: Weimiao

last: Wu

first: April

last: Pruitt

first: David

middle: S

last: Jin

first: Priyanka

last: Jamadagni

first: Marina

last: Carlson

first: Cheryl

last: Lacadie

first: Kristen

middle: D

last: Enriquez

first: Ningshan

last: Li

first: Dejian

last: Zhao

first: Sundas

last: Ijaz

first: Catalina

last: Sakai

first: Christina

last: Szi

first: Brendan

last: Rooney

first: Marcus

last: Ghosh

first: Ijeoma

last: Nwabudike

first: Andrea

last: Gorodezsky

first: Sumedha

last: Chowdhury

first: Meeraal

last: Zaheer

last: McLaughlin

first: Joseph

last: Fernandez

first: Jia

first: Jeffrey

last: Eilbott

first: Brent

last: Vander Wyk

first: Jason

last: Rihel

first: Xenophon

last: Papademetris

first: Zuoheng

last: Wang

first: Ellen

last: Hoffman


title: A hyper-quiescent chromatin state formed during aging is reversed by regeneration [ChIP-seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Epigenetic alterations are a key hallmark of aging but have not been extensively explored in tissues. Here, using naturally aged murine liver as a model and extending study to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach and the first direct visualization of aged chromatin, we find that old cells show global H3K27me3-driven broad heterochromatinization and transcription suppression. At the local level, site-specific loss of H3K27me3 from promoters of genes encoding developmental transcription factors leads to expression in liver of non-hepatocyte markers. Interestingly, liver regeneration reverses H3K27me3 patterns and rejuvenates multiple molecular and physiological aspects of the aged liver.

overall_design:
ChIP-seq of H3K27me3 in 3 young and 3 old mouse livers, 4 young and 4 old mouse kidneys.
ChIP-seq of 3 young and 3 old mouse livers before and after regeneration. ChIP-seq of EZH2 in 4 young and 4 old mouse livers.
ChIP-seq of various histone modifications in 3-4 young (10-14 weeks) and 3-4 old (79-95 weeks) mouse tissues.

last: Yang

first: Payel

last: Sen


title: A hyper-quiescent chromatin state is a barrier to productive regeneration during aging. [RNA-Seq]

summary: Epigenetic alterations are one of the key hallmarks of aging. Emerging evidence in model organisms, senescent cell cultures and limitedly, murine, and human tissue samples suggest local effects impacting genes and regulatory elements. However, how chromatin changes broadly affect euchromatin-heterochromatin balance, three-dimensional chromatin conformation, histone composition and global transcriptome has not been addressed. Furthermore, the cause and impact of these alterations on tissue function and age-related loss of regeneration is not well-understood. Here, using murine liver as a model for regeneration and an integrated multi-omics approach, we find that aged cells assume a severely repressed hyper-quiescent chromatin state characterized by a condensed chromatin, broad heterochromatinization driven by H3K27me3, global suppression of the transcriptome and inability of the chromatin to self-interact over long distances. Interestingly, concomitant targeted chromatin opening occurs over developmental gene promoters leading to loss of cell identity. We extend our findings to other quiescent tissues including human liver biopsies. Our findings reveal that global chromatin alterations promote a cellular state that is refractory to injury sensing and repair. Local chromatin changes compromise cellular identity. Together, this study provides possible explanations for age-related loss of regeneration and tissue function at the chromatin level.

overall_design: Transcriptomics over 6 time points during regeneration in young (4 month) and old (18 month) mouse liver. n=3 biological replicates per group, 36 libraries in total.

first: James

last: Occean


title: Constitutive active STING signaling in MC38 tumor cells [CITE-seq]

first: Jürgen

last: Ruland

summary: Parental MC38 tumor cells were transduced with the STING-N153S mutant

overall_design: CITE-Seq analysis of RNA-seq data from parental versus STING-N153S mutant MC38 tumor cells

first: Larsen

last: Vornholz

first: Daniel

middle: C

last: Strobl


title: A hyper-quiescent chromatin state is a barrier to productive regeneration during aging. [CUT&Tag ]

overall_design: CUT&Tag of H3K27me3 in 3 young and 5 old human livers.