title: Astrocytic ZBTB7A promotes orbitofrontal cortex dysfunction associated with Major Depressive Disorder [bulk RNA-Seq]

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

summary: Overall risk for Major Depressive Disorder (MDD) is determined by complex interactions between genetic and environmental factors that influence epigenetic regulation of neuroplasticity and stress pathways1,2. These mechanisms are specific to the distinct regulatory context within regionally-defined brain cell-types3,4. Here, we employed genome-wide chromatin accessibility profiling of neuronal vs. non-neuronal cells in orbitofrontal cortex (OFC) to capture regulatory signatures of MDD. We mapped genetic risk for MDD to active promoters of non-neuronal cell-types in OFC and identified MDD-specific open chromatin regions, which were differentially accessible exclusively in non-neuronal cells. Characterization of these loci revealed a key role for astrocyte dysfunction, and implicated the chromatin remodeling protein ZBTB7A, which coordinates wide-ranging cellular activation programs, including NF-kB inflammatory transcription5. In mice, astrocyte-specific knockdown of Zbtb7a reversed chromatin remodeling, reactive astrocyte transcription, and behavioral deficits associated with chronic stress. Conversely, ZBTB7A overexpression in OFC astrocytes induced stress-related behavioral deficits, promoted widespread inflammatory gene expression, and drove pathophysiological OFC neuronal hyperactivity in response to a mild subthreshold stressor. Our data highlight a critical role for OFC astrocytes in the bidirectional regulation of stress vulnerability and pinpoint ZBTB7A as a key factor mediating maladaptive astrocyte plasticity and OFC neuronal hyperexcitability in MDD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of mouse orbitofrontal cortex bulk tissue.For Zbtb7a knockdown experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-Zbtb7a-KD-mir virus or the AAV6-GFAP-mirNeg control virus to knockdown Zbtb7a expression specifically in OFC astrocytes, mice were randomly assigned to either the control group, or chronic stress group (10 days of chronic social defeat stress).     For ZBTB7A-OE experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-ZBTB7A OE virus or the AAV6-GFAP-GFP empty vector control virus to overexpress ZBTB7A specifically in OFC astrocytes and put through acute stress (1 day of social defeat stress).

first: Ian

last: Maze


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers

status: Public on Aug 11 2023

city: Helsinki

first: Konsta

last: Karttunen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Astrocytic ZBTB7A promotes orbitofrontal cortex dysfunction associated with Major Depressive Disorder [MDD]

status: Public on Aug 08 2023

country: USA

overall_design: Comparative gene expression profiling analysis of RNA-seq data of human postmortem orbitofrontal cortex bulk tissue.

middle: L


title: Astrocytic ZBTB7A promotes orbitofrontal cortex dysfunction associated with Major Depressive Disorder [MACS]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MACs-isolated astrocytes and neurons from virally-transduced male mouse OFC tissue. For Zbtb7a knockdown experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-Zbtb7a-KD-mir virus or the AAV6-GFAP-mirNeg control virus to knockdown Zbtb7a expression specifically in OFC astrocytes, mice were randomly assigned to either the control group, or chronic stress group (10 days of chronic social defeat stress). For ZBTB7A-OE experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-ZBTB7A OE virus or the AAV6-GFAP-GFP empty vector control virus to overexpress ZBTB7A specifically in OFC astrocytes and put through acute stress (1 day of social defeat stress).

last: L Fulton


title: Identification of a transcriptomic signature of X chromosome overdosage in  Saudi Klinefelter syndrome iPSCs.

status: Public on Aug 02 2023

city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

summary: Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by an extra copy of the X chromosome,while the non-mosaic form of KS with 47,XXY  karyotype is the most frequent (80-90%), less common non-disjunction events during the early mitotic division of the zygote result in mosaic forms of KS (47,XXY/46,XY). Here, using a paradigmatic cohort of KS-inducible pluripotent stem cells (iPSCs) carrying 47,XXY karyotypes we present the first iPSC-based disease-modeling study performed on KS patients from Saudi Arabia. We profiled the transcriptome of these Saudi KS-iPSCs, virtually characterized by subduedcgenetic backgrounds. Moreover, we performed a comparative transcriptomic analysis to assess the aberrant gene expression profile due to X dosage imbalance in four Saudi and five European and North American 47,XXY patients-derived iPSCs from our previously published study on KS and high-grade sex chromosome aneuploidies (SCAs). We identified a transcriptomic signature including ten PAR1 genes and thirteen non-PAR escape genes consistently upregulated in KS compared to 46,XY controls in both groups, as well as 193 consistenty disregulated autosomal genes. Our results indicate that the global transcriptional impact of X chromosome overdosage in KS is largely attributable to X-linked genes escaping X inactivation, regardless of the geographical area of origin, ethnicity, and genetic background.

overall_design: Bulk transcriptomic profiles of iPSC derived from 4 Klinefelter syndrome patients and 1 control.  For each patien three independent clones have been generated and for each clone three independent RNA-Seq libraries have been processed.

first: Veronica

last: Astro

first: Elisabetta

last: Fiacco

first: Kelly

middle: J

last: Cardona-Londoño

first: H

middle: S

last: Alzahrani

first: J

last: Alama

first: Amal

last: Kokandi

first: Taha

last: Abo-Almagd

first: Majed

last: Felemban


title: Alveolar macrophage immunobiology and functional genomics: Unlocking human to human variation in host response to M. tuberculosis

status: Public on Aug 07 2023

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: An innovative, high-throughput approach was proposed to identify key gene expression profiles and regulatory polymorphisms affecting innate immunity to TB by studying interactions between M.tb and human alveolar macrophages (AMs). We systematically analyzed interactions of a virulent M.tb strain with freshly isolated human AMs from 28 healthy adult donors, measuring host RNA expression and secreted candidate proteins associated with TB pathogenesis over 72h. We observed large inter-individual differences in bacterial uptake and growth, with tenfold variation in M.tb load at 72h, reflected by large variation of gene expression programs. Systems analysis of differential and variable RNA and protein expression identifies TB-associated genes and networks (e.g., IL1B and IDO1). RNA time profiles document early stimulation of M1-type macrophage gene expression followed by emergence of an M2-type profile.

overall_design: Assesment of transcriptome profiles from cells infected with Mycobacterium tuberculosis using AmpliSeq.

first: Wolfgang

last: Sadee

first: Larry

last: Schlesinger

first: Audrey

last: Papp

first: Abul

last: Azad


title: Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability.

city: San Antonio

state: TX

address: 8715 W. Military Dr

department: Host-Pathogen Interaction Program

institute: Texas Biomedical Research Institute

summary: This is a replication study on human alveolar macrophages (HAMs) from a smaller cohort from South Africa in order to support the RNA data of a relatively larger cohort from the US (Ohio & Texas). In this replication cohort, using full RNA-seq, a substantial portion of significant differentially expressed RNAs overlap with those identified with Ampliseq from the larger cohort over time, yielding similar enriched functional terms, e.g., interferon, interleukin, and IDO1 signaling.

overall_design: HAMs from healthy control subjects

middle: H

last: Cheeseman

middle: K


title: intact Hi-C from mucosa of descending colon (ENCSR206OUF)

status: Public on Jul 25 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
w80-mucosa-of-descending-colon-intact dnase HiC

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


title: Astrocytic ZBTB7A promotes orbitofrontal cortex dysfunction associated with Major Depressive Disorder

first: Sasha

last: Fulton

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: intact Hi-C from right cardiac atrium (ENCSR994DPD)

status: Public on Jul 24 2023

summary:
w76 right cardiac atrium intact dnase hic

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


title: intact Hi-C from left cardiac atrium (ENCSR975NRV)

summary:
w78 left cardiac atrium

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


title: intact Hi-C from natural killer cell (ENCSR971CJS)

summary:
NK intact Hi-C

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


title: intact Hi-C from prostate gland (ENCSR557QRO)

summary:
entex prostate intact dnase hic

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


title: intact Hi-C from mucosa of descending colon (ENCSR595UCM)

summary:
W76 mucosa of descending colon

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


title: intact Hi-C from heart left ventricle (ENCSR998LLZ)

summary:
uw67-heart-left-ventricle intact HiC

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


title: intact Hi-C from left colon (ENCSR972FIP)

summary:
w72 left colon intact dnase hic

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


title: intact Hi-C from posterior cingulate gyrus (ENCSR968JCS)

summary:
rush brain posterior cingulate gyrus healthy dnase hic

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


title: intact Hi-C from ovary (ENCSR872ZCP)

summary:
w80-ovary intact HiC

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


title: intact Hi-C from testis (ENCSR870SXX)

summary:
entex testis intact dnase hic

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


title: intact Hi-C from heart left ventricle (ENCSR942NSE)

summary:
uw036-heart-left-ventricle intact HiC

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


title: intact Hi-C from heart left ventricle (ENCSR967VFA)

summary:
uw076-heart-left-ventricle intact HiC

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


title: intact Hi-C from cardiac septum (ENCSR556QHB)

summary:
w61 cardiac septum intact dnase hic

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


title: intact Hi-C from aorta (ENCSR554SLA)

summary:
w73-aorta intact HiC

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


title: intact Hi-C from psoas muscle (ENCSR538PNC)

summary:
W80 psoas muscle intact dnase hic

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


title: BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

summary: Pseudouridine (Ψ) is an abundant RNA modification that is present in and impacts the functions of diverse non-coding RNA species, including rRNA, tRNA, snRNA, etc. Pseudouridine also exists in mammalian mRNA and likely exhibits functional roles; however, functional investigations of pseudouridine in mammalian mRNA have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed Bisulfite-Induced Deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol to generate highly reproducible results, displaying nearly zero background deletions at unmodified uridines after bisulfite treatment and uncovering 8,407 Ψ sites starting from as little as 10 ng mouse embryonic stem cell (mESC) polyA+ RNA, with the steps that are fast in both library preparation and data analysis. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS), and data analysis. The library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe (https://github.com/y9c/pseudoU-BIDseq), a user-friendly data analysis pipeline for BID-seq, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from NGS data.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: [dataset1] 24 samples (Sample 1-24):  "Input" and "Treated" samples in BID-seq to detect pseudouridine in synthetic RNA oligos. [dataset2] 6 samples (Sample 25-30):  "Input" and "Treated" samples in BID-seq to detect pseudouridine in mESC polyA+ RNA.

first: Chang

last: Ye

first: Chuan

last: He


title: Examining the brain's response to intestinal permeability and inflammation in the dextran sulfate sodium-induced colitis model.

status: Public on Aug 01 2023

city: Gainesville

first: Jake

last: Boles

state: FL

address: LG-152, 1149 Newell Dr

department: Neuroscience

institute: University of Florida

summary: The gut and brain are increasingly linked in human disease, with neuropsychiatric conditions classically long attributed to the brain showing an involvement of the intestine and inflammatory bowel diseases displaying an ever-lengthening list of neurological comorbidities. To identify molecular systems that underpin this gut-brain connection and thus discover therapeutic targets, experimental models of gut dysfunction must be evaluated for brain effects. In the present study, we examine disturbances along the gut-brain axis in a widely used murine model of colitis, the dextran sodium sulfate (DSS) model, using high-throughput transcriptomics and an unbiased network analysis strategy coupled with standard outcome measures, yielding a comprehensive approach to identify key disease processes in both colon and brain. We examine the reproducibility of colitis induction with this model and its resulting genetic programs during different phases of disease, finding that DSS-induced colitis is largely reproducible with a few site-specific molecular features. We focus on the circulating immune system, which exhibits an activation of pro-inflammatory innate immunity during colitis, as the vessel between gut and brain. Our unbiased approach provides supporting evidence for immune activation in the brain during colitis, suggests that myelination may be a vulnerable system with intestinal permeability, and identifies a possible role for oxidative stress and brain oxygenation. Overall, we provide a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.

overall_design: C57Bl6/J mice were treated with 2.5% DSS, assigned to various treatment schedules to create a time-series as follows: untreated controls, 5d DSS, 7d DSS, 7d DSS + 2d recovery, 7d DSS + 5d recovery, 7d DSS + 7d recovery, and 7d DSS + 14d recovery. After their respective schedules, mice were euthanized via rapid decapitation and tissues were harvested. Distal and proximal segments of the colon were taken to assess molecular processes associated with colitis and evaluate the reproducibility of these systems. From the brain, cortex, hippocampus, ventral midbrain, and striatum were taken to examine both global and regionally-specific transcriptomic perturbances that emerge in response to gut leakiness. All tissues were assayed with high-throughput RNA sequencing.

first: Malú

middle: G

last: Tansey


title: intact Hi-C from heart right ventricle (ENCSR941KKW)

summary:
uw68 heart right ventricle

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


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCSR923PPH)

summary:
naive CD4+ T cell Th0 effector _activated intact mnase

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


title: intact Hi-C from aorta (ENCSR797MWY)

summary:
w61-aorta intact dnase HIC

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


title: intact Hi-C from posterior vena cava (ENCSR941AMF)

summary:
w73 posterior vena cava

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


title: intact Hi-C from HCT116 (ENCSR533VUS)

summary:
HCT116 Pol2RA auxin untreated degron intact mnase hic

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


title: intact Hi-C from endothelial cell of umbilical vein (ENCSR788FBI)

summary:
HUVEC intact Hi-C

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


title: intact Hi-C from GM12878 (ENCSR916MFV)

summary:
GM12878 intact mnase hi-c

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


title: intact Hi-C from ovary (ENCSR782YIX)

summary:
w73 ovary intact dnase hi-c

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


title: intact Hi-C from heart right ventricle (ENCSR530DID)

summary:
uw076-heart-right-ventricle intact HiC

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


title: intact Hi-C from heart left ventricle (ENCSR529BKV)

summary:
w72 heart left ventricle intact dnase hic

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


title: intact Hi-C from HCT116 (ENCSR777YML)

summary:
HCT116 SMARCA5 auxin untreated degron intact hic

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


title: intact Hi-C from Right ventricle myocardium inferior (ENCSR921BHU)

summary:
W78 right ventricle myocardium inferior intact HIC

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


title: intact Hi-C from B cell (ENCSR847RHU)

summary:
Bcell intact Hi-C

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


title: intact Hi-C from right cardiac atrium (ENCSR503LWK)

summary:
w78-right-cardiac-atrium-intact dnase hic

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


title: intact Hi-C from heart left ventricle (ENCSR518LPK)

summary:
uw054-heart-left-ventricle-intact dnase

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


title: intact Hi-C from heart right ventricle (ENCSR771MVF)

summary:
UW65-heart-right-ventricle intact HiC

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


title: intact Hi-C from PC-9 (ENCSR859DRK)

summary:
PC9 intact Hi-C

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


title: intact Hi-C from adrenal gland (ENCSR898ANZ)

summary:
W61 adrenal gland intact dnase hic

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


title: intact Hi-C from lower leg skin (ENCSR720WEB)

summary:
entex skin (sun exposed) lower leg intact dnase hic

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


title: intact Hi-C from pancreas (ENCSR502GIO)

summary:
w62-pancreas intact hic dnase

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


title: intact Hi-C from heart left ventricle (ENCSR498AFT)

summary:
w73 heart left ventricle intact dnase hic

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


title: intact Hi-C from lower lobe of right lung (ENCSR749PID)

summary:
W78 lower lobe of right lung intact HIC

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


title: intact Hi-C from HCT116 (ENCSR481XZF)

summary:
HCT116 CDK7 degron untreated intact mnase

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


title: intact Hi-C from spleen (ENCSR692QWS)

summary:
w80 spleen permafrost intact dnase hic

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


title: intact Hi-C from mammary epithelial cell (ENCSR707XVJ)

summary:
HMEC intact Hi-C

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


title: intact Hi-C from HepG2 (ENCSR888DEJ)

summary:
HepG2 intact Hi-C

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


title: intact Hi-C from left lung (ENCSR892BZA)

summary:
w62-left-lung intact HiC

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


title: intact Hi-C from HCT116 (ENCSR490HOI)

summary:
HCT116-MED14-auxin untreated degon-intact

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


title: intact Hi-C from K562 (ENCSR479XDG)

summary:
K562 intact Hi-C

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


title: intact Hi-C from upper lobe of right lung (ENCSR673UZF)

summary:
W78 upper lobe of right lung intact HIC

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


title: intact Hi-C from HCT116 (ENCSR669VZH)

summary:
HCT116-CTCF auxin treated intact HIC

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


title: intact Hi-C from vagina (ENCSR886JAM)

summary:
entex vagina intact dnase hic

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


title: intact Hi-C from HCT116 (ENCSR477GZK)

summary:
HCT116 intact Hi-C

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


title: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR458VJJ)

summary:
Naive CD4+ T cell (CD45RO-CCR7+) Intact Mnase

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


title: intact Hi-C from HCT116 (ENCSR642MGQ)

summary:
HCT116 SMARCA5 auxin treated degron intact hic

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


title: intact Hi-C from MCF-7 (ENCSR660LPJ)

summary:
MCF-7 intact Hi-C

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


title: intact Hi-C from head of caudate nucleus (ENCSR874HTT)

summary:
rush brain anterior caudate healthy intact dnase hic

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


title: intact Hi-C from heart right ventricle (ENCSR908NSV)

summary:
uw038-heart-right-ventricle intact HiC

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


title: intact Hi-C from HCT116 (ENCSR878JLT)

summary:
HCT116 BRD4 degron treated intact mnase

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


title: intact Hi-C from adrenal gland (ENCSR832NED)

summary:
entex adrenal gland intact dnase

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


title: intact Hi-C from tibial artery (ENCSR601RFS)

summary:
entex tibial artery intact dnase hic

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


title: intact Hi-C from Panc1 (ENCSR584RBV)

summary:
Panc1 intact Hi-C

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


title: intact Hi-C from activated T-helper 2 cell (ENCSR474VTW)

summary:
naive CD4+ T cell Th2 effector _activated intact mnase

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


title: intact Hi-C from A673 (ENCSR455KLX)

summary:
A673 intact Hi-C

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


title: intact Hi-C from ascending aorta (ENCSR464RYO)

summary:
entex aorta intact dnase hic

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


title: intact Hi-C from T-helper 2 cell (ENCSR832CKD)

summary:
naive CD4+ T cell Th2 effector resting intact mnase

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


title: intact Hi-C from stomach (ENCSR569OBN)

summary:
entex stomach intact dnase hic

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


title: intact Hi-C from Caco-2 (ENCSR820DYU)

summary:
Caco-2 intact Hi-C

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


title: intact Hi-C from CD4-positive, alpha-beta T cell (ENCSR335JYP)

summary:
CD4+ intact Hi-C

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


title: intact Hi-C from pancreas (ENCSR387RQD)

summary:
w73 pancreas intact dnase

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


title: intact Hi-C from heart right ventricle (ENCSR812PIJ)

summary:
UW036 heart right ventricle intact dnase hic

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


title: intact Hi-C from left ventricle myocardium superior (ENCSR333BMU)

summary:
w78-leftventmyosup intact Mnase HiC

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


title: intact Hi-C from HCT116 (ENCSR565SZK)

summary:
HCT116-SUPT16H-treated intact HIC

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


title: intact Hi-C from breast epithelium (ENCSR326YHP)

summary:
entex breast intact dnase hic

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


title: intact Hi-C from heart left ventricle (ENCSR385MKW)

summary:
uw040-heart-left-ventricle-intact Dnase

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


title: intact Hi-C from CD14-positive monocyte (ENCSR444SKT)

summary:
Monocytes CD14+ LP23 intact Mnase HiC

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


title: intact Hi-C from heart right ventricle (ENCSR462CIE)

summary:
w73 heart right ventricle intact dnase hic

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


title: intact Hi-C from HCT116 (ENCSR176ICO)

summary:
HCT116-SUPT16H-auxin-untreated-intact HiC

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


title: intact Hi-C from CD4-positive, alpha-beta memory T cell (ENCSR379TIE)

summary:
Memory CD4+ T cell (CD45RO+CCR7+/-) LP11 resting Intact mnase

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


title: intact Hi-C from CD8-positive, alpha-beta T cell (ENCSR321BHC)

summary:
CD8+ intact Hi-C

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


title: intact Hi-C from right cardiac atrium (ENCSR173VDQ)

summary:
w73-right-cardiac-atrium intact hic dnase

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


title: intact Hi-C from colonic mucosa (ENCSR439ILZ)

summary:
w61 colonic mucosa

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


title: intact Hi-C from transverse colon (ENCSR258OVY)

summary:
entex transverse colon intact dnase hic

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


title: intact Hi-C from right lobe of liver (ENCSR753CKM)

summary:
w63 right lobe of liver intact HIC

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


title: intact Hi-C from heart right ventricle (ENCSR374OJL)

summary:
uw067-heart-right-ventricleintactHiC

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


title: intact Hi-C from MCF 10A (ENCSR370TFL)

summary:
MCF10A intact Hi-C

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


title: intact Hi-C from HCT116 (ENCSR233DHQ)

summary:
HCT116 BRD4 degron untreated intact mnase

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


title: intact Hi-C from HCT116 (ENCSR218URU)

summary:
HCT116 Pol2RA auxin treated degron intact mnase hic

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


title: intact Hi-C from sciatic nerve (ENCSR119TFS)

summary:
w61 sciatic nerve intact dnase hic

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


title: intact Hi-C from left lung (ENCSR305GRJ)

summary:
w76 left lung intact dnase hic

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


title: intact Hi-C from left ventricle myocardium inferior (ENCSR352EGR)

summary:
W78 left ventricle myocardium inferior intact Hi-C

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


title: intact Hi-C from esophagus muscularis mucosa (ENCSR274FJN)

summary:
entex esophagus muscularis intact dnase hic

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


title: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR215PTV)

summary:
naive CD4+ T cell Th0 effector resting intact mnase

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


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCSR421CGL)

summary:
LP6 CD4+ T Cells activated intact Hi-C

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


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCSR351NAI)

summary:
CD8+ activated intact Hi-C

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


title: intact Hi-C from CD14-positive monocyte (ENCSR236EYO)

summary:
Monocytes intact Hi-C

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


title: intact Hi-C from left colon (ENCSR298UUL)

summary:
W73 left colon intact HIC

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


title: intact Hi-C from heart left ventricle (ENCSR324EJR)

summary:
uw38-heart-left-ventricle intact HiC

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


title: intact Hi-C from heart left ventricle (ENCSR210LEF)

summary:
w76 heart left ventricle intact dnase hic

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


title: intact Hi-C from right cardiac atrium (ENCSR168PIR)

summary:
W72 right cardiac atrium intact HIC

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


title: intact Hi-C from heart left ventricle (ENCSR348KEP)

summary:
uw65-heart-left-ventricle intact HiC

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


title: intact Hi-C from pancreas (ENCSR408HOG)

summary:
w80-pancreas intact HiC

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


title: intact Hi-C from left cardiac atrium (ENCSR434MBR)

summary:
w73 left cardiac atrium intact dnase hic

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


title: intact Hi-C from heart right ventricle (ENCSR315OOJ)

summary:
UW040-heart-right-ventricle intact HiC

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


title: intact Hi-C from activated naive CD4-positive, alpha-beta T cell (ENCSR195ETV)

summary:
naive CD4+ T cell, activated Day 2 intact mnase

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


title: intact Hi-C from IMR-90 (ENCSR345VTI)

summary:
IMR-90 intact Hi-C

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


title: intact Hi-C from psoas muscle (ENCSR173QPK)

summary:
w61-psoas-muscle intact HiC

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


title: intact Hi-C from placenta (ENCSR395DZW)

summary:
human placenta intact hi-c dnase

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


title: intact Hi-C from HCT116 (ENCSR343ELD)

summary:
HCT116 MED14degron treated intact mnase

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


title: intact Hi-C from HCT116 (ENCSR087JOM)

summary:
HCT116-RAD21 auxin treated intact HIC

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


title: intact Hi-C from ovary (ENCSR160XGG)

summary:
w61-ovary intact hic dnase

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


title: intact Hi-C from Calu3 (ENCSR118AQZ)

summary:
Calu3 intact Hi-C

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


title: intact Hi-C from gastrocnemius medialis (ENCSR136MVS)

summary:
entex skeletal muscle gatsrocnemius medialis

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


title: intact Hi-C from thyroid gland (ENCSR043XTM)

summary:
entex thyroid intact dnase hic

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


title: intact Hi-C from lower lobe of left lung (ENCSR068FXF)

summary:
w78 lower lobe of left lung intact dnase hic

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


title: intact Hi-C from kidney (ENCSR044YKV)

summary:
w71-kidney intact dnase hic

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


title: intact Hi-C from OCI-LY7 (ENCSR088BOG)

summary:
OCI-LY7 intact Hi-C

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


title: intact Hi-C from heart right ventricle (ENCSR297CCU)

summary:
w72 heart right ventricle intact dnase hic

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


title: intact Hi-C from body of pancreas (ENCSR121ALS)

summary:
entex pancreas intact dnase hic

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


title: Gene expression profile at single cell level of normal neurons or peri-infarct neurons of Padi4-deficient and wild-type mice on day 4 after ischemic stroke

city: Bunkyo-ku

first: Akari

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

summary: To investigate the gene expression difference in peri-infarct neurons of Padi4-deficient and control mice on day 4 after ischemic stroke onset, we performed gene expression profiling analysis using data obtained from RNA-seq of peri-infarct neurons from neuron-specific Padi4-deficient and control mice.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data in peri-infarct neurons from neuron-specific Padi4-deficient (Slc17a7-Cre; Slc32a1-Cre; Padi4 flox/flox) and control (Padi4 flox/flox) mice.

first: Seiichiro

last: Sakai

first: Yuichiro

last: Hara

first: Hideya

last: Kawaji

first: Takashi

last: Shichita


title: intact Hi-C from dorsolateral prefrontal cortex (ENCSR165UJN)

summary:
rush brain midfrontal cortex healthy intact dnase hic

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


title: intact Hi-C from ovary (ENCSR181LJD)

summary:
entex ovary intact dnase hic

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


title: Chromatin accessibility in peri-infarct neurons on day 4 after ischemic stroke [ATAC-seq]

summary: To investigate chromatin accessibility in peri-infarct neurons on day 4 after ischemic stroke, we performed assay for transposase-accessible chromatin with sequencing (ATAC-seq) in peri-infarct neurons from Padi4 non-dificient mice.

overall_design: ATAC-seq in peri-infarct neurons from Padi4 flox/flox (Cre-) mice.

first: Jun

last: Tsuyama


title: intact Hi-C from activated CD4-positive, alpha-beta memory T cell (ENCSR291EBI)

summary:
Memory CD4+ T cell, activated Day 2 LP11 Intact mnase

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


title: intact Hi-C from uterus (ENCSR008CUR)

summary:
entex uterus intact dnase hic

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


title: Differential gene expression in brain tissues of Pla2g2e-deficient and wild-type mice

summary: To investigate the gene expression in brain tissues of Pla2g2e-deficient and wild-type mice, we performed gene expression profiling analysis using data obtained from Microarray of brain tissues collected from neuron-specific Pla2g2e-deficient and wild-type mice.

overall_design: Comparative gene expression profiling analysis of Microarray data for brain tissues from Pla2g2e-deficient and wild-type mice.

first: Yasumasa

last: Nishito


title: intact Hi-C from HCT116 (ENCSR086RCC)

summary:
HCT116-CTCF-auxin untreated degon-intact

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


title: Differential gene expression in brain tissues of Pla2g2e-deficient and wild-type mice on day 3 after ischemic stroke onset

summary: To investigate the gene expression in brain tissues of Pla2g2e-deficient and wild-type mice on day 3 after ischemic stroke onset, we performed gene expression profiling analysis using data obtained from Microarray of brain tissues from Pla2g2e-deficient and wild-type mice.


title: Differential gene expression in peri-infarct neurons of 15-HETrE-administered mice (compared with vehicle-administered mice) on day 4 after ischemic stroke onset

summary: To investigate the gene expression difference in peri-infarct neurons of vehicle- and 15-HETrE-administered mice on day 4 after ischemic stroke onset, we performed gene expression profiling analysis using data obtained from RNA-seq of peri-infarct neurons collected from the brain of vehicle- and 15-HETrE-administered mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from peri-infarct neurons between vehicle- and 15-HETrE-administered mice.


title: Single-cell transcriptional profiling of advanced renal fibrosis identifies novel specific fibroblast marker and disease target

status: Public on Jun 14 2023

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Dissecting the molecular and cellular nature of advanced renal fibrosis is principal for mechanistic understanding of chronic kidney disease (CKD) and developing targeted strategies against its progression. Aberrant renal fibroblast activation and unresolved tubular epithelial injury are key contributors to excessive extracellular matrix (ECM) production and kidney function loss. However, the transcriptional and cellular identities of activated renal fibroblasts remain poorly characterized. Moreover, historically used markers compromise specificity of activated renal fibroblasts tracing and targeting. Here, we created comprehensive single cell transcriptional profiles of two clinically relevant long-term renal fibrosis models and revealed three distinctive “secretory”, “contractile” and “migratory” fibroblast clusters. We identified a novel specific renal activated fibroblast marker expressed in all three populations. Advanced kidney fibrotic remodeling elicited sustaining developmental signature and pronounced epithelial-to-stromal crosstalk. Furthermore, we mechanistically validated AHNAK as a putative novel target of kidney injury in a primary human in vitro model of epithelial-to-mesenchymal transition.

overall_design: UIR and UUO injured kidneys were compared to controls vis single-cell RNAseq. The Ctrl, N, and AN samples are all controls. The controls were done in three different batches.

first: Steve

last: Potter

first: Prasad

last: Devarajan


title: Analysis of microbiota composition within breast tumor and healthy breast tissues in males and females

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Total DNA was extracted from FFPE specimens of breast tumor and surrounding healthy tissue, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

sample_organism:
Homo sapiens
other sequences

platform_organism:
Homo sapiens
other sequences

overall_design: Differential analysis of microbial abundance at different taxonomic ranks

first: Amedeo

last: Amedei

first: Simone

last: Baldi

first: Leandro

last: di Gloria


title: Single-cell RNAseq analysis of Gli1-GFP+ tooth roor progenitor cells and PTHrP+ dental follicle cells of the murine molar

status: Public on Jul 19 2023

city: Houston

first: Mizuki

last: NAGATA

address: 7500 Cambridge St

department: Orthodontics

institute: UTHealth

summary: A single cell transcriptional profile of both epithelial and mesenchymal cells in the tooth bud of the murine molar marked by Gli1-GFP+ tooth root progenitor cells or PTHrP+ dental follicle cells at postnatal day 6 (P6)

overall_design: GFP+, tdTomato+ and GFP+tdTomato+ cells were FACS-isolated from postnatal day 6 (P6) tooth bud of Gli1-GFP; PTHrP-creER; R26R-tdTomato mice (tamoxifen at P3). 10,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina NovaSeq 6000

first: Noriaki

last: Ono


title: PTHrP+ dental follicle cells

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


title: intact Hi-C from HCT116 (ENCSR129NAE)

first: ENCODE

last: DCC

summary:
HCT116 CDk7 degron treated intact mnase

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


title: TFEB-vacuolar ATPase signaling regulates lysosomal activity and immune response in tauopathy

status: Public on Jun 02 2023

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

summary: Transcription factor EB (TFEB) mediates gene expression through binding to the Coordinated Lysosome Expression And Regulation (CLEAR) sequence. We created a knock-in mouse line in which the CLEAR sequence of ATP6V1H was mutated. Crossing the CLEAR mutant with PS19 mice led to higher tau pathology but dampened glial cell activation. snRNA-seq revealed that the CLEAR mutant failed to be activated in tauopathy conditions.

overall_design: single nuclear RNA sequencing (snRNA-seq) of hippocampus of wild-type and PS19 tau transgenic mice and CLEAR mutant and CLEAR mutant crossing with PS19 mice at 9 month-of-age; and bulkRNAseq in WT and PS19 with 4 or 9 months old.

first: Hui

last: Zheng


title: intact Hi-C from sigmoid colon (ENCSR123ZFD)

summary:
entex sigmoid colon intact dnase hic

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


title: EZH1/2 dual inhibitors suppress HTLV-1-infected cell proliferation and hyperimmune response in HTLV-1-associated myelopathy

status: Public on Jun 01 2023

city: Tokyo

first: Makoto

last: Yamagishi

address: 4-6-1, Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: Gene expression profiling in PBMC and CD4+ T cells was performed to define gene expression changes in HTLV-1 infected cells from HAM/TSP patients.

overall_design: Total RNA samples from sorted patient cells were subjected to Cy-3 labeling followed by human whole genome gene expression microarray analyses.

first: Tomo

last: Satoh

first: Yoshihisa

last: Yamano


title: Comparative bulk RNAseq analysis of Control and Ptch1-deficient PTHrP+ dental follicle cells.

summary: We set out to reveal the transcriptome change induced by Ptch1 deficiency in PTHrP+ dental follicle cells

overall_design: tdTomato+ cells were FACS-isoalted from postnatal day 8 (P8) dental follicles of Ptch1 conditional Het and conditional KO mandibular molars (tamoxifen pulse at P3). mRNA were amplifed by SMARTer mRNA-seq kit (Clonetech/Takara) before deep-sequenced by Illumina HiSeq4000.


title: intact Hi-C from esophagus squamous epithelium (ENCSR015CVF)

summary:
entex esophagus mucosa intact dnase hic

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


title: Distribution of histone-3-citrullinated sites in peri-infarct neurons on day 4 after ischemic stroke

first: Akari

last: Nakamura

summary: To investigate distribution of histone-H3-citrullinated sites in peri-infarct neurons on day 4 after ischemic stroke and sham-operated mice, we performed cleavage under targets and tagmentation (CUT&Tag) assay for citrullinated histone H3 of peri-infarct neurons from Padi4-dificient or control mice .

overall_design: CUT&Tag assay for citrullinated histone H3 in peri-infarct neurons from Padi4-deficient (Slc17a7-Cre; Slc32a1-Cre; Padi4 flox/flox) and control  (Padi4 flox/flox) mice.

first: Seiichiro

last: Sakai

first: Jun

last: Tsuyama

first: Takashi

last: Shichita


title: Single-cell RNA sequencing defines disease-specific differences between chronic nodular prurigo and atopic dermatitis

status: Public on May 24 2023

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Chronic nodular prurigo (CNPG) is a chronic inflammatory skin disease that is maintained by a chronic itch-scratch cycle likely rooted in neuro-immunological dysregulation. This condition may be associated with atopy in some patients, and there are now promising therapeutic results from blocking type-2 cytokines such as IL-4, IL-13 and IL-31. Nevertheless, underlying pathomechanisms as well as the molecular relationship with atopy remain ill-defined.
Methods: We profiled skin lesions from patients with CNPG in comparison to atopic dermatitis (AD) and healthy control (HC) individuals using single-cell RNA sequencing combined with T-cell receptor sequencing.
Results: We found type-2 immune skewing in both CNPG and AD, as evidenced by CD4+ helper T cells expressing IL13. However, only AD harbored an additional, oligoclonally expanded CD8A+ IL9R+ IL13+ cytotoxic T cell population, and immune activation pathways were highly upregulated in AD, but less so in CNPG. Conversely, CNPG showed signatures of extracellular matrix organization, collagen synthesis, and fibrosis, including a unique population of CXCL14- IL24+ secretory-papillary fibroblasts. Besides known itch mediators such as IL31 and oncostatin M (OSM), we also detected increased levels of neuromedin B (NMB) in fibroblasts of CNPG lesions compared to AD and HC, with NMB receptors detectable on some nerve endings.
Conclusion:  These data show that CNPG does not harbor the strong disease-specific immune activation pathways that are typically found in AD, but is rather characterized by upregulated stromal remodeling mechanisms that might directly impact itch fibers.

overall_design:
Comparison of skin cells obtained from PN, AD and HC donors.
Raw data is not provided due to patient privacy concerns.
Healthy Control samples 112 – HC1, 115 – HC2, 116 – HC3 and 121 – HC4 used in this manuscript are already publicly available via Gene Expression Omnibus GSE173205.

first: Frank

middle: P

last: Assen

first: Tamara

last: Arnoldner

first: Wolfgang

middle: M

last: Bauer

first: Marco

middle: A

last: Medjimorec

first: Lisa

middle: E

last: Shaw

first: Katharina

last: Rindler

first: Gregor

last: Holzer

first: Philipp

last: Weber

last: Weninger

first: Christian

last: Freystätter

first: Tamar

last: Kinaciyan

first: Matthias

last: Farlik

first: Constanze

last: Jonak

first: Johannes

last: Griss

first: Christine

last: Bangert

first: Patrick

last: Brunner


title: A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities

status: Public on May 30 2023

city: Durham

first: Amy

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

overall_design: Refer to individual Series


title: Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas [Bulk ATAC-seq]

status: Public on Apr 27 2023

city: New York City

first: Cassandra

last: Burdziak

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: In pancreatic cancer, select cells within a homogeneous epithelium drive tumorigenesis in response to an environmental trigger, suggesting key uncharacterized roles for epigenetics and cellular context. To investigate epigenetic plasticity in early tumorigenesis, we performed single-cell transcriptional and chromatin accessibility sequencing of Kras-mutant pancreatic cancer models, encompassing initiation to malignant stages and wild-type tissue. Our analysis identifies a few progenitor states that correspond to known cells-of-origin, exhibit the greatest measured epigenetic plasticity, and are primed for diverse neoplastic fates. Plasticity is strongly associated with accessibility near receptor and ligand loci. We delineated robust communication modules and a feedback loop between IL33-expressing epithelial and immune cells with broad tissue impacts, which we confirmed by genetic perturbation in mice. Our results promise to nominate early interception strategies for this lethal cancer.

overall_design: Characterization of bulk chromatin accessibility (ATAC-seq) profiles of lineage-traced pancreatic epithelial cells (mKate2+) freshly-isolated by FACS-sorting from benign neoplastic lesions: To characterize early benign neoplasia (K3), KC;RIK (Ptf1a-Cre;RIK;LSLKrasG12D) mice were treated with caerulein at 5 weeks of age, and mKate2+ cells were subjected to ATAC-seq analyses 3 weeks thereafter. To characterize benign neoplasia emerging a later time-point without injury (K4), Kras-mutant pancreatic epithelial cells were isolated from KC;RIK mice at 41 weeks of age. Data from additional stages (N1, N2, K1, K2, K5) were extracted from GSE137069. 3 biological replicates (independent mice) were used per experimental condition.

first: Direna

last: Alonso-Curbelo

first: Dana

last: Pe'er

first: Scott

middle: W

last: Lowe


title: Unexpected consequences  of combined glucocerebrosidase and acid sphingomyelinase deficiency in a model of Parkinson’s disease

status: Public on Apr 24 2023

city: Edinburgh

first: Marcus

last: Keatinge

state: Midlothian

address: Ground Floor, Chancellors building, little france

country: United Kingdom

institute: University of Edinburgh

summary: Heterozygous variants in GBA1, encoding glucocerebrosidase (GCase), are the most common genetic risk factor for Parkinson’s disease (PD). Moreover, sporadic PD patients also have a substantial reduction of GCase activity. Genetic variants of SMPD1 are also overrepresented in PD cohorts, whereas a reduction of its encoded enzyme (acid sphingomyelinase or ASM) activity is linked to an earlier age of PD onset. Despite both converging on the ceramide pathway, how the combined deficiencies of both enzymes might interact to modulate PD has yet to be explored. Therefore, we created a double-knockout (DKO) AQ4 zebrafish line for both gba1 (or gba) ¶ and smpd1 to test for an interaction in vivo, hypothesising an exacerbation of phenotypes in the DKO line compared to those for single mutants

overall_design: Genes GBA and SMPD were knocked-out and compared to wild-type zebrafish. A double-knock out was also created. Each biological condition was repeated four times, in two experimental batches

first: Mark

last: Dunning

first: Ryan

middle: B

last: MacDonald

first: Deepak

last: Ailani


title: Overexpression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo

status: Public on Apr 26 2023

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI


title: Human Vg9Vd2 T cells develop within the postnatal thymus via a three-stage pathway defined by distinct molecular and cellular changes

status: Public on May 11 2023

city: Parkville

first: Peter

last: Hickey

summary: We identify precursors to the Vg9Vd2 T cell lineage in the postnatal thymus and use RNA-sequencing to understand their changes in gene expression throughout development

overall_design: Vg9Vd2 T cells were cell sorted from the postnatal thymus and periperal blood of human donors for RNA-seq analysis.

first: Daniel

last: Pellicci

first: Louis

last: Perrimen

middle: F

first: William

last: Ho


title: Overexpression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo I.

status: Public on Apr 28 2023

summary: RNAseq of Adult Liver in ADAR1 E861A, ADARp110, ADAR p150, ADAR1 knock in mice generated by deep sequencing.

overall_design: Whole liver from 3 replicates of each genotype were subjected to RNA sequencing.

first: Shannon

last: Ruiz

first: Ankita

last: Gupte

first: Jacki

last: Heraud-Farlow

first: Carl

middle: R

last: Walkley


title: A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

status: Public on Apr 20 2023

city: Boston

first: Stefano

last: Nardone

state: MASSACHUSETTS

address: 3,blackfan circle

department: Endocrinology

institute: Beth Israel Deaconess Medical Center

summary: The “dorsal pons”, or “dorsal pontine tegmentum” (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed the unique marker genes of many neuronal subtypes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study’s translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.

overall_design: Single nuclei were isolated from 1mm thick bilateral dissections of the dorsal pontine tegmentum (PnTg). To guide the dissection of the dorsal PnTg, we selectively labeled two different brain regions, the Parabrachial nucleus (PB) and the Barrington nucleus (Bar) (also known as PMC), that define its extension. A total of 9 and 8 batches (3-5 mice each) of male and female mice, respectively, of age between 8 and 10 weeks old, were used for the DroNc-seq assay.   In total, 447,833 nuclei were recovered.

first: Roberto

last: De Luca

first: Antonino

last: Zito

first: Natalie

last: Klymko

first: Dimitris

last: Nicoloutsopoulos

first: Oren

last: Amsalem

first: Cory

last: Brannigan

first: Jon

last: Resch

first: Christopher

last: Jacobs

first: Deepti

last: Pant

first: Molly

last: Veregge

first: Harini

last: Srinivasan

last: Grippo

first: Zongfang

last: Yang

last: Andermann

last: Zeidel

first: Kenneth

middle: D

last: Harris

first: Linus

middle: T

last: Tsai

first: Elda

last: Arrigoni

first: Anne

last: Verstegen

first: Clifford

last: Saper

first: Bradford

last: Lowell


title: Molecular features driving cellular and regulatory complexity of human brain evolution

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens


title: Mappinig the foci of rejuvenation interventions across the mouse central nervous system

status: Public on Apr 17 2023

city: South San Francisco

first: Oliver

last: Hahn

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

summary: Dietary, genetic and pharmacological interventions can extend health- and lifespan in diverse model organisms whilst delaying the onset of age-related pathologies. In the context of the brain, several of these interventions have shown to improve molecular, structural and cognitive hallmarks of brain aging. However, there is limited quantitative knowledge on where in the brain these interventions are most active and to what degree their molecular mechanisms overlap.  Here we performed region-resolved RNA-seq of the brain of aged mice either subjected to acute dietary restriction (aDR), injection of young mouse plasma (YMP), as well as their corresponding controls (ad libitium feeding and PBS injection, respectively). This encompasses 229 samples dissected from 15 regions. We reveal that each rejuvenation intervention impacts gene expression in a region-dependent manner, varying in timing, magnitude and biological function.

overall_design: mRNA-seq data of 15 distinct brain regions sampled from 19-months-old C57BL/6JN mice) were generated by deep sequencing using Illumina sequencing. One group of mice (Young Plasma Injection group) received retro-orbital injections of either Young Mouse Plasma (YMP) or PBS (n = 3-4 males per treatment). The second group (Dietary intervention group) of mice was either dietary restricted (aDR) or received ad libitum (AL) feeding (n = 4-5 females per diet). mRNA-seq of liver tissue of all mice in the Dietary Intervention group was additionally generated to assess efficacy of dietary restriction protocol.

first: Aulden

last: Foltz

first: Blen

last: Kedir

first: Micaiah

last: Atkins

first: Patricia

last: Moran-Losada

first: Christy

last: Munson

first: Ian

last: Guldner

first: Fabian

last: Kern

first: Róbert

last: Pálovics

first: Lu

last: Nannan

first: Benoit

last: Lehallier

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray


title: Differential gene expression in peri-infarct neurons compared between Padi4-deficient and wild-type mice on day 4 after ischemic stroke

first: Akari

last: Nakamura

summary: To investigate the gene expression difference in peri-infarct neurons compared between Padi4-deficient and wild-type mice on day 4 after ischemic stroke onset, we performed gene expression profiling analysis using data obtained from RNA-seq of peri-infarct neurons collected from neuron-specific Padi4-deficient and control mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from peri-infarct neurons between neuron-specific Padi4-deficient (Slc17a7-cre; Slc32a1-cre; Padi4flox/flox) and control (Padi4flox/flox) mice.

first: Seiichiro

last: Sakai

first: Takashi

last: Shichita


title: Overexpression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo II.

first: Alistair

last: Chalk

summary: RNAseq of Osteosarcoma model from ADAR1 knock in mice generated by deep sequencing.

overall_design: Murine osteoblasts immortalised from primary long bone derived osteoblasts with engineered deletion of p53 (R26-CreERT2 Tp53fl/fl derived cells) were collected at day 7, 14 and 21 post tamoxifen addition. 3 replicates of each genotype were subjected to RNA sequencing.

first: Shannon

last: Ruiz

first: Ankita

last: Gupte

first: Jacki

last: Heraud-Farlow

first: Carl

last: Walkley


title: Analysis of wild type and GAT201 deletion mutant strain reactivation in RPMI supplemented with and without 10% heat-inactivated fetal calf serum at 37°C.

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

summary: We wanted to find out the transcriptomic response of growth arrested wild type (KN99α) and Gat201 deletion mutant Cryptococcus yeast cells reactivating in cell culture media with and without serum.

overall_design: 56-sample RNA-seq timecourse of reactivation of growth-arrested 2 x wild type (KN99a + KN99α) and 2x Gat201 deletion mutant (Madhani and Bahn deletion collection) Cryptococcus neoformans in two different cell culture media at 37°C. Two biological samples of cells were pre-grown for 5 days in 20mL YPD at 30°C, 200rpm. A 2ml sample of this was taken as the "0 minute" control timepoint. We then inoculated 3.5ml in 2 different cultures of 100mL pre-warmed media: (RPMI, RPMI+Serum) at 37°C and grew for 30, 120 or 240 min. 15ml of culture was collected at each time point and fixed in 33& ice cold methanol, spun down astored at -80°C.

first: Elizabeth

last: Hughes

last: Ballou


title: Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex

status: Public on Apr 06 2023

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama 1 Rd. Wangmai Pathumwan

country: Thailand

institute: Chulalongkorn University

summary:
In this study, we investigated the effects of prenatal bisphenol-A (BPA) exposure on transcriptome profiles in the frontal cortex of the rat offspring. Transcriptome profiling by RNA-seq analysis of frontal cortex tissues isolated from neonatal pups prenatally exposed to BPA revealed that a list of differentially expressed genes (DEGs) associated with autism spectrum disorder (ASD), including Ntng1, Auts2, and Ankrd11 was dysregulated in a sex-specific pattern. The gene ontology analysis revealed that the BPA-responsive genes in the offspring’s frontal cortex were significantly associated with ASD-related neurological functions. These results indicated that prenatal BPA exposure may increase the risk of ASD by impacting ASD-related genes in the offspring’s frontal cortex.
We conducted experiments using the frontal cortex from neonatal pups prenatally exposed to BPA or vehicle control (BPA treament; pooled 3 pups frontal cortex, vehicle control; pooled 3 pups frontal cortex). 10-week-old female rats were daily treated with BPA at the concentration of 5,000 microgram/kilogram of maternal body weight or vehicle control from gestation day 1 (GD1) until parturition. Total RNAs were isolated and cDNAs were synthesized. The transcriptome profiles were performed using a high-throughtput RNA-seq.

overall_design: Expression profiling by high throughput sequencing

first: Songphon

last: Kanlayaprasit

first: Surangrat

last: Thongkorn

first: Pawinee

last: Panjabud

first: Depicha

last: Jindatip

first: Valerie

last: Hu

first: Takako

last: Kikkawa

first: Noriko

last: Osumi


title: Single-cell atlas of mouse leptomeningeal immune cells

status: Public on Mar 27 2023

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

summary: Metastasis to the cerebrospinal fluid (CSF)-filled leptomeninges, or leptomeningeal metastasis (LM), represents a fatal complication of cancer. Proteomic and transcriptomic analyses of human CSF reveal a substantial inflammatory infiltrate in LM. We find the solute and immune composition of CSF in the setting of LM changes dramatically, with notable enrichment in IFN-gamma signaling. To investigate the mechanistic relationships between immune cell signaling and cancer cells within the leptomeninges, we developed syngeneic lung, breast, and melanoma LM mouse models. We find that transgenic host mice, lacking IFN-gamma or its receptor, fail to control LM growth. Overexpression of Ifng through a targeted AAV system controls cancer cell growth independent of adaptive immunity. Instead, leptomeningeal IFN-gamma actively recruits and activates peripheral myeloid cells, generating a diverse spectrum of dendritic cell subsets. These migratory, CCR7+ dendritic cells orchestrate the influx, proliferation, and cytotoxic action of natural killer cells to control cancer cell growth in the leptomeninges. This work uncovers leptomeningeal-specific IFN-gamma signaling and suggests a novel immune-therapeutic approach against tumors within this space.

overall_design: 10x single-cell proteogenomics of mouse leptomeningeal immune cells in steady state and metastasis

first: Russell

last: Kunes

first: Ronan

last: Chaligné

first: Dana

last: Pe'er

first: Adrienne

last: Boire


title: Molecular features driving cellular and regulatory complexity of human brain evolution [RNA-seq]

first: Genevieve

last: Konopka

summary: Genomic changes acquired in human evolution contribute to the unique abilities of human brain. However, characterizing the molecular underpinnings of human-specific traits is a multifaceted challenge due to the cellular heterogeneity of human brain and complex regulation of gene expression. Here, we performed single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC-seq (snATAC-seq) in human, chimpanzee, and rhesus macaque brain tissue (brodmann area 23, posterior cingulate cortex). Human-specific changes were distinct among neuronal subtypes indicating that human brain evolution was accompanied by molecular alterations in finer cellular resolution.  We also observed more human-specific alterations in epigenome compared to transcriptome. Interestingly, human-specific accessibility changes in neurons were not as concordant with gene expression changes in comparison to other species, partially explaining this discrepancy. These cis-regulatory elements were enriched for immediate early gene motifs, identifying accelerated evolution of activity regulated genes in humans. We also uncovered associations between human evolution and brain disease genes at the cell type level. Together, these results reveal multiple mechanisms for human brain evolution at cell type resolution and establish the first direct evidence for accelerated human-specificity of activity-dependent molecular changes.

platform_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Brodmann Area 23 was dissected from human, chimpanzee and rhesus macaque (Macaca Mulatta). Each species contained 4 adult, post-mortem samples. Each sample was obtained from a different individual. Droplet-based single-nuclei RNA-seq libraries were prepared using the  Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina NovaSeq 6000.

first: Emre

last: Caglayan

first: Fatma

last: Ayhan

first: Todd

last: Preuss

first: Soojin

middle: V

last: Yi


title: Immunocompetent models of brain parenchymal and leptomeningeal metastasis

summary: Using iterative in vivo selection strategy, we generated a series of mouse metastatic lines with increased tropism for brain parenchyma or leptomeninges, to faithfully recapitulate the hallmarks of human disease.

overall_design: RNA was collected from in vitro cultured parenchymal or leptomeningeal metastatic cells and along with parental cells subjected for transcriptomic analysis.


title: Single-cell atlas of human leptomeningeal immune cells

summary: Profiling of immune cells in CSF from patients without leptomeningeal malignancy.

overall_design: 10x single-cell RNA-sequencing of human leptomeningeal immune cells


title: Molecular features driving cellular and regulatory complexity of human brain evolution [ATAC-seq]

overall_design: Brodmann Area 23 was dissected from human, chimpanzee and rhesus macaque (Macaca Mulatta). Each species contained 4 adult, post-mortem samples. Each sample was obtained from a different individual. Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.


title: SARS-CoV-2 induces dopaminergic neuronal loss in midbrain organoids during short and prolonged cultures

status: Public on Mar 20 2023

city: Esch-sur-Alzette

first: Javier

last: Jarazo

address: 6A, avenue des Hauts-Fourneaux

country: Luxembourg

institute: OrganoTherapeutics

summary: SARS-CoV-2 induces transcriptional dysregulation in midbrain organoids that can be linked to neurodegeneration

overall_design: Midbrain organoids of 30-33 days old were incubated with SARS-CoV-2 and differentially expressed genes were assessed 4 and 28 days post infection.

first: Eveline

last: Santos da Silva

first: Enrico

last: Glaab

first: Danielle

last: Bercoff

first: Jens

last: Schwamborn


title: Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas

first: Cassandra

last: Burdziak

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

overall_design: Refer to individual Series


title: Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas [scRNA-seq]

overall_design: Characterization of single-cell transcriptional profiles of lineage-traced pancreatic epithelial cells (mKate2+) isolated directly by FACS-sorting from normal (N1), regenerating (N2), pre-neoplastic (K1, K2), bening neoplastic (PanIN, K3, K4), malignant (PDAC, K5) and metastasis (K6) murine pancreatic tissues: To assess the effects of injury-induced inflammation on mutant Kras-expressing or Kras wild-type pancreatic epithelia, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe, and were analyzed 2 o 21 days thereafter. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+ or p48Cre;RIK;LSL-KrasG12D;p53R127H/+). 2-3 biological replicates (independent mice) were used per experimental condition.

first: Direna

last: Alonso-Curbelo

first: Scott

last: Lowe


title: Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas [ATAC-seq]

overall_design: Characterization of single-cell chromatin accessibility (scATAC-seq) profiles of lineage-traced pancreatic epithelial cells (mKate2+) freshly-isolated by FACS-sorting from benign neoplasia (K3) or malignant (K5)  pancreatic tissues: To characterize benign neoplasia (K3), KC;RIK (Ptf1a-Cre;RIK;LSLKrasG12D) mice were treated with caerulein at 5 weeks of age, and mKate2+ cells were subjected to scATAC-seq analyses 3 weeks thereafter. To characterize invasive disease (K5), pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPC;RIK (Ptf1a-Cre;RIK;LSL-KrasG12D;p53fl/+). Data from additional pre-malignant stages (K1, K2) were extracted from GSE137069, from KC-RIK mice treated with caerulein or PBS at 5 weeks of age, and analyzed 2 days thereafter. 2 biological replicates (independent mice) were used per experimental condition.


title: Feeder-Free Generation and Characterization of Endocardial and Cardiac Valve Cells from Human Pluripotent Stem Cells

status: Public on Mar 03 2023

city: New York

first: Clifford

middle: Z.

last: Liu

address: 1470 Madison Ave, Hess 8-301

institute: Icahn School of Medicine at Mount Sinai

summary: Valvular heart disease presents a significant health burden, yet advancements in valve biology and novel therapeutics have been hindered by the lack of accessibility to human valve cells. In this study, we have developed a scalable and feeder-free method to differentiate human induced pluripotent stem cells (iPSCs) into endocardial cells. Importantly, we show that these endocardial cells are transcriptionally and phenotypically distinct from vascular endothelial cells and can be directed to undergo endothelial-to-mesenchymal transition (EndMT) to generate cardiac valve cell populations. Following this, we identified two distinct populations—one population undergoes EndMT to become valvular interstitial cells (VICs), while the other population reinforces their endothelial identity to become valvular endothelial cells (VECs). We then characterized our iPSC-derived cell populations and identified putative markers for these populations through bulk RNAseq transcriptome analyses. Lastly, we validated our VIC and VEC populations by comparing our transcriptomic data to pseudobulk data generated from single-cell RNAseq of normal valve tissue from a 15-week-old human fetus. By increasing the accessibility to these cell populations, we aim to accelerate discoveries for cardiac valve biology and disease.

overall_design: Two wild-type iPSC lines (MSN02-4 and WTC11) were used. Each of these lines were differentiated to endocardial, endothelial, valvular interstitial cells (VICs), and valvular endothelial cells (VECs). These differentiated cell populations were sorted and total RNA was extracted for bulk RNAseq. Paired-end 150bp reads were performed at a depth of ~20 million reads per sample. A total of 3 replicates for each cell type, from each iPSC line was sequenced.

middle: Z

first: Aditi

last: Prasad

first: Bharati

last: Jadhav

first: Yu

first: Mingxia

last: Gu

first: Andrew

middle: J

last: Sharp

first: Bruce

last: Gelb


title: Spatial transcriptomics of the mouse brain across three age groups

first: Oliver

last: Hahn

summary: Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we use the 10X Visium platform to perform spatial transcriptomics (Spatial-seq) of equivalent coronal sections  of the mouse brain at young (6 months), middle (18 months) and old (21 months) age.

overall_design: Spatial RNA-seq of coronal brain sections from young, middle and old mice using 10x Genomics Visium for OCT embedded tissue (v3').

first: Aulden

middle: G

last: Foltz

first: Micaiah

last: Atkins

first: Blen

last: Kedir

first: Patricia

last: Moran-Losada

first: Christy

last: Munson

first: Ian

last: Guldner

first: Fabian

last: Kern

first: Róbert

last: Pálovics

first: Nannan

last: Lu

first: Benoit

last: Lehallier

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray


title: Tetrandrine regulates NAADP-mediated calcium signalling through a novel LIMP-2-dependent, sphingosine-mediated mechanism

status: Public on Mar 04 2023

city: Hung Hom, Kowloon, Hong Kong

first: Ricky

last: Chan

address: 11 Yuk Choi Rd

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Tetrandrine (Tet) is a highly potent inhibitor of Ebola virus replication by blocking NAADP-dependent calcium release through endolysosomal two-pore channels (TPCs) and is a moderately potent anti-tumor agent. Using a clickable, photoaffinity probe of Tet, we identified lysosomal integral membrane protein-2 (LIMP-2) as the genuine molecular target of Tet and a novel regulator for NAADP-dependent calcium release. Tet binds to the ectodomain of LIMP-2 and inhibits its cholesterol and sphingosine transport function, resulting in the alteration of lipid profiles and metabolic pathways in cells and development of acute hypercholesterolemia and hepatosteatosis in mice. Cells treated with Tet or depleted for LIMP-2 similarly inhibits NAADP-dependent calcium release, which can be restored by eliminating lysosomal cholesterol and sphingosines. Importantly, addition of sphingosine dose-dependently triggers lysosomal calcium release through TPCs, and restores NAADP-dependent calcium release in Tet-treated or LIMP-2-depleted cells. At higher concentrations, Tet induced apoptosis associated with unfolded protein response activation in a LIMP-2-independent manner.  We identified Tet as the first known inhibitor of LIMP-2, discerned its pharmacological principle in regulating calcium signalling and cell death, and discovered a novel LIMP-2-regulated, sphingosine-dependent lysosomal calcium signalling pathway. Our findings have profound implications in the understanding of lysosomal calcium signalling mechanisms and development of Tet and LIMP-2 inhibitors into clinical therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells treated with DMSO or diferent concentration of Tetrandrine or AD-Tetrandrine

first: Ben

middle: C

last: Ko

first: Wing-Cheung

first: Pauline

last: Chiu

first: Qian

last: Zhao

first: Hok-Him

last: Tang

first: Daniel

middle: K

last: Mok

first: Lakhansing

last: Pardeshi

first: Ye Chun

last: Ruan

first: Yang

last: Yang

first: Chi-Ming

last: Wong

first: Clarence

first: Yong-Juan

first: Ka Ying

first: Zengsheng

last: Yin

first: Howard

middle: H

last: Leung

first: Xiyang

last: Ma

first: Po Ki

last: Chau

first: Franco

first: Ying-Ying

last: Lui

first: Shannon

last: Au

first: Kailei

last: Sun

first: Chin Yu

first: Fang

last: Wang

first: Cong

first: Yuxuan

last: He

first: Xiang-Yang

last: Ye

first: Man Lung

last: Yeung

first: Yajing

last: Zhang

first: Yan Xiang

first: Jiang

last: Liu

first: Xiang

last: Li

first: Gary

last: Tse

first: Larry

last: Chow

first: Ka-Hing

first: Man-Kin

first: Xiao

last: Shen


title: Single-nuclei sequencing of the mouse hippocampus and caudate putamen at young and old age

first: Oliver

last: Hahn

summary: Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed single-nuclei sequencing (Nuc-seq) of hippocampus and caudate putamen isolated from young (3 months) and old (21 months) old mice.

overall_design: Single-nuclei RNA transcriptomes of hippocampus and caudate putamen obtained from brains of young and old mice using 10x Genomics Drop-seq (v3.1).

first: Aulden

last: Foltz

first: Micaiah

middle: E

last: Atkins

first: Blen

last: Kedir

first: Patricia

last: Moran-Losada

first: Christy

last: Munson

first: Ian

last: Guldner

first: Fabian

last: Kern

first: Róbert

last: Pálovics

first: Lu

last: Nannan

first: Benoit

last: Lehallier

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray


title: Single-nuclei sequencing of the mouse hippocampus of dietary restricted mice

summary: Dietary restriction (DR), reduced food intake while avoiding malnutrition, profoundly extends lifespan in most model and non-model organisms. Both chronic (i.e. life-long)  and acute (i.e. late-onset) DR have been shown to improve cognitive performance in aged mice compared to animals with an unrestricted access to food (ad libitium feeding; AL). Yet so far, quantitative analyses of the molecular dynamics in the brain of DR fed animals have been limited. Here we performed single-nuclei sequencing (Nuc-seq) of whole hippocampus isolated from young (5 months) and old (24 months) AL fed animals, as well as old chronic DR (DR started at 3 months) and acute DR (aDR) mice.

overall_design: Single-nuclei RNA transcriptomes of whole frozen hippocampus obtained from brains of young (5 months) and old (24 months) mice fed ad libitum (AL) as well as old mice that were dietary restricted from the age of 5 months (long-term DR; DR) or 20 months of age (acute DR; aDR) using 10x Genomics Drop-seq (v3.0). All animals were of the C3B6F1 hybrid strain.

first: Sebastian

last: Grönke

first: Linda

last: Partridge


title: A spatiotemporal map of the mouse brain reveals white matter tracts as vulnerable foci of aging

summary: Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we performed spatiotemporal RNA-seq of the brain across the adult mouse lifespan, encompassing 847 samples dissected from 15 regions spanning 7 age groups. We reveal that aging impacts gene expression in a region-dependent manner, varying in timing, magnitude and biological function.

overall_design: mRNA-seq data of 15 distinct brain regions sampled from 59 C57BL/6JN mice ( n = 3-6 males per age; aged 3, 12, 15, 18, 21, 26 and 28 months; n = 5 females per age; aged 3, 12, 15, 18 and 21 months; all C57BL/6JN strain) were generated by deep sequencing using Illumina sequencing.


title: USP25 Ameliorates Pathological Cardiac Hypertrophy by Stabilizing SERCA2a in Cardiomyocytes

status: Public on Mar 01 2023

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

country: China

institute: Wenzhou Medical University

summary: Pathological cardiac hypertrophy can lead to heart failure and is one of the leading causes of death globally. Understanding the molecular mechanism of pathological cardiac hypertrophy will contribute to the treatment of heart failure. Deubiquitinating enzymes (DUBs) are essential to cardiac pathophysiology by precisely controlling protein function, localization, and degradation.This study set out to investigate the role of a DUB, USP25, in pathological cardiac hypertrophy, reveal its molecular mechanism, and hopefully provide a new therapeutic target for heart failure.We revealed increased protein level of USP25 expression in the cardiomyocytes in response to Ang II stimulation. USP25 deficiency aggravated cardiac hypertrophy and cardiac dysfunction under Ang II and TAC treatment. Mechanistically, LC-MS/MS analysis combined with Co-IP was used to identify SERCA2a, an anti-hypertrophy protein, as an interacting protein of USP25. Also, our data showed that USP25 bound to SERCA2a directly via its USP domain and cysteine at position 178 of USP25 exerts deubiquitination to maintain the stability of the SERCA2a protein by removing the K48 ubiquitin chain and preventing proteasomal pathway degradation, thereby maintaining calcium content in cardiomyocytes. Moreover, restoration of USP25 expression via with AAV9 vectors in USP25-/- mice attenuated Ang II-induced cardiac hypertrophy and cardiac dysfunction, whereas SERCA2a myocardial overexpression could offset the effect of USP25.

overall_design: We performed RNA sequencing analysis on the heart tissues of three control group mice and three Ang II-induced mice.

first: Bozhi

last: Ye

first: Guang

last: Liang