title: Isoliensinine ameliorates renal injury via the TGF-β1/SMAD2/3 pathway in spontaneously hypertensive rats [kidney tissue]

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in renal tissues of WKY and SHR with or without isoliensinine treatment. The SHRs (n=12) were randomly divided into 2 groups: SHR, and SHR + isoliensinine (5mg/kg/d) groups (n=6 for each group). WKY rats (n=6) were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O); while rats in  SHR + isoliensinine (5mg/kg/d) group were intragastrically with 5mg/kg/d of  isoliensinine for 10 weeks.  Then the renal tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with kidney of rats in 3 groups: WHY, SHR, SHR + isoliensinine - M (5mg/kg/d) treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Mengying

last: Yao

first: Dawei

last: Lian

first: Meizhu

last: Wu


title: Effect of depletion of FAP on gene expression in ovarian cancer cell OVCAR8

status: Public on Sep 20 2023

city: Gainesville

first: Shuang

last: Huang

state: FL

address: 2033 mowry road

country: USA

institute: University of Florida

type: Expression profiling by high throughput sequencing

summary: To investigate the effcet of FAP KD in ovarian cancer cells

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of ovcar8 cells after 4-day KD

first: Bin

last: Li


title: Age-associated changes in murine endothelial gene expression and chromatin accessibility correlate with impaired blood-brain barrier integrity and elevated risk of intracerebral hemorrhage [ATAC-seq]

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Intracerebral hemorrhage (ICH), a devastating form of stroke, is a leading global cause of human death and disability. The major risk factors for ICH include increasing age, hypertension and cerebral amyloid angiopathy. Despite high mortality and morbidity associated with ICH, the mechanisms leading to blood-brain barrier (BBB) dysfunction with age and development of hemorrhagic stroke is poorly understood. In the vasculature of the central nervous system, endothelial cells (ECs) constitute the core component of the BBB and provide a physical barrier due to tight junctions, adherens junctions, and basement membrane layers. In this study, we show in brains of mice that incidents of intracerebral bleeding increase with advancing age. After isolation of an enriched population of cerebral ECs, we studied gene expression in ECs isolated from murine brains of increasing ages of 2, 6, 12, 18, and 24 months. The study reveals age-dependent dysregulation of 1388 genes in the ECs, including many involved in the maintenance of BBB and vascular integrity. Since epigenetic mechanisms regulate gene expression, we also investigated age-dependent changes at the levels of CpG methylation and accessible chromatin in cerebral ECs. Our study reveals correlations between age-dependent changes in chromatin structure and gene expression. We find significant age-dependent downregulation of the apelin receptor (Aplnr) gene along with an age-dependent reduction in chromatin accessibility of the promoter of this gene. Aplnr is known to play a crucial role in positive regulation of vasodilation and is implicated in vascular health. Interestingly, we also observe an age-dependent reduction in the protein expression levels of the apelin receptor in the brain, potentially implicating the apelin receptor to be critical for the increased risk of intracerebral hemorrhage with ageing.

overall_design: Assay for Transposase-Accessible Chromatin (ATAC) -seq.

first: Kshitij

last: Mohan

first: Abdulrahman

last: Salhab

first: Michael

last: Orlich

first: Robert

last: Geffers

first: Steve

last: Hoffmann

first: Ralf

middle: H

last: Adams

first: Jörn

last: Walter

first: Alfred

last: Nordheim


title: Global gene profilings in embryo and seed coat of lentil during embryogenesis

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: We present an atlas of global gene expression covering embryo and seed coat development in lentil, providing insights into the evolution of gene expression in embryogenesis of lentil species.

overall_design: We investigate the dynamics and evolution of gene expression throughout eight stages of embryo development, and one unfertilized ovule stage in lentil.

first: Daoquan

last: Xiang

first: Bianyun

last: Yu


title: Transcriptome Alteration Between Young and Senile Human Bone MSC

city: Chengdu

first: Fanyuan

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

country: China

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: In order to uncover mechanisms of hBMSC senescence, we performed high-throughput RNA-seq using young and senile human bone MSC (hBMSC).

overall_design: We used three independent samples in each groups. And the young hBMSC was set as control group.

first: Feifei


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [CUT&Tag]

city: Guangzhou

first: Rui

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
Herein, we describe the landscape of m6A on super enhancer RNAs (seRNAs) in pancreatic ductal adenocarcinoma (PDAC) and demonstrate a regulatory axis involving m6A-seRNAs, H3K4me3 modification, chromatin accessibility and oncogenic transcription.
our study has revealed the CFL1-YTHDC2-MLL1 epigenetic regulatory axis plays critical roles of dynamic m6A deposition in seRNAs and local chromatin state, which may be a novel oncogenic mechanism in PDAC and shed light on the crosstalk between epitranscriptome and epigenome.

overall_design: H3K4me3、YTHDC2、MLL1 CUT&Tag of PANC-1

first: Hongzhe

last: Zhao

first: Xudong


title: Role of Caveolin 1 in metabolic programming of fetal brain (bulk RNA-seq data)

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: Caveolae are plasma membrane invaginations found in most cells of mammals. Caveolin-1 (Cav1) encodes a major protein of the lipid rafts of these membrane structures. Cav1-null mice, though viable, show various phenotypic defects. At an early adult age, these mice show brain aging that resemble brain of one and half year old wildtype mice, and exhibit symptoms that are hallmarks of Alzheimer’s disease. It is not known if the ablation of Cav1 in these mice impacts the brain at the fetal stage that then influences brain function later in life. RNA-seq was performed to profile gene expression of fetal brain (gestation day 15) and aging brain (week 70) of  Cav1 knockout mice. The  data was comapred with genes expression data of fetal brain (gestation day 15) and aging brain (week 70) of  wildtype  mice from our earlier study.

overall_design: RNA-seq was performed with fetal brain (gestation day 15) of wild-type and Cav1 knockout mice. Aging brain (week 70) from Cav1 knockout mice was also sequenced and compared with RNA-seq data  of WT mice generated from our earlier study.

first: Maliha

last: Islam

middle: K


title: Distinct circular DNA profile in hSOD1G93A ALS that intersects with ALS proteome changes

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: Numerous genes mutated in amyotrophic lateral sclerosis (ALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. DNA instability and repair mechanisms segregate extrachromosomal circular DNAs (ec/eccDNAs) that can modulate gene expression somatically. Here, circulome profiling in a hSOD1G93A genotoxicity model of ALS revealed a 6-fold enrichment of small-size eccDNAs relative to controls. DifCir-based differential analysis identified 189 genes with patterned segregation of differentially produced per gene circles (DPpGCs) from ALS but not from control samples, implicating an inter-sample recurrence rate of at least 89% for the top 6 DPpGCs. Mass spectrometry-based ALS circulome-proteome cross-referencing revealed 31 corresponding differentially expressed proteins (DEPs), with 12 DPpGC-DEP pairs being itemized in ALS risk GWAS databases. DPpGC-DEP hotspots mainly convey neuron-specific functions counteracting ALS detriments. This is unanticipated evidence for non-random, profiled eccDNA accumulation in ALS neurodegeneration, involving putative interactions with their gene products as well as biomarker perspectives.

overall_design: The data C (Control,C57BL/6J) is performed with 10 replicates. The data A (ALS,B6.Cg-Tg(SOD1*G93A)1Gur/J) is performed with 9 replicates.

first: Daniela

last: Gerovska

first: Julie

last: Boertmann Noer

first: Yating

last: Qin

first: Ivonne

last: Heinze

first: Joanna

last: Kirkpatrick

first: Quratul

last: Ain

first: Matthias

last: Schwab

first: Otto

middle: W

last: Witte

first: Alessandro

last: Ori

first: Birgitte

middle: J

last: Regenberg

first: Alexandra

last: Kretz


title: Tumor immune profiling of gingivo-buccal oral cancer patients reveals two groups with significant differences in prognosis and immune contextures

city: Kalyani

first: Partha

middle: P.

last: Majumder

state: West Bengal

country: India

institute: National Institute of Biomedical Genomics

summary: Interactions between cancer and immune cells determine the formation and progression of a tumor. Variability of immune contextures in tumor and margins among patients with oral squamous cell carcinoma of the gingivobuccal region (OSCC-GB) – the most prevalent subtype of oral cancer in India and southeast Asia – and the relationship of these contextures with prognosis are largely unknown.  Treatment naïve, HPV negative, OSCC-GB patients (n=46) were recruited, treated, followed-up for two years and recurrence/death noted.  Immune contextures of tumor and negative margins were studied using RNA-sequencing and immunohistochemistry (n=43; margin tissues were unavailable from three patients). Expressions of 544 immune related genes (IRGs) revealed a subgroup of patients (28%) with poor prognosis (high recurrence and death). The compositions of immune cell-types of normal and negative margin tissues were similar among patients irrespective of prognoses; differences were observed only in tumor.

first: Ankita

last: Chatterjee

middle: P


title: 4DNESRE7AK5U - Replicate experiments of in situ Hi-C on globose cell of olfactory epithelium with DpnII

status: Public on Sep 19 2023

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. These contacts are orchestrated by intergenic olfactory receptor enhancers, the 'Greek islands', which first contribute to the formation of olfactory receptor compartments and then form a multi-chromosomal super-enhancer that associates with the single active olfactory receptor gene. The Greek-island-bound transcription factor LHX2  and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans  interactions in gene expression.

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNESRE7AK5U
condition: Globose basal cells of the olfactory epithelium
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESRE7AK5U/
number_of_experiments: 1

experiment: 4DNEXCDN8ONW; replicate_number: Biorep 1, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/dee195fc-ef83-478a-95ba-d563930120c1/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFI4PDERVK.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIWAA9Q8H.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/dee195fc-ef83-478a-95ba-d563930120c1/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFI4PDERVK.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFI1TBYKV3.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/dda3ff58-73f9-443c-b88a-e9c7e69c91c6/
genome_assembly: GRCm38
derived_from: 4DNFI1TBYKV3.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFILUQCWPA.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/dda3ff58-73f9-443c-b88a-e9c7e69c91c6/
genome_assembly: GRCm38
derived_from: 4DNFI1TBYKV3.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIZ6CYXH7.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/200ab2d4-7378-4c6e-ae48-b29b6067737a/
genome_assembly: GRCm38
derived_from: 4DNFI1TBYKV3.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIB8IUKAB.bw


title: Long-term NAD+ supplementation prevents the progression of age-related hearing loss in mice

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Age-related hearing loss (ARHL) is the most common sensory disabling condition associated with aging in humans. Yet, there are still no approved measures for preventing or treating this debilitating condition. With its slow progression, continuous and safe treatment approaches are critical for ARHL treatment. Nicotinamide Riboside (NR), a NAD+ precursor, is well-tolerated even for long-term use and is already shown effective in various disease models including Alzheimer’s and Parkinson’s Disease. However, its beneficial impact on ARHL is not known. In this study, we investigated transcriptomic profile in the cochlea of the mice (mtKeima strain) that are treated with NR for 10 months vs. non-treated.

overall_design: NR administration to mtKeima mice started at 2 months and treatment lasted for 10 months until mice were 12 months of age. The cochlea was dissected for further gene expression profiling at the end of the NR administration.

first: Mustafa

middle: N

last: Okur

first: Risako

last: Kimura

first: Burcin

middle: D

last: Sahbaz

first: Uri

last: Manor

first: Jaimin

last: Patel

first: Leo

last: Andrade

first: Kala

last: Puligilla

first: Deborah

middle: L

last: Croteau

first: Vilhelm

middle: A

last: Bohr


title: c-Fos mediates cell proliferation, invasion and drug-resistance of lung adenocarcinoma through MAPK signal pathway

city: Shanghai

first: Shaohua

last: Wang

address: No 12 Middle Wulumuqi Road

institute: Department of Thoracic Surgery

summary: Lung cancer is the main cause of cancer-related death in men and women all over the world. Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer, with the overall 5-year survival rate is less than 20% . We found the mRNA expression of c-Fos in LUAD clinical samples was decreased significantly compared to adjacent normal control. Overexpression of c-Fos inhibited LUAD cell proliferation, colony formation, and induced cell apoptosis while c-Fos knockdown promoted cell proliferation, colony formation, and suppressed cell apoptosis. Cell cycle showed little difference after c-Fos knockdown but overexpression of c-Fos increased the distribution of G1 phase when decreased G2 phase cells. Knockdown of c-Fos reduced the sensitivity of LUAD cells to cisplatin but overexpression of c-Fos increased the efficacy of cisplatin both in vitro and in vivo. MAPK signaling pathway was enriched after c-Fos was overexpressed in LUAD cells. The expression of c-Jun, c-Myc and DUSP1 was greatly inhibited after c-Fos overexpression but incresed after c-Fos knockdown, which suggests c-Fos regulated MAPK signaling pathway in LUAD. Furthermore, c-Fos was shown to interact with c-Jun and overexpression of c-Jun partially recovered the expression of c-Jun, c-Myc and DUSP1 caused by c-Fos overexpression. Cell proliferation was also rescued when apoptosis was decreased followed by c-Jun overexpression. In contrast, knockdown of c-Jun inhibited cell proliferation and promoted cell apoptosis in LUAD cells when reduced the level of c-Jun, c-Myc and DUSP1. In summary, c-Fos inhibits cell proliferation, promotes apoptosis and increses cisplatin-sensitivity of lung adenocarcinoma cells via regulating MAPK signaling by interacting with c-Jun in certain LUADs.

overall_design: mRNA profiles of SOX9 shRNA #1 vs. shCtrl & mRNA profiles of SOX9 shRNA #2 vs. shCtrl


title: RNA-Seq investigating the global landscape of the host molecular response to infection by SARS-CoV-2 variants of concern

city: San Francisco

first: Mehdi

last: Bouhaddou

state: CA

institute: University of California San Francisco

summary:
Purpose: RNA-Seq was performed for gene expression analysis following infection of human cells with different VOC depending on the experiment group to investigate changes in the host and viral molecular response.
Methods: RNA was extracted from 10^6 cells using the Qiagen RNeasy extraction kit according to the manufacturer's protocol and quantified by nanodrop. Samples were submitted for RNA-Seq to Genewiz (Azenta) for library preparation and subsequent steps.
Results: We have identified SARS-CoV-2 VOC-specific differences in RNA expression, including for N, Orf9b, and Orf6. We have also measured ISG expression and proinflammatory gene suppression across the VOC, determining changes in ISG expression and proinflammatory gene suppression during amongst VOC during SARS-CoV-2 evolution.
Conclusions: Our study examines changes in the host molecular response to VOC infection to identify changes in gene expression, especially those related to the innate immune response, that have occurred during SARS-CoV-2 evolution.

overall_design: A total of 340 samples consisting of triplicates across six experiment groups were submitted for RNA-Seq. Mock and early-lineage VOC infection samples were used as controls throughout the experiments.

last: cBouhaddou

first: Nevan

last: Krogan


title: 4DNES425UDGS - Replicate experiments of in situ Hi-C on immediate neuronal precursor cell with DpnII

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNES425UDGS
condition: Immediate Neuronal Precursor cells
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES425UDGS/
number_of_experiments: 2

experiment: 4DNEXKO3TRJT; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXTDMNUOO; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI1QBCSKR.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFICUQ1N7S.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI2YHK51M.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFICXGHQP3.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/96e31197-b1ca-4921-b833-9b6c1132d770/
genome_assembly: GRCm38
derived_from: 4DNFICUQ1N7S.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIKXATLSH.bw


title: Modelling Porcine NAFLD by Deletion of Leptin and defining the role of AMPK in hepatic fibrosis

city: Beijing

first: Tan

last: Tan

address: Yuanmingyuan West Road 2#, Haidian District

department: College of Biological Science

institute: China Agricultural University

summary: Liver fibrosis occurs during chronic liver disease. Advanced liver fibrosis results in cirrhosis, liver failure and often requires liver transplantation. However, due to the lack of human models, mechanisms underlining the pathogenesis of liver fibrosis remain unclear. Recent studies implicated a central role of deranged lipid metabolism in its pathogenesis. In this study, we generated LEPTIN-deficient (LEPTIN-/-) pigs using zinc finger nuclease technology to investigate the mechanisms of liver fibrosis associated with obesity. The LEPTIN-/- pigs showed increased body fat and significant insulin resistance by 12 months of age. To resemble non-alcoholic fatty liver disease (NAFLD) patients, LEPTIN-/- pig developed the phenotypic features of fatty liver, non-alcoholic steatohepatitis (NASH) and hepatic fibrosis with age. Meanwhile, LEPTIN absence reduced phosphorylation of JAK2-STAT3 and AMPK. The alteration of JAK2-STAT3 enhanced fatty acid β-oxidation, whereas inactivation of AMPK led to mitochondrial autophagy, and both contributed to increased oxidative stress in hepatocytes. Although Leptin deletion in the rat liver altered JAK2-STAT3 phosphorylation, it activated the AMPK pathway and prevented liver fibrogenesis in contrast with the LEPTIN-/- pig. To our knowledge, the LEPTIN-/- pig provides the first model recapitulating the full pathogenesis of NAFLD and its progression toward liver fibrosis. The activity of AMPK signaling pathway suggests a potential target for development of  new strategies for the diagnosis and treatment of NAFLD.

overall_design: Liver mRNA profiles of 22-35 months old wild type (WT) and LEPTIN-/- pigs

first: Xing

last: Yiming

first: Song

last: Zhiyuan


title: human head and neck squamous cell carcinoma (HNSCC) to compare different tissue dissociation methods

city: Palo Alto

first: Andrew

last: Gentles

address: 1265 Welch Rd

institute: Stanford University

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

overall_design: Refer to individual Series


title: RNA-seq of human head and neck squamous cell carcinoma (HNSCC) to compare different tissue dissociation methods [bulkRNA]

summary: Tissue dissociation, mechanical and/or enzymatic, is a method of disaggregating 3D connective tissue to release cells for downstream single cell analysis.  Without proper controls for tissue dissociation experiments, potential artifacts can be mistaken for baseline tissue data. We hypothesized that enzymatic (collagenase/hyaluronidase) compared to mechanical dissociation leads to dissociated related artifacts not found in endogenous tumor tissue. To distinguish artifacts between enzymatic and mechanical dissociation, we compared separate enzymatic and mechanical dissociated samples with baseline samples from healthy and tumor patient whole blood, melanoma and head and neck squamous cell carcinoma (HNSCC) tumor tissues in flow cytometry, RNA sequencing and CODEX experiments. In bulk sorted tumor tissue, there is a significant difference between enzymatic and mechanical digested samples in cell stress, heat shock proteins and cell death related genes. These genes were also significantly upregulated in enzymatic over mechanical samples in the single cell RNA sequencing HNSCC tissue data. Fibroblasts and CD39+CD103+ CD8 T cells from tumor tissue, appear to require enzymatic digestion for efficient release from tissue compared to the mechanical digested samples. CD39+CD103+ CD8 tumor infiltrating lymphocytes (TILs) show different phenotypes depending on dissociation technique and tumor tissue. In tumor tissue, CD3+CD8+CD69+ T cells and gene expression were elevated in the enzymatic samples over the mechanical and baseline frozen tissue. Tissue dissociation techniques and tissue analysis from downstream applications have the potential for dissociation related artifacts that can mislead both protein and RNA sequencing data analysis in cancer research.

overall_design: RNA-seq profiling from sorted populations from head and neck squamous carcinomas and melanomas

first: Serena

last: Chang

first: Almudena

middle: E

last: Perez

first: Weiruo

last: Zhang


title: RNA-seq of YAP's role in hDPCs.

first: Fanyuan

last: Yu

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in YAP2SA-lentivirus-infected adult human dental pulp stromal cells (hDPCs).To overexpress YAP2SA in hDPCs we transfected cells with YAP2SA-lentivirus. Cells were derived from a 18~22-year-old healthy male human donor. Total mRNA was collected using TRIzol ® (Invitrogen, CA, USA) solution. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues.  After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 3 replicates which were from 3 independent experimental repeats.

overall_design: Examination of RNA expression in hDPCs after YAP2SA lentivirus infection.

first: Lin

last: Yao


title: RNA-seq analysis revealed that chloroquine(CQ) intervenes nephrotoxicity of nilotinib in an autophagy-independent manner

city: hangzhou

first: huang

last: xiangliang

address: hanzghou, China

institute: zhejiang university

summary: Nilotinib is a second-generation BCR-ABL1 tyrosine kinase inhibitor for the first-line treatment of Philadelphia chromosome-positive chronic myeloid leukemia. However, its nephrotoxicity has become prominent with the increase of clinical use, which greatly limits its long-term application. So far, the mechanism of nilotinib’s nephrotoxicity is still unknown leading to a lack of clinical intervention strategies. Here, we found that nilotinib could promote intrinsic apoptosis of both vascular endothelial cells and renal tubular epithelial cells, which was mediated by the excessive ubiquitin-proteasome degradation of anti-apoptotic protein BCL-XL. Moreover, we confirmed that Chloroquine (CQ) could intervene nilotinib-induced apoptosis by reversing the decreased BCL-XL whose mechanism was not relied on autophagy inhibition. Furthermore, RNA-seq analysis was applied to identify the potential target of CQ and the result suggested that CQ could alleviate nilotinib-induced ANKRD1 reduction. Further, we found ANKRD1 abrogated cell apoptosis by preventing ubiquitination of BCL-XL and hence inhibiting BCL-XL degradation. In conclusion, our research reveals the molecular mechanism of nilotinib’s nephrotoxicity, wherein the excessive degradation of BCL-XL via ubiquitin-proteasome pathway promotes kidney cells apoptosis, and provides CQ analogs as the clinical intervention strategy of nilotinib’s nephrotoxicity whose pharmacological effect is dependent on ANKRD1 instead of autophagy inhibition.

overall_design: Control Sample, Nilotinib-treated Sample, CQ-treated Sample, Nilotinib plus CQ-treated Sample

first: Hao

last: Yan

first: Peihua

last: LUO


title: A time-course transcriptome analysis of a double challenge bleomycin-induced lung fibrosis rat model

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary:
Backgroud: Idiopathic pulmonary fibrosis (IPF) is an irreversible disorder with a poor clinical outcome. The partial understanding of IPF pathogenesis and, consequently, the lack of appropriate relevant animal models is limiting the development of effective treatments. In this context, the intratracheal bleomycin (BLM) administration murine model is regarded as the most reliable preclinical approximation of human IPF. We present, here, the results of an integrated histological and transcriptome analysis that was used to monitor the time-course of BLM-induced lung fibrosis development in a rat model of disease and to assess its overlap with IPF.
Methods: Male rats were injected intratracheally (IT) with a double dose of BLM or saline (day 0 – 4) and sacrificed at day 7, 14, 21, 28 and 56. Histomorphometric analysis of lung fibrosis was performed on Masson’s trichrome stained sections on the left lung lobe. Transcriptome profiling by RNAseq was performed on total RNA extracted from the right lung lobe
Results and Conclusions: Transcriptomic analysis provided a detailed overview of BLM-induced lung fibrosis development and identified three clusters of differentially co-regulated genes whose expression was modulated in a time-dependent manner in response to BLM. One of these clusters centred on extracellular matrix-related pathways and process was found to be significantly correlated with histological parameters and gene sets derived from human IPF studies, thus indicating its translational potential as a signature biomarker for future IPF-related target validation and drug discovery studies.

overall_design: Evaluation of right lung mRNA profiles derived from a time course study of a rat model of lung fibrosis induced by a double bleomycin administration

first: Martina

last: Bonatti

first: Simona

last: Cantarella


title: Identification of early glutamine-responsive genes in Arabidopsis

city: Taipei City

first: Yi-Jie

last: Hung

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: To understand the global effect of Gln on gene expression, we performed RNA-seq analysis to compare the gene expression profiles between Arabidopsis seedlings treated with Gln for 0hr and 0.5hr.

overall_design: Total RNA extracted from 14-day-old Arabidopsis seedlings grown on liquid medium containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) and then treated with Gln for 0hr and 0.5hr was used for RNAseq analysis.

first: Hong-Sheng

last: Liao

first: Sang-Chu

last: Lin

first: Wei-Yu

last: Hsieh

first: Ming-Hsiun


title: 4DNES54YB6TQ - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

last: DCIC

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNES54YB6TQ
condition: Mature Olfr16 expressing olfactory sensory neurons
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES54YB6TQ/
number_of_experiments: 2

experiment: 4DNEXMM7MN7V; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXBSGTVWJ; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIBEV8M9E.pairs.gz, 4DNFI3O8M6SZ.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIOW2L46Z.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIBEV8M9E.pairs.gz, 4DNFI3O8M6SZ.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIMV54HXI.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/
genome_assembly: GRCm38
derived_from: 4DNFIMV54HXI.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIQI43DO2.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/
genome_assembly: GRCm38
derived_from: 4DNFIMV54HXI.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIP7U355R.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a5b6ce84-8f6d-4f57-a496-97c4a27adc27/
genome_assembly: GRCm38
derived_from: 4DNFIMV54HXI.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI5F17SZD.bw


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [RNA-seq]

first: Rui

last: Li

overall_design: RNA-seq data of PANC-1

first: Hongzhe

last: Zhao

first: Xudong

last: Huang


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [ATAC-seq]

overall_design: ATAC-seq of PANC-1


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [PAR-CLIP]

overall_design: CFL1/METTL3/YTHDC2 PAR-CLIP-seq of PANC-1


title: Mechanistic insights into small-molecule inhibitor MS-444 arresting embryonic development revealed by low-input RNA-seq and dSTORM

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The HuR small-molecule inhibitor MS-444 has been used in many cancer treatment studies, but its reproductive toxicity in females is unknown.Here, we used low-input RNA-seq and dSTORM to reveal the molecular mechanism and nanoscale organization changes by which MS-444 arrests embryonic development at the 2-cell stage.

overall_design: Two groups [MS-444, DMSO] of embryos were examined, with three replicates in each group.

first: Yongqaing

last: Nie


title: DiMNF treated NHBE cells with HCoV-OC43 Infection

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

summary: The emergence of novel betacoronaviruses has posed significant financial and human health burdens, necessitating the development of appropriate tools to combat future outbreaks. In this study, we have characterized a human cell line, IGROV-1, as a robust tool to detect, propagate, and titrate betacoronavirus SARS-CoV-2 and HCoV-OC43. IGROV-1 cells can be used for serological assays, antiviral drug testing, and isolating SARS-CoV-2 variants from patient samples. Using time-course transcriptomics, we confirmed that IGROV-1 cells exhibit a robust innate immune response upon SARS-CoV-2 infection, recapitulating the response previously observed in primary human nasal epithelial cells. We performed genome-wide CRISPR knockout genetic screens in IGROV-1 cells and identified Aryl hydrocarbon receptor (AHR) as a critical host dependency factor for both SARS-CoV-2 and HCoV-OC43. Using DiMNF, a small molecule inhibitor of AHR, we observed that the drug selectively inhibits HCoV-OC43 infection but not SARS-CoV-2. Transcriptomic analysis in primary normal human bronchial epithelial cells revealed that DiMNF blocks HCoV-OC43 infection via basal activation of innate immune responses. Our findings highlight the potential of IGROV-1 cells as a valuable diagnostic and research tool to combat betacoronavirus diseases.

overall_design: To identify mechanisms underlying antiviral activity of DiMNF, an AHR inhibitor, on human coronavirus OC43, normal human bronchial epithelial cells (NHBE) have been infected with the virus in the presence or absence of DiMNF. Transcriptome profiles are subsequently analyzed for the differential gene expressions.

first: Meisam

last: Yousefi

first: Yaw

middle: S

last: Ooi

middle: O


title: Identification of AHR as a pro-viral host factor of human betacoronaviruses SARS-CoV-2 and HCoV-OC43 using IGROV-1 cells


title: Single-cell RNA sequencing analysis of hypopharyngeal carcinoma treated with TPF chemotherapeutic regimen in combination with cinobufotalin treatment

first: Meng

last: Lian

address: 1 Dongjiaomin Alley

institute: Beijing Tongren Hospital

summary: In order to understand the effect of chemotherapy with cinobufotalin combined with TPF on Fadu cell line (hypopharyngeal squamous carcinoma cells), we performed single-cell RNA sequencing on three samples with different treatments.

overall_design: Fadu cell line and TPF (paclitaxel, cisplatin and 5-fluorouracil) were used for the construction of TPF-resistant hypopharyngeal squamous carcinoma cell lines. After obtaining a stable TPF-resistant cell line, pre-configured cinobufotalin was added to the culture dishes of Fadu cell line and TPF-resistant cell line, respectively.

first: Boxuan

last: Han

first: Jiaming

last: Chen

first: Shaoshi

first: Xixi

last: Shen

first: Lizhen

last: Hou

first: Jugao

last: Fang


title: Toll-like receptor 9 signaling in chronic lymphocytic leukemia cell lines

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

summary: To investigate Toll-like receptors (TLR) signaling in Chronic lymphocytic leukemia (CLL) cell lines, we analyzed HG-3, MEC-2 and PCL-12 CLL cell lines before and after TLR9 stimulation by RNA-sequencing followed by bioinformatic analyses and validation experiments.

overall_design: Cells from different CLL cell line were plated, stimulated and RNAseq was performed. In each replicate series, one sample was stimulated 4h with CpG-ODN2006 and an unstimulated sample was used as control.

first: Miriam

last: Meloni

first: Ilenia

last: Sana

first: Maria

last: Mantione

first: Marta

last: Muzio


title: Single Cell analysis of Cells from a IL10 B cell conditional KO Kidneys

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary: CD45+ Cells were sorted from kidneys from IL10 Fl/FL CD19 Cre mice or controls and analysed by 10x

overall_design: 2 lanes of 10x, each lane contained wither KO cells or controls with the cells originating from a pool of 5 mice per lane.

first: J

middle: R

first: Z

last: Tuong

first: O

last: Suchanek

first: M

last: Clatworthy


title: Glioma synapses recruit mechanisms of adaptive plasticity: Gene expression in SU-DIPG21 and SU-DIPG25 cell cultures

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

department: Neurology

summary: The nervous system plays an increasingly appreciated role in the regulation of cancer. In gliomas, neuronal activity drives tumor progression through paracrine signaling factors such as neuroligin-3 and brain-derived neurotrophic factor (BDNF), and also through electrophysiologically functional neuron-to-glioma synapses mediated by AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors. The consequent glioma cell membrane depolarization drives tumor proliferation. In the healthy brain, activity-regulated secretion of BDNF promotes adaptive plasticity of synaptic connectivity and strength. Here, we show that malignant synapses exhibit similar plasticity regulated by BDNF. Signaling through the receptor TrkB (tropomyosin receptor kinase B), BDNF promotes AMPA receptor trafficking to the glioma cell membrane, resulting in increased amplitude of glutamate-evoked currents in the malignant cells. This potentiation of malignant synaptic strength shares mechanistic features with synaptic plasticity that contributes to memory and learning in the healthy brain. BDNF-TrkB signaling also regulates the number of neuron-to-glioma synapses. Abrogation of activity-regulated BDNF secretion from the brain microenvironment or loss of TrkB in human glioma cells robustly inhibits tumor progression. Blocking TrkB genetically or pharmacologically abrogates these effects of BDNF on glioma synapses and substantially prolongs survival in xenograft models of pediatric glioblastoma and diffuse intrinsic pontine glioma (DIPG). Taken together, these findings indicate that BDNF-TrkB signaling promotes malignant synaptic plasticity and augments tumor progression.

overall_design:
Bulk RNA sequencing was performed in patient-derived SU-DIPG21 and SU-DIPG25 cells. RNA was sequenced on the Illumina NextSeq 500 and fpkm values were quantified using featureCounts (Liao et al, 2014). Replicates were performed as indicated in the metadata spreadsheet. Due to patient privacy concerns, we are witholding raw sequencing files at this time.
-----------------------------------
Submitters state "Due to patient privacy concerns, we are witholding raw sequencing files at this time."

first: Kathryn

last: Taylor

first: Surya

last: Nagaraja

first: Rebecca

last: Mancusi


title: Mechanism of monoallelic expression and allelic rheostat role of DNA methylation (RRBS)

first: Saumya

last: Gupta

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: In mammalian cells, large groups of genes show epigenetically controlled unequal transcription of maternal and paternal alleles. Thousands of autosomal genes subject to monoallelic expression (MAE) comprise the largest such group. The initial random allelic choice in these loci is followed by mitotically stable transmission of the allele-specific state, leading to stable epigenetic and functional differences between clonal cell lineages. Molecular mechanisms underpinning MAE maintenance are not known. We devised and performed a drug screen for reactivation of epigenetically silenced alleles in mouse cells, using a new strategy based on deep targeted allele-specific RNA sequencing, which can read out multiple loci simultaneously. We found that, contrary to previous observations, DNA methylation plays a key role in mitotic memory of MAE in multiple autosomal loci. Having established that a specific perturbation can affect multiple loci, we assessed genome-wide impact of the drug exposure in several clonal cell lines, identifying over 600 genes with allele-specific expression changing with DNA methylation. We found that multiple distinct states of allele-specific expression correspond to the extent of DNA methylation and can be stably maintained, indicating allelic rheostat role of DNA methylation. Our findings reveal a previously unappreciated interplay of genetic and epigenetic control of allele-specific expression and reinforce the role of such regulation in maintaining differences between developmentally equivalent clonal cell lineages.

overall_design: RRBS was performed in immortalised B cell line, Abl.1 clonal cell line of 129xCastF1 background [1,2] before and after treatment with 5-aza-2'-deoxycytidine (5-aza-dC). Libraries (minimum 2 replicates per sample, except otherwise mentioned) were sequenced and data was analyzed. [1] Zwemer, L.M., Zak, A., Thompson, B.R., Kirby, A., Daly, M.J., Chess, A., and Gimelbrant, A.A. (2012). Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10. [2] Nag, A., Savova, V., Fung, H.-L., Miron, A., Yuan, G.-C., Zhang, K., Gimelbrant, A.A., and Gingeras, T. (2013). Chromatin signature of widespread monoallelic expression. eLife 2, e01256.

first: Alexander

last: Gimelbrant


title: CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

overall_design: Refer to individual Series


title: A high-glucose diet stimulates an anti-tumor immune response to glioblastoma via gut microbiota modulation

city: Duarte

first: Jaeho

last: Kim

address: 1500 E Duarte Rd

department: RadiationOncology

institute: City of Hope

summary: A high-sugar diet induces lifestyle-associated metabolic diseases, such as obesity and diabetes, which may underlie the pro-tumor effects of a high-sugar diet. We supplied GL261 syngeneic glioblastoma (GBM) model mice with a short-term high-glucose diet (HGD) and found an increased survival rate with no evidence of metabolic disease. Modulation of the gut microbiota by an HGD was critical for enhancing the anti-tumor immune response. Single-cell RNA sequencing showed that modulation of the gut microbiota by an HGD increased the T cell-mediated anti-tumor immune response in GBM mice. We found that the cytotoxic CD4+ T cell population in GBM mice increased due to synergy with anti-PD-1 immune checkpoint inhibitors, but this depended on an HGD. Thus, we determined that an HGD enhanced anti-tumor immune responses in GBM mice through changes in the gut microbiota and suggest that the role of an HGD in GBM should be re-examined.

overall_design: We analyzed glioma infiltrated immune cells by single cell RNA sequencing (scRNAseq) with 10X genomics. For the high glucose diet experimental model, we supplied  C57BL/6 wild type mice with 20% dextrose water for 5 weeks before and 2 weeks after GL261 mouse glioma tumor cell inoculation intracranially. Cells in tumor were isolated at 20 days after inoculation and sorted CD45-positive immune cells were analyzed.  For Desulfovibrio colonization, we supplied C57BL/6 wild type germ-free mice with Desulfovibrio vulgaris 1 × 10^8 cells/100 μl or DPBS for control through oral gavage, three times a week for 2 weeks before and after GL261 tumor inoculation. Cells in tumor were isolated at 20 days after inoculation and sorted CD45-positive immune cells were analyzed.  For anti PD-1 samples, we supplied  C57BL/6 wild type mice with 20% dextrose water for 5 weeks before and 2 weeks after GL261 mouse glioma tumor cell inoculation intracranially. For anti-PD-1 ICI administration, 200 µg of anti-mouse PD-1 depletion antibody was injected intraperitoneally into each mouse on days 9, 12, 15 after GL261 tumor inoculation. Cells in tumor were isolated at 20 days after inoculation and sorted CD45-positive immune cells were analyzed.

first: Hyun-Jin

first: Yumin

first: Jeoungwoo

last: La

first: Won

middle: H

last: Park

first: Keun

middle: B

last: Ku

first: Byeong

last: Kang

first: Myoung

last: Kwon

first: Juhee

last: Lim

first: Sang

first: Chae

first: Hyeon

middle: C

first: Heung

last: Lee


title: 4DNESEPDL6KY - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. These contacts are orchestrated by intergenic olfactory receptor enhancers, the 'Greek islands', which first contribute to the formation of olfactory receptor compartments and then form a multi-chromosomal super-enhancer that associates with the single active olfactory receptor gene. The Greek-island-bound transcription factor LHX2  and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans  interactions in gene expression.

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNESEPDL6KY
condition: Mature olfactory sensory neurons
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESEPDL6KY/
number_of_experiments: 2

experiment: 4DNEX5ICY4Q2; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXVCPZOH3; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/93f9b9e4-d2bd-4530-b844-bde42b8a2104/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIVN95UEZ.pairs.gz, 4DNFI2HQA2EE.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIOWTBACC.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/93f9b9e4-d2bd-4530-b844-bde42b8a2104/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIVN95UEZ.pairs.gz, 4DNFI2HQA2EE.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIUH9FJR6.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97f6f8cb-5a53-4e5f-9b8e-1cb5804a807b/
genome_assembly: GRCm38
derived_from: 4DNFIUH9FJR6.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI9N6Q3JW.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97f6f8cb-5a53-4e5f-9b8e-1cb5804a807b/
genome_assembly: GRCm38
derived_from: 4DNFIUH9FJR6.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI9CVDG7P.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/fa2c218d-99d0-4ce4-bcc6-d15037341633/
genome_assembly: GRCm38
derived_from: 4DNFIUH9FJR6.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI75Q5IUV.bw


title: Host Saliva RNA Responses to COVID-19 Infection

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: RNA-Seq was used to study changes in gene expression in saliva samples from 266 human subjects after SARS-COV-2 infection, vaccination, or combined infection and vaccination (breakthrough). Approximately equal numbers of males and females, matched for age, were profiled after subjects tested positive for COVID-19 by PCR and sequencing of the variant. In addition to samples from uninfected controls with and without vaccination, samples from infected subjects with and without vaccination that represent eight major SARS-COV-2 lineages are included: epsilon, iota, alpha, delta, omicron BA.1, omicron BA.2, omicron BA.4, and omicron BA.5. Stranded single-end sequencing was performed using standard Illumina protocols. Reads were quantified to hg38 human transcriptome using Salmon after adapter trimming. Quantified reads were filtered to remove features with fewer than one count in 80% of the samples, and normalized using TPM, followed by quantile and log2 transformation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from human saliva RNA following COVID-19 infection, vaccination, or breakthrough infection.


title: Boric acidon intercepts 80S ribosome migration from AUG-stop by stable eRF1 immobilization

city: Hirosawa Wako city, Saitama prefecture, Japan

first: Shintaro

last: Iwasaki

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: Upon the environmental changes, cells flexibly and rapidly alter the gene expression by the translation control. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through the upstream open reading frame (uORF), which comprises only AUG and stop codons, in response to the shortage of boric acid. However, the molecular details of how the minimum uORF controls the translation of downstream main ORF depending on the boric acid concentration remained unclear. Here we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment for downstream translation initiation and that the presence of boric acid impedes the process by stable confinement of eukaryotic release factor 1 (eRF1) on 80S on AUG-stop. Ribosome profiling along the in vitro-translated reporter mRNA revealed that the number of the ribosomes on AUG-stop and that along the downstream are anti-correlated in response to boric acid, reflecting the 80S scanning leaving AUG-stop for translation initiation from downstream ORF. Moreover, cryo-electron microscopy (cryo-EM) analysis revealed that, in the presence of boric acid, the initiator methionyl-tRNA (Met-tRNAi) in the P site stably contacts eRF1 in the A site on AUG-stop. In contrast, the absence of boric acid led to weaker eRF1 density, suggesting that eRF1 cannot be stably positioned without boric acid. Consistent with the structural features, the hydrolysis of Met-tRNAi on AUG-stop was accelerated by boric acid, which is likely to be the checkpoint for the subsequent 80S scanning of the downstream. Our results provide a molecular insight into the translation regulation by a minimum and environment-responsive uORF.

overall_design: Ribosome profiling

first: Mayuki

last: Tanaka

first: Takeshi

last: Yokoyama

first: Hironori

last: Saito

first: Madoka

last: Nishimoto

first: Kengo

last: Tsuda

first: Naoyuki

last: Sotta

first: Hideki

last: Shigematsu

first: Mikako

last: Shirouzu

first: Takuhiro

last: Ito

first: Toru

last: Fujiwara


title: Dimethyl Itaconate selectively targets chronic lymphocytic leukemia cells

first: Michela

last: Riba

summary: Chronic Lymphocytic Leukemia (CLL) is strictly dependent on the complex interplay between the intrinsic features of the leukemic cells and microenvironmental stimulations including inflammatory stimuli by Toll Like Receptors (TLR) which protect CLL cells from drug induced apoptosis by upregulating NFKBIZ, an atypical co-transcription factor. To face the challenge of targeting transcription factors, we exploited the capacity of Dimethyl Itaconate (DI), an electrophilic synthetic derivative of Itaconate, to block NFKBIZ acting as anti-inflammatory agent. Primary CLL cells isolated from the peripheral blood of patients, leukemic splenocytes isolated from TCL1 transgenic mice, and circulating leukocytes isolated from healthy donors were treated in vitro with increasing concentrations of DI either alone or in combination with the TLR ligands. DI abrogated the induction of NFKBIZ as well as its target genes IL6 and IL10. Remarkably, DI reduced metabolic activation and cell viability of leukemic cells even if added after a robust TLR pre-stimulation; in contrast, no toxic effect was evident in normal leukocytes including T- and B-lymphocytes. DI induced apoptosis of malignant cells by reducing BCL-XL and MCL1 levels while inducing PARP cleavage. RNA sequencing highlighted that DI abrogated the TLR9-mediated upregulation of transcripts related to the metabolism of rRNAs, interferon and cytokine signaling. Notably, in addition to the expected electrophilic stress signature observed after DI treatment, novel pathways emerged including the downregulation of distinct MHC class II complex genes. In conclusion, DI not only abrogated the pro-inflammatory effects of TLR stimulation but also targeted a specific vulnerability in CLL cells.

overall_design: CLL primary cells were isolated from peripheral blood of 6 patients with CLL. Cells were plated, treated/stimulated and RNAseq was performed. In each replicate series, one sample was pre-treated with DI overnight followed by 4h of CpG-ODN2006 (human specific) stimulation, one sample was only treated with DI for 20h, one was only stimulated 4h with CpG-ODN2006 and an unstimulated and untreated sample was used as control.

first: Ilenia

last: Sana

first: Maria

last: Mantione

first: Miriam

last: Meloni

first: Pamela

last: Ranghetti

first: Lydia

last: Scarfò

first: Paolo

last: Ghia

first: Marta

last: Muzio


title: Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [leChRO-seq]

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

institute: University of Stuttgart

summary: A major hurdle to the application of precision oncology in pancreatic cancer is the lack of molecular stratification approaches and targeted therapy for defined molecular subtypes. In this work, we sought to gain further insight and identify molecular and epigenetic signatures of the basal-like A pancreatic ductal adenocarcinoma (PDAC) subgroup that can be applied to clinical samples for both patient stratification and for choice of therapy. We generated and integrated global gene expression and epigenome mapping data from patient-derived xenograft (PDX) models to identify subtype-specific enhancer regions that were validated in patient-derived samples. In addition, complementary nascent transcription and chromatin topology (HiChIP) analysis revealed a basal-like A subtype-specific transcribed enhancer program (B-STEP) in PDAC characterized by enhancer RNA (eRNA) production that is associated with higher chromatin interactions and subtype-specific gene activation. Importantly, we successfully confirmed the validity of eRNA detection as a possible histological approach for PDAC patient stratification by performing RNA in situ hybridization analyses for subtype-specific eRNAs on pathological tissue samples. Thus, the finding in this study provides proof-of-concept that subtype-specific epigenetic changes relevant for PDAC progression can be detected at a single cell level in complex, heterogeneous, primary tumor material.

overall_design: Length extension chromatin run-on assay followed by sequencing (leChRO-Seq) was performed in L3.6pl cells in control or P63 knockdown condition as well as in pancreatic ductal adenocarcinoma (PDAC) patient derived xenograft (PDX) tissue with basal-like A phenotype.

first: Zeynab

last: Najafova

first: Steven

last: Johnsen


title: Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma

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


title: 4DNES18BMU79 - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

city: Boston

last: DCIC

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNES18BMU79
condition: Mature olfactory sensory neurons with conditional Ldb1 knockout
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES18BMU79/
number_of_experiments: 2

experiment: 4DNEXVJSLZI5; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXH98PC96; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/11161c28-5235-403b-80fb-060c28e779d8/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIC2O325X.pairs.gz, 4DNFIPWEWCY3.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIC5AHBPV.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/11161c28-5235-403b-80fb-060c28e779d8/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIC2O325X.pairs.gz, 4DNFIPWEWCY3.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIVPAXJO8.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/05b1faea-e612-417e-98fe-aaf75eb6e5a6/
genome_assembly: GRCm38
derived_from: 4DNFIVPAXJO8.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIR3XCIMA.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/05b1faea-e612-417e-98fe-aaf75eb6e5a6/
genome_assembly: GRCm38
derived_from: 4DNFIVPAXJO8.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIXKKNMS7.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/58e9509a-c2e9-4ccb-95be-ca351bbb5894/
genome_assembly: GRCm38
derived_from: 4DNFIVPAXJO8.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIN13N8C1.bw


title: Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [ChIP-seq]

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) was performed in basal-like pancreatic ductal adenocarcinoma (PDAC)  patient-derived xenograft  for H3K27ac, P63. In L3.6pl cells ChIP-Seq for  H3K4me3, H3K4me1  was performed in untreated cells, whereas for H3K27ac was done in untreated as well as P63 knockdown conditions.


title: 4DNESNYBDSLY - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNESNYBDSLY
condition: Mature Olfr17 expressing olfactory sensory neurons
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESNYBDSLY/
number_of_experiments: 2

experiment: 4DNEXDSNPZOU; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXH1YN2XB; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c6fae89c-faa9-411f-8eba-b48c8f2c5f8a/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFICY5CI8Q.pairs.gz, 4DNFIEIEFZMD.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIB5G24G6.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c6fae89c-faa9-411f-8eba-b48c8f2c5f8a/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFICY5CI8Q.pairs.gz, 4DNFIEIEFZMD.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFI3M6726I.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/1bcfaf49-e8a4-467c-9114-5ca0649f0246/
genome_assembly: GRCm38
derived_from: 4DNFI3M6726I.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIHLVUQ26.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/1bcfaf49-e8a4-467c-9114-5ca0649f0246/
genome_assembly: GRCm38
derived_from: 4DNFI3M6726I.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIBS5F7ZO.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a7516038-8612-41f7-a73f-7aa51aa9774f/
genome_assembly: GRCm38
derived_from: 4DNFI3M6726I.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFITAKTJ26.bw


title: 4DNESH4UTRNL - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

overall_design:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
accession: 4DNESH4UTRNL
condition: Mature Olfr1507 expressing olfactory sensory neurons
submitted_by: Adan Horta
dataset_label: Hi-C on Mouse Olfactory System cells
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESH4UTRNL/
number_of_experiments: 2

experiment: 4DNEXOHPSJTN; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX4KRGMAQ; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/b5eb0694-e9c3-4572-a71d-2799074c9e23/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFI72AHX9H.pairs.gz, 4DNFI3CBEV3I.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI5AFARSZ.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/b5eb0694-e9c3-4572-a71d-2799074c9e23/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFI72AHX9H.pairs.gz, 4DNFI3CBEV3I.pairs.gz, 4DNFI3HVC1SE.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIHBTUDO9.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a0a1490-ccea-4fdc-a0b1-8599e3707219/
genome_assembly: GRCm38
derived_from: 4DNFIHBTUDO9.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIRHK3EVK.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a0a1490-ccea-4fdc-a0b1-8599e3707219/
genome_assembly: GRCm38
derived_from: 4DNFIHBTUDO9.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIYHAG3V2.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/b673122f-812c-479c-9aa2-f2ff2c7f3db7/
genome_assembly: GRCm38
derived_from: 4DNFIHBTUDO9.mcool, 4DNFIOFXJOUA.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIUDAACUL.bw


title: Dual RNA sequencing of Helicobacter pylori and host cell transcriptomes reveals ontologically distinct host-pathogen interaction

city: Shen Zhen

first: Zhiyong

last: Zhai

state: Guang Dong

address: No.1333, XinAn Street, BaoAn District

institute: Shenzhen Hospital of Southern Medical University

summary: Helicobacter pylori (H. pylori) is a highly successful pathogen that constitutes a serious threat to human health. However, the dynamic interaction between H. pylori and human gastric epithelium has not been fully documented. Here, by leveraging the advantage of dual RNA sequencing technology, we characterized a cytotoxin-associated genes A (CagA)-modulated bacterial adoption strategy by reinforcing the expression of ATP-binding cassette (ABC) transporter-related genes, metQ and HP_0888 upon co-culturing with human gastric epithelial cells (GES-1), thus, to benefit intracellular H. pylori survival through facilitating the uptake of host-provided nutrients. We further detected a generally repressed impact on electron transportation-associated genes by CagA, leading to the activation of oxidative phosphorylation. Temporal profiling of host mRNA signatures revealed down-regulation of multiple splicing regulators elicited by bacterial infection. Consequently, aberrant pre-mRNA splicing of functional genes that were involved in cell cycle process in response to H. pylori infection were identified. Moreover, we verified a protective effect for gastric H. pylori colonization against chronic dextran sulfate sodium (DSS)-induced colitis. Mechanistically, we profiled a cluster of short chain fatty acids (SCFA)-producing bacteria, Muribaculaceae that was selectively enriched in H. pylori-pre-colonized mice colon, contributing to the restoration of intestinal barrier function damaged by DSS treatment. Taken together, this study represents the first dual-transcriptome analysis of H. pylori during dynamic interaction with gastric epithelium and provide new insights into H. pylori pathogenesis.

sample_organism:
Helicobacter pylori
Homo sapiens

platform_organism:
Helicobacter pylori
Homo sapiens

overall_design: GES-1 cells were infected with H. pylori with a multiplicity of infection (MOI) of 1:100 for 3 h, then exposed to gentamycin (100 μg/ml; Sigma-Aldrich, 345814-M) for 1 h to kill the extracellular bacteria. Cells were washed with phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4) buffer 3 times, then incubated in fresh medium for another 12 h or 24h. Cells were extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) to obtain total RNA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. rRNA is removed by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA).Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

first: Wei

last: Hu

first: Zhaoyu

last: Huang


title: RNAseq experiment to identify differentially expressed genes in dvl/rtfl mutants and DVL overexpresion lines in inflorescence apices of Arabidopsis thaliana

city: Valencia

first: Ana

last: Alarcia

address: Campus de la Univ. Politécnica de Valencia. CPI Edif. 8E. Av de los Naranjos s/

country: Spain

institute: Instututo de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary: The lack of visible phenotypes of multiple dvl/rtfl mutants prompted us to compare the transcriptomic signatures of inflorescence apices of wildtype and mutant combinations (specifically dvl1 dvl8 dvl11 rtfl11 dvl19 and dvl8 dvl11 rtfl9 rtfl11 dvl19), as well as dvl1-D mutant, where DVL1 is overexpressed, and 35Spro:DVL8 line. Significant changes in gene expression were caused by the mutation of DVL genes in both quintuple mutant  and overexpression backgrounds.

overall_design:
We collected whole inflorescences where the oldest flower was in anthesis in three independent biological replicates that were used for RNA sequencing. RNA was extracted and sequenced on Illumina Novaseq6000

Please note that the following samples were excluded from data processing as outliers:
WT Col.0.4
DVL1.1D.4
35S.DVL8.2.4
dvl1.1
rtfl9.3
and therefore the 'DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv' contains total 15 data columns.

first: Cristina

last: Ferrandiz


title: RNA-seq analysis for DMSO- or RSL3-treated H1299 cells

city: Shanghai

first: Wanxin

last: Guo

address: West Huaihai Road No.241

institute: Shanghai Chest Hospital

summary: Ferroptosis suppresses tumor growth. Finding out potent pro-ferroptosis regulators via new approaches is extremely helpful for guiding and improving ferroptosis-based anti-tumor therapy. To seek pro-ferroptosis regulators, we proposed a novel screening strategy which focuses on molecules consistently upregulated even after long-time treatment of ferroptosis inducer. RNA-seq of RSL3-treated cells was performed as to be analysed together with RNA-seq data of ferroptosis-resistant cells in GEO dataset. Cysteine-rich angiogenic inducer 61 (CYR61) was identified as a novel pro-ferroptosis regulator via our new mining strategy.

overall_design:
The goal of this experiment was to characterize ferroptosis-related molecules.
RNA-seq of H1299 cells treated with DMSO or RSL3 for 24 h in three replicates


title: Discovery of a long half-life AURKA inhibitor to treat MYC-amplified solid tumors as a monotherapy and in combination with everolimus

status: Public on Sep 18 2023

city: Miaoli County

first: Ya-Hui

last: Chi

address: 35 Keyan Road, Zhunan Town

department: Institute of Biotechnology and Pharmaceutical Research

institute: National Health Research Institutes

summary: Aurora kinase inhibitors such as alisertib can destabilize MYC-family oncoproteins and have demonstrated compelling anti-tumor efficacy. In this study, we report 6K465, a novel pyrimidine-based Aurora kinase A (AURKA) inhibitor that reduces levels of c-MYC and N-MYC oncoproteins more potently than alisertib. In an analysis of the antiproliferative effect of 6K465, the sensitivities of small cell lung cancer (SCLC) and breast cancer (BC) cell lines to 6K465 were strongly associated with the protein levels of c-MYC and/or N-MYC. We also report DBPR728, an acyl-based prodrug of 6K465 bearing fewer hydrogen-bond donors that exhibited 10-fold improved oral bioavailability. DBPR728 induced persistent tumor regression of c-MYC- and/or N-MYC- overexpressing xenografts including SCLC, triple-negative breast cancer (TNBC), hepatocellular carcinoma and medulloblastoma using a 5-on-2-off or once-a-week dosing regimen on a 21-day cycle. A single oral dose of DBPR728 at 300 mg/kg induced c-MYC reduction and cell apoptosis in the tumor xenografts for more than 7 days. The inhibitory effect of DBPR728 at a reduced dosing frequency was attributed to its uniquely high tumor/plasma ratio (3.6-fold within 7 days) and the long tumor elimination half-life of active moiety 6K465. Furthermore, DBPR728 was found to synergize with the mTOR inhibitor everolimus to suppress c-MYC- or N-MYC- driven SCLC cancers. Collectively, these results suggest DBPR728 has the potential to treat cancers overexpressing c-MYC- and/or N-MYC.

overall_design: Next-generation sequencing (i.e. RNA-Seq) was used to examine the molecular signatures affected by a small molecule AURKA inhibitor DBPR728 in the NCI-H446 tumor xenografts within 24 and 48 hours of drug exposure. Differentially expressed genes between 24-hour vs mock and 24-hour vs mock were compared.


first: Michela

last: Riba

overall_design: CLL primary cells were isolated from peripheral blood of 7 patients with CLL. Cells were plated, stimulated and RNAseq was performed. In each replicate series, one sample was stimulated 4h with CpG-ODN2006 and an unstimulated sample was used as control.

first: Ilenia

last: Sana

last: Mantione


title: Effects of exercise on whole blood transcriptome profile in children with overweight/obesity

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

summary: Background:   The current knowledge about the molecular mechanisms underlying the health benefits of exercise is still limited, especially in the pediatric population. We set out to investigate the effect of a 20-week exercise intervention on whole blood transcriptome profile (RNA-seq) in children with overweight/obesity.  Methods:   Twenty-four pre-pubertal children (10.21 ± 1.33 years, 46% girls) with overweight/obesity, were randomized to either a 20-week exercise program (intervention group; n=10), or to a non-exercise control group (usual lifestyle, n=14). Whole blood transcriptome profile was analysed using RNA-seq STRT2 technique. Gene expression analysis was carried out with the Limma R/Bioconductor software package, and the gene ontology (GO) and pathway enrichment analyses were performed using R. Ingenuity Pathway Analysis (IPA) was performed for gene network detection. The transcriptome data were in silico validated using PHENOPEDIA and meta-analysis database extrameta.org.    Results:   161 genes were differentially expressed between the exercise and the control groups among boys, and 121 genes among girls (p-value < 0.05), while after multiple correction, no significant difference between groups persisted in gene expression profiles (FDR > 0.05). Based on non-corrected analyses, the enriched GO processes and molecular pathways highlighted the effect of exercise on different immune response related pathways in boys (antigen processing and presentation, infections, and T cell receptor complex) and girls (Fc epsilon RI signaling pathway) (FDR < 0.05). In silico data mining and validation analyses (using PHENOPEDIA and meta-analysis database extrameta.org)  highlight top genes regulated by exercise such as CD6, HLA-C, TNFRSF1A, MYD88, and NFKBIA genes in boys and RAC1, ANXA6, FYN, INPP5D, PIK3CD and SPARC genes in girls.  Conclusion:   These results suggest that 20-week exercise program influences different immune processes in children with overweight/obesity. The transcriptome differences between boys and girls could partly be explained, in addition to the gender differences, by the distinct intensity in the exercise intervention as boys had stronger exercise stimulus in training. Our findings should be considered exploratory and preliminary given the relatively small sample size. Larger and more powered randomized controlled trials should confirm or contrast our findings.

overall_design: Total whole blood mRNA profiles of 24 children with overweight/obesity were analyzed by 5’-end RNA sequencing at two different time points (before and after a 20-week exercise intervention).

first: Signe

last: Altmäe

first: Abel

last: Plaza-Florido

first: Francisco

last: Esteban

first: Augusto

last: Anguita-Ruiz

first: Kaarel

last: Krjutškov

first: Shintaro

last: Katayamah

first: Elisabet

last: Einarsdottir

first: Juha

last: Kere

first: Shlomit

last: Radom-Aizik

last: Ortega


title: Preclinical development of brain permeable ERβ agonist for the treatment of glioblastoma

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the mechanisms by estrogen receptor beta agonist CIDD-0149897 regulates glioma progression. Glioma stem cells (GSCs) were treated with CIDD-0149897 , and total RNA was isolated for RNA-seq analysis. Our results demonstrated that treatment with CIDD-0149897 showed upregulation of apoptotic and p53 pathways and downregulates several pathways including MYC and E2F.

overall_design: Total RNA from vehicle (0.1% DMSO v/v) and  CIDD-0149897 (20 µM) treated cells were isolated using RNeasy mini kit (Qiagen).  Samples were prepared in triplicates and sequenced on the Illumina NovaSeq 6000 platform (Illumina Inc.) using the 150bp paired-end sequencing module.

first: Ratna

middle: K

last: Vadlamudi

first: Uday

last: Pratap

first: Zhao

last: Lai


title: Neuronal HLH-30 regulates glp-1 longevity independent of neuronal MML-1/MXL-2

city: Suita

first: Tatsuya

last: Shioda

state: Osaka

address: Yamadaoka 1-1

institute: Osaka University

summary: Accumulating evidence has demonstrated the presence of inter-tissue communication regulating systemic aging, but the underlying molecular network has not been fully explored. We and others previously showed that two basic helix-loop-helix transcription factors, MML-1 and HLH-30, are required for lifespan extension in several longevity paradigms, including germline-less Caenorhabditis elegans. However, it is unknown what tissues these factors target to promote longevity. Here, using tissue-specific knockdown experiments, we found that MML-1 and its heterodimer partners MXL-2 and HLH-30 act primarily in neurons to extend longevity in germline-less animals. Neuronal functions of MML-1/MXL-2 and HLH-30 are also essential to prevent aging in non-neuronal tissues, including muscle and the intestine. Interestingly, however, both the temporal requirement and the downstream function of MML-1 in neurons were distinct from those of HLH-30. MML-1 was active early, while HLH-30 functioned later in life to sustain longevity in germline-less animals. Moreover, neuronal RNA interference (RNAi)-based transcriptome analysis revealed that the glutamate transporter GLT-5 is a novel downstream target of MML-1 but not HLH-30. Furthermore, the MML-1–GTL-5 axis in neurons is critical to prevent an age-dependent collapse of proteostasis and increased oxidative stress through autophagy and peroxidase MLT-7, respectively, in long-lived animals. Collectively, our study revealed that systemic aging is regulated by a novel molecular network involving neuronal MML-1 function in both neural and peripheral tissues.

overall_design: Neuronal knockdown of hlh-30, atg-2, or atg-18 in germline-less glp-1 nematodes

first: Shuhei

last: Nakamura

first: Tamotsu

last: Yoshimori


title: Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1 at the A site

city: Wako

last: Iwasaki

address: 2-1 Hirosawa

summary: In response to environmental changes, cells flexibly and rapidly alter gene expression, through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through upstream open reading frames (uORFs) that comprise only AUG and stop codons, in response to a shortage of boric acid in the environment. However, the molecular details of how the minimum uORF controls the translation of the downstream main ORF, in a boric acid concentration-dependent manner, have remained unclear. Here, combining ribosome profiling, TCP-Seq, structural analysis with cryo-electron microscopy, and biochemical assays, we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 (eRF1) on the 80S on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.

overall_design: Translation complex profile sequencing (TCP-seq)

first: Mayuki

last: Tanaka

first: Takeshi

last: Yokoyama

first: Hironori

last: Saito

first: Madoka

last: Nishimoto

first: Kengo

last: Tsuda

first: Naoyuki

last: Sotta

first: Hideki

last: Shigematsu

first: Mikako

last: Shirouzu

first: Takuhiro

last: Ito

first: Toru

last: Fujiwara


title: Single-cell RNA-seq of human head and neck squamous cell carcinoma (HNSCC) to compare different tissue dissociation methods

city: Palo Alto

first: Andrew

last: Gentles

address: 1265 Welch Rd

institute: Stanford University

summary: Tissue dissociation, mechanical and/or enzymatic, is a method of disaggregating 3D connective tissue to release cells for downstream single cell analysis.  Without proper controls for tissue dissociation experiments, potential artifacts can be mistaken for baseline tissue data. We hypothesized that enzymatic (collagenase/hyaluronidase) compared to mechanical dissociation leads to dissociated related artifacts not found in endogenous tumor tissue. To distinguish artifacts between enzymatic and mechanical dissociation, we compared separate enzymatic and mechanical dissociated samples with baseline samples from healthy and tumor patient whole blood, melanoma and head and neck squamous cell carcinoma (HNSCC) tumor tissues in flow cytometry, RNA sequencing and CODEX experiments. In bulk sorted tumor tissue, there is a significant difference between enzymatic and mechanical digested samples in cell stress, heat shock proteins and cell death related genes. These genes were also significantly upregulated in enzymatic over mechanical samples in the single cell RNA sequencing HNSCC tissue data. Fibroblasts and CD39+CD103+ CD8 T cells from tumor tissue, appear to require enzymatic digestion for efficient release from tissue compared to the mechanical digested samples. CD39+CD103+ CD8 tumor infiltrating lymphocytes (TILs) show different phenotypes depending on dissociation technique and tumor tissue. In tumor tissue, CD3+CD8+CD69+ T cells and gene expression were elevated in the enzymatic samples over the mechanical and baseline frozen tissue. Tissue dissociation techniques and tissue analysis from downstream applications have the potential for dissociation related artifacts that can mislead both protein and RNA sequencing data analysis in cancer research.

overall_design: Two samples from the same human HNSCC patient with mechanical and enzymatic digestions respectively

first: Serena

last: Chang

first: Almudena

last: Perez

first: Weiruo

last: Zhang


title: Acid-base homeostasis orchestrated by NHE1 defines the pancreatic stellate cell phenotype in pancreatic cancer

city: Münster

first: Zoltan

last: Pethö

state: NRW

address: Robert-Koch Str. 27B

department: Physiology II

institute: University of Münster

summary: Pancreatic ductal adenocarcinoma (PDAC) progresses in an organ with a unique pH landscape, where the stroma acidifies after each meal. We hypothesized that disrupting this pH landscape during PDAC progression triggers pancreatic stellate cells (PSCs) and cancer-associated fibroblasts (CAFs) to induce PDAC fibrosis. We revealed that alkaline environmental pH is sufficient to induce PSC differentiation to a myofibroblastic phenotype. We then mechanistically dissected this finding focusing on the involvement of the Na+/H+ exchanger NHE1. Perturbing cellular pH homeostasis by inhibiting NHE1 with cariporide partially alters the myofibroblastic PSC phenotype. To show the relevance of this finding in vivo, we targeted NHE1 in murine PDAC (KPfC). Indeed, tumor fibrosis decreases when mice receive the NHE1-inhibitor cariporide in addition to gemcitabine treatment. Moreover, the tumor immune infiltrate shifts from granulocyte-rich to more lymphocytic. Taken together, our study provides mechanistic evidence on how the pancreatic pH landscape shapes pancreatic cancer through tuning PSC differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C57BL6/J mouse-derived pancreatic stellate cells (PSCs), cultured for 120h at pH6.6 or at pH7.4. 3 biological replicates are included for each group.

first: Albrecht

last: Schwab


title: Effect of DNA damage and chromatin damage on transcription in HT1080 cells with wild type p53 and p53 inhibited by dominant negative mutant

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: DNA-targeting drugs may damage DNA or chromatin. Many anti-cancer drugs do both, making difficult understanding their mechanism of actions. Using molecules causing DNA breaks without altering nucleosome structure (bleomycin) or destabilizing nucleosomes without damaging DNA (curaxin), we investigated consequences of DNA or chromatin damage in normal and tumor cells. As expected, DNA damage caused p53-dependent growth arrest followed by senescence. Chromatin damage caused higher p53 accumulation than DNA damage, but growth arrest was p53-independent and did not result in senescence. Chromatin damage activated transcription of multiple genes, including classical p53 targets, in a p53-independent manner. These activated genes, though they were not highly expressed, have chromatin organization around transcription start sites (TSS) characteristic for the most highly expressed genes and the highest level of paused RNA polymerase. We proposed that nucleosomes around TSS of these genes are the most sensitive to chromatin damage, and therefore nucleosome loss upon curaxin treatment enables transcription without assistance of sequence-specific transcriptional factors. We confirmed this by showing greater loss of nucleosomes around TSS of these genes upon curaxin treatment and activation of specific p53 reporter in p53-null cells by chromatin damaging agents, but not DNA damaging agents.

overall_design: HT1080 cells, parental or expressing p53 dominant negative mutant GSE56 were treated with 400ug/ml of bleomycin or 0.5 uM of CBL0137 for 24 hours.  After 24 hr, cells were incubated with 1 mM EU for 20 min. RNA was isolated using the Monarch Total RNA Miniprep Kit (New England BioLabs, cat #T2010) following the manufacturer's protocol. Nascent RNA was labeled with biotinylated azide and captured on magnetic beads using the Click-iT Nascent RNA Capture Kit (Molecular Probes, cat # C10365). cDNA was synthesized from RNA bound to the beads using the SuperScript VILO cDNA Synthesis Kit (ThermoFisher Scientific, cat #11754-050). cDNA was sequenced with the Illumina NextSeq 500/550 at the Roswell Park Comprehensive Cancer Center Genomics Shared Resource using Illumina NextSeq 500/550.

first: Katerina

middle: V

last: Gurova

first: Jianmin

last: Wang


title: RNA-Sequencing of Saliva Samples from COVID-Infected and Vaccinated Subjects

first: Frank

last: Middleton

summary: SARS-CoV-2 virus is known to infect the oral cavity and can be readily detected using PCR-based testing. In this study, we examined the host transcriptomic response to PCR-confirmed SARS-CoV-2 virus infection, vaccination against SARS-CoV-2, or breakthrough infection following vaccination using RNA-sequencing. The identification of the viral variant for all samples was obtained using full viral genome sequencing.  Approximately equal numbers of males and females were used for every major variant lineage. Results indicate strong anti-viral responses in each case, with some differences due to variant strain and vaccination history, as well as age and sex.

overall_design: Human subjects participating in COVID-19 surveillance testing provided consent and submitted a saliva sample using a swab-based collection device. PCR testing was performed and SARS-CoV-2 genome sequencing completed on all positive subjects. Vaccine histories were also obtained. RNA was purified and used to create strand-specific libraries for next generation sequencing (RNA-Seq) with single-end reads. Resulting reads were mapped and quantified at the transcript level using Salmon, and filtered to remove features with less than 1 observed count in fewer than 80% of the samples. Normalization was applied using TPM + 1, followed by quantile normalization and log2 transformation.

first: John

last: Cleary

first: Sawyer

last: Hicks

first: Josh

last: Wallace

first: Tanner

last: Waldman

first: Claudia

last: Lennon

last: Berglund


title: IL-17 mediated downregulation of miR-101 facilitates expression of EZH2 to promote epidermal hyperplasia in psoriasis

city: Singapore

first: Candida

last: Vaz

address: 30 Medical drive

department: Human Development

institute: Singapore Institute for Clinical Sciences

summary: Epidermal hyperplasia, a characteristic feature of psoriatic skin lesions, is epigenetically driven by Enhancer of Zeste homolog 2 (EZH2). EZH2 and EZH2-mediated trimethylation of histone H3 lysine 27 (H3K27me3) are both abnormally upregulated in psoriatic lesions. To identify microRNAs that could potentially target these epigenetic regulators we profiled miRNAs from psoriatic lesional skin in comparison with healthy skin. Analysis of the differentially expressed miRNAs revealed miR-101, as one of the most significant miRNA, consistently downregulated in psoriatic lesions compared to the healthy skin. A clear inverse correlation in the expression of miR-101 versus EZH2 was apparent in normal skin versus psoriatic lesional skin indicating that EZH2 is a potential target of miR-101, which was further confirmed by luciferase assay. Investigating the upstream effectors of the miR-101- EZH2 pathway in psoriasis, we identified the pro-inflammatory cytokine IL-17 as regulator of miR-101 expression. Here we propose a model, depicting a pathway triggered by IL-17 – mediated modulation of miR-101 expression, which in turn elicit sustained expression of EZH2, leading to enhanced keratinocyte proliferation and epidermal hyperplasia in psoriasis. Taken together, this indicates that miR-101 is a potential therapeutic target to alleviate the downstream effects of IL-17 mediated epidermal hyperplasia in psoriasis.

overall_design: Total RNA was extracted from healthy and psoriatic lesional skin by trizol lysis followed by extraction with Exiqon miRcury RNA extraction kit and subjected to exiqon microRNA microarray

first: Prabha

last: Sampath

first: Gopinath

last: Sundaram


title: Transcriptome analysis in mouse ES cells deficient for Zfp352 or both Zfp352/Zfp353

city: Kumamoto

first: Mitsuhiro

last: Endoh

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

institute: Kumamoto University

summary: Mouse ES cell population contains a minor sub-population expressing the genes that are specifically expressed in 2-cell stage embryos. This sub-population, consists of the 2-cell-gene labelled cells (2CLCs), is generated by the transient activation of the 2-cell specific genes initiated by the master regulator Dux. However, the mechanism regulating the transient expression remains largely unclear. Here we reported a novel function of Zfp352, one of the 2-cell specific genes, in the regulation of the 2CLC sub-population. Zfp352 encodes zinc-finger transcription factor belonging to the Klf family. Zfp352 is transiently activated by Dux after the activation of Zscan4c and expresses in a subset of 2CLC subpopulation. Interestingly, in the reporter assay, the transcriptional activation of Zscan4c by Dux is strongly repressed by the co-expression of Zfp352. However, knockout of Zfp352 resulted in the repression of a subset of the 2-cell specific genes. These data suggest the dual roles of Zfp352 in the regulation of the transient activation of the 2-cell specific genes.

overall_design: In the EB5 mouse ES cell line (derived from male E14tg2a mESCs, 129Ola, Oct3/4IRES-BSD-pA/+, deposited to RIKEN Cell Bank) , only the Zfp352 gene or both Zfp352/Zfp353 genes were deleted using the CRISPR-Cas9 method. Total RNA was extracted using the QuickGene RNA cultured cell kit S (Kurabo). After checking the quality of the extracted RNA using the BioAnalyzer 2100 (RIN > 8), the library DNA was prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced with Illumina NextSeq 500 (Illumina) using Nextseq 500/550 High Output v2.5 Kit (Illumina) to obtain single end 75 nt reads.

first: Shingo

last: Usuki

first: Hitoshi

last: Niwa


title: Identification of AHR as a pro-viral host factor of human betacoronaviruses SARS-CoV-2 using IGROV-1 cells

first: Wharton

last: Chan

address: 8 College Road

institute: Duke-NUS Medical School

summary: The emergence of novel betacoronaviruses has posed significant financial and human health burdens, necessitating the development of appropriate tools to combat future outbreaks. In this study, we have characterized a human cell line, IGROV-1, as a robust tool to detect, propagate, and titrate betacoronavirus SARS-CoV-2 and HCoV-OC43. IGROV-1 cells can be used for serological assays, antiviral drug testing, and isolating SARS-CoV-2 variants from patient samples. Using time-course transcriptomics, we confirmed that IGROV-1 cells exhibit a robust innate immune response upon SARS-CoV-2 infection, recapitulating the response previously observed in primary human nasal epithelial cells. We performed genome-wide CRISPR knockout genetic screens in IGROV-1 cells and identified Aryl hydrocarbon receptor (AHR) as a critical host dependency factor for both SARS-CoV-2 and HCoV-OC43. Using DiMNF, a small molecule inhibitor of AHR, we observed that the drug selectively inhibits HCoV-OC43 infection but not SARS-CoV-2. Transcriptomic analysis in primary normal human bronchial epithelial cells revealed that DiMNF blocks HCoV-OC43 infection via basal activation of innate immune responses. Our findings highlight the potential of IGROV-1 cells as a valuable diagnostic and research tool to combat betacoronavirus diseases.

overall_design: SARS-CoV2 infection of IGROV-1 and Huh7 cells at 0, 24, 48 and 72 hours post infection

first: Meisam

last: Yousefi

first: Yaw

last: Ooi