title: Epithelial-mesenchymal plasticity induced by discontinuous exposure to TGFβ1 increases tumorigenic potential of normal epithelial cells

status: Public on Jul 30 2021

city: Vizela

first: Marta

middle: Patrícia

last: Ferreira

state: Braga

address: Rua da junuqeira, Santo Adrião

country: Portugal

summary: In this manuscript, we used a non-genetically manipulated EMT/MET cell line model to demonstrate that epithelial mesenchymal plasticity occurring in normal cells generates co-existing phenotypically and functionally divergent cell subpopulations with increased tumorigenic potential in vivo.

overall_design: RNAseq data of 3 isogenic cell lines dereived from EpH4 murine cells

first: Patrícia

last: Oliveira

first: David

last: Huntsman

first: Alireza

last: Heravi-Moussavi

first: Angela

last: Burleigh

first: Calvin

last: Roskelley

first: Carla


title: Distinct transcriptional programs characterize neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade [single-cell RNA-seq]

status: Public on Jul 21 2021

city: Baltimore

first: Kellie

middle: Nicole

last: Smith

state: MD

address: 1650 Orleans Street, CRB1, 4M

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: Immune checkpoint blockade (ICB) has revolutionized cancer treatment, but most patients do not respond. PD-1 blockade “unleashes” CD8 T cells, including those specific for mutation-associated neoantigens (MANA), but factors in the tumor microenvironment can inhibit responses by dampening MANA-specific T cell function. Recent advances in single cell transcriptomics are revealing global T cell dysfunction programs in tumor-infiltrating lymphocytes (TIL). However, the vast majority of TIL do not recognize tumor antigens and little is known about transcriptional programs of true MANA-specific TIL. Here, we use an integrated approach to identify MANA-specific T cell clones using the MANA functional expansion of specific T cells (MANAFEST) assay in neoadjuvant anti-PD-1-treated lung cancers and use their TCR CDR3 as barcodes to track them and analyze their transcriptional programs and function in the tumor microenvironment using single cell RNA sequencing. We find both MANA-and virus-specific clones in TIL and adjacent normal lung, regardless of response status. MANA-specific, influenza (flu)-specific and EBV-specific TIL each have unique transcriptional programs. Most MANA-specific clones are tissue resident memory (TRM) cells, an incompletely activated cytolytic program, including EOMES deficiency, and higher levels of genes encoding T cell inhibitory molecules and Tox2. Notably, MANA-specific T cells express low levels of IL-7R and are functionally less responsive to IL-7 compared with tissue-resident flu-specific clones. MANA-specific clones from anti-PD-1 non-responding tumors express TCR with markedly lower ligand-dependent signaling capability, are largely confined to HOBIThi TRM subsets and coordinately up-regulate genes encoding specific checkpoints, killer inhibitory receptors, and intracellular inhibitors of T cell activation and cytotoxicity. These findings provide mechanistic and potential therapeutic insights into overcoming resistance to PD-1 blockade.

overall_design:
We utilized peripheral blood and surgical resection specimens obtained from the first-in-human clinical trial of neoadjuvant anti-PD-1 (nivolumab) in resectable non-small cell lung cancer (NCT02259621). MANAFEST (Mutation Associated NeoAntigen Functional Expansion of Specific T cells) was used to detect in vivo antigen-experienced T cell responses and identifies the clonal identity of the T cell receptor (TCR) corresponding to these cells in 6 paitents.

Each sample includes processed data for both GEX and VDJ or TCR.

Raw data have been submitted to EGA under accession ID: EGAS00001005343

middle: N

first: Justina

last: Caushi

first: Jiajia

last: Zhang


title: RNA-sequencing in rat hippocampus following chronic ethanol and withdrawal

status: Public on Jun 15 2021

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

summary: The objective of  The Center for Alcohol Research in Epigenetics (CARE) is to identify gene regulatory pathways in hippocampus that are altered in response to chronic ethanol administration and withdrawal.

overall_design: Adult male rats (6 per group) were used for each experimental group:  control diet-fed, chronic ethanol diet-fed and 24h withdrawal following chronic ethanol exposure. Hippocampus tissues were dissected out and immediately frozen.  Altogether, there was a total of 18 samples (3 groups x 6 rats).  The RNAseq libraries were quantitated by qPCR and the 18 libraries were paired-end sequenced on 11 lanes (Illumina Hiseq 4000). Fastq files  generated and demultiplexed with bcl2fastq and adaptor sequences were trimmed from the 3’-end of the reads.

first: Amy

middle: W

last: Lasek

first: Harish

middle: R

last: Krishnan

first: Huaibo

first: Ying

last: Chen

first: Alvaro

middle: G

last: Hernandez

first: Jenny

last: Drnevich

first: Dennis

last: Grayson


title: Distinct transcriptional programs characterize neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade

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

overall_design: Refer to individual Series


title: The innate and adaptive immune landscape of SARS-CoV-2-associated multisystem inflammatory syndrome in children (MIS-C) from acute disease to recovery

status: Public on Sep 10 2021

city: Birmingham

first: Graham

last: Taylor

address: Vincent Drive

department: Institute of Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

summary: Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening disease occurring several weeks after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Deep immune profiling showed acute MIS-C patients had highly activated neutrophils, classical monocytes and memory CD8+ T-cells; increased frequencies of B-cell plasmablasts and double-negative B-cells. Post treatment samples from the same patients, taken when symptoms were resolving, identified recovery-associated immune features including CD163+ monocytes, emergence of a new population of immature neutrophils and, in some patients, a transient increase in arginase. Plasma profiling identified multiple features shared by MIS-C, Kawasaki Disease and COVID-19 and that therapeutic inhibition of IL6 may be preferable to IL1 or TNF-a. We identified potential new mechanisms of action for IVIG, the most commonly used drug to treat MIS-C. Finally, we showed systemic complement activation with high plasma C5b-9 levels is common in MIS-C, suggesting complement inhibitors could be used to treat the disease.

overall_design: 4 Samples analysed by 10X single cell RNA seq, with additional CITE-seq performed in parallel using the following antibodies (all from Biolegend): anti-gamma/delta, anti-CD45RO, Totalseq-B TBNK cocktail (CD3, CD4, CD8, CD11c, CD16, CD19, CD45 and CD56).

first: G

middle: S

first: E

middle: A

last: Fennel

first: P

last: Vrljicak

first: R

last: Stark

first: S

last: Ott


title: Targeting MTDH-SND1 interaction

status: Public on Sep 07 2021

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University


title: Pertubations of gene expresion  by lapatinib or THZ1 in HER2 positive breast cancer cell lines.

status: Public on May 21 2021

city: Albuquerque

first: Viswanathan

last: Palanisamy

state: NM

address: 2325 Camino de Salud NE,

department: Internal Medicine

institute: University of New Mexico

summary: Gene expression profiling were examined by Human HT-12 v4.0 Expression BeadChip arrays  in SKBR3 and BT474 cells treated with HER2 inhibitor lapatinib or CDK7 inhibitor THZ1.

overall_design: SKBR3 and BT474 cells were treated with  lapatinib(1 μM) or THZ1 (250 nM) for 6 hours. RNA was extracted with TRIzol reagent (Invitrogen)  and RNeasy mini kit (Qiagen). HumanHT-12 v4.0 Expression BeadChip arrays were used for analyses of transcriptomic changes caused by HER2 or CDK7 inhibition.

first: Qi

last: Wang

last: Hazard

first: Robert

last: Wilson


title: Nucleosome conformation dictates the histone code

status: Public on May 06 2021

city: Durham

first: Bryan

middle: J

last: Venters

state: NC

address: 6 Davis Drive

institute: EpiCypher

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized “codes” that are read by specialized domains (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP - histone PTM] specificity, and in doing so to decipher the histone code. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order considerations. Here we show that histone PTM specificity is in fact dependent on nucleosomal context, necessitating we re-define the ‘histone code’ concept and further interrogate it at the nucleosomal level.

overall_design: We performed CUT&RUN for one NURF complex protein, three Histone PTMs, and one IgG control for paired-end sequencing.


title: Effect of Soluble Guanylyl Cyclase Stimulator Compound 1 on Renal function in ZSF-1 model of diabetic nephropathy

status: Public on Aug 02 2021

city: South San Francisco

first: Yang

last: Liu

state: California

address: 213 E Grand Ave

institute: Merck

summary: Diabetic nephropathy is associated with endothelial dysfunction and oxidative stress, in which nitric oxide-soluble guanylate cyclase-cyclic guanosine monophosphate (NO-sGC-cGMP) signaling pathway is impaired.  We hypothesize that sGC stimulator,  Compound 1, can enhance  NO signaling, reduce proteinuria in diabetic nephropathy pre-clinical model with diminished NO-bioavailability and increased oxidized sGC. We therefore, evaluated the effect of sGC stimulator Compound 1 on renal effect in obese ZSF1 rats.  Materials and Methods: The sGC stimulator Compound 1, the standard of care agent enalapril, and combination of Compound 1 with enalapril was administered chronically to ZSF1 rats for 6 months. Mean arterial pressure, heart rate, creatinine clearance for estimate glomerular filtration rate (eGFR), urinary protein excretion to creatinine ratio (UPCR), and urinary albumin excretion ratio (UACR) were determined during the study. Histopathology of glomerular and interstitial lesions were assessed at the completion of the study. Results: While both Compound 1 and Enalapril significantly reduced blood pressure the combination of Compound 1 and enalapril normalized blood pressure level. Compound 1 improved eGFR and reduced UPCR and UACR. Combination of enalapril and Compound 1 resulted in marked reduction in UPCR and UACR and improved GFR. Conclusion: The sGC stimulator Compound 1 as a monotherapy slowed renal disease progression and the combination of sGC stimulator with enalapril provided a greater renal protection in a rodent model of diabetic nephropathy.

overall_design: Examine transcriptional changes in kidney after treatment of compound 1 and enalapril

first: Gayathri

last: Swaminath


title: The Anti-Fibrotic Drug Nintedanib Promotes Expansion of Lung Macrophages with a Distinct Transcriptional Repair Program in Bleomycin-Exposed Mice

status: Public on May 05 2021

city: Biberach an der Riss

first: Fidel

last: Ramírez

state: BW

address: Birkendorfer Str. 65

department: Computational Biology

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Idiopathic pulmonary fibrosis (IPF) is a progressing chronic and fibrotic lung response with poor prognosis. The current standard-of-care for IPF is the kinase inhibitor nintedanib, which has a broad target range. The mechanism of nintedanib’s action remains unclear as it inhibits diverse kinases expressed in lung epithelia, endothelia and putatively the immune populations distributed throughout the lung. Given the proposed role of multiple pulmonary macrophage populations in mediating both protective and pathogenic roles in lung fibrosis, we sought to identify repair-associated macrophage populations in mice influenced by nintedanib after bleomycin challenge for 7 and 14 days using single cell RNA sequencing. Bleomycin exposure triggered expansion of inflammatory MHCIIhigh macrophage populations, which was partially reversed after nintedanib treatment. Concurrently, nintedanib promoted the expansion of MHCIIlow macrophages, which were linked to attenuation of lung fibrosis. Concomitantly, nintedanib promoted an increased expression of mRNA for canonical macrophage repair markers in MHCIIlow macrophages. Finally, exposure of inflammatory macrophages to nintedanib in vitro resulted in attenuation of expression of transcripts for MCHII. In conclusion, a component of nintedanib’s protective mode of action in lung fibrosis relies on expanding distinct MHCIIlow macrophage populations and redirecting them toward a reparative phenotype. This study provides a rationale for further refinement of therapeutic kinase inhibition in fibrotic diseases.

overall_design: 6 conditions were evaluated in mouse: Mouse + Bleomycin, sacrificed 7 and 14 days after exposure, mouse + Bleomycin + Nintedanib, sacrificed 7 and 14 days after exposure, and control mouse + NaCl, sacrificed 7 & 14 days after exposure. Nintedanid was given from day 0 to day 6 for mice sacrificed on day 7 and from day 7 to day 13 on mice sacrificed on day 14. Each treatment had three replicates for a total of 18 single celll RNA samples. Each replicate was composed of three mice pooled together.

first: Carolin

middle: K

last: Koss

first: Christian

middle: T

last: Wohnhaas

first: Carmen

last: Lerner

first: Coralie

last: Viollet

first: Cornelia

last: Tilp

first: Heinrich

last: Huber

first: Matthew

last: Thomas

first: Florian

last: Gantner

first: Peter

last: Murray

last: Ramirez

first: Karim

last: El Kasmi


title: Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

status: Public on May 10 2021

city: Philadelphia

first: Xin

last: Sheng

institute: University of Pennsylvania

summary: The functional interpretation of GWAS remains challenging due to the cell-type dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTL) for 659 microdissected human kidney samples and identified cell-type eQTLs by mapping interactions between cell type abundance and genotype. By partitioning heritability using stratified LD-score regression to integrate GWAS with scRNA-seq and snATAC-seq data, we prioritized proximal tubules in kidney function and endothelial cells and distal tubule segments in blood pressure pathogenesis. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of commonly used antihypertensive and renal protective drugs and identifies drug repurposing opportunities for kidney disease.

overall_design: 10x snATAC-seq for 2 human kidney samples

first: Ziyuan

last: Ma

first: Junnan

last: Wu

first: Katalin

last: Susztak


title: Single cell transcriptional zonation of human psoriasis whole skin

status: Public on Apr 26 2021

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

country: Sweden

institute: Karolinska Institute

summary:
To explore the cellullar and molecular alteration of human psoriasis, we collected full-thickness skin from the lesion region of 3 patients and the similar region of 3 healthy donors, and submit for single cell RNA sequencing (scRNAseq) with 10x genomics (V3.1). The transcriptional landscape of human psoriasis whole skin provide a unique view of immuno-regulation among skin cell types.

1. "Single cell transcriptional zonation of human psoriasis skin identifies an alternative immunoregulatory axis",<Cell Death Dis.>, 2021 May 6;12(5):450.
https://yz-studio.shinyapps.io/shinyapph5ad/

2. "Integrative single-cell transcriptomic investigation unveils long non-coding RNAs associated with localized cellular inflammation in psoriasis" <Front Immunol>2023 Sep 26:14:1265517.
Integrated dataset: 106,675 cells from 11 healthy human skin and 79,887 cells from 9 psoriatic human skin
https://yz-studio.shinyapps.io/psoriaticskincellatlas2/

overall_design:
Single cell RNA-seq study of human psoriasis skin

*** Revision: The raw data has been uploaded to the Genome Sequence Archive (GSA) for human data, and the GSA ID is HRA004936, link: https://ngdc.cncb.ac.cn/gsa-human/browse/HRA004936 ***

first: Yuge

last: Gao

first: Yuan

last: Li


title: Dysregulated myogenesis and autophagy in genetically induced pulmonary emphysema

status: Public on Jul 20 2021

city: Albany

first: Ariel

last: Jaitovich

email: balnisj@amc.edu, jaitova@amc.edu

state: NY

address: 47 New Scotland Ave.

department: MCP

institute: Albany Medical College

summary: Patients with chronic obstructive pulmonary disease (COPD)-pulmonary emphysema often develop locomotor muscle dysfunction, which is independently associated with disability and higher mortality in that population. Muscle dysfunction entails reduced muscle mass and force-generation capacity, which are influenced by fibers integrity. Myogenesis, which is muscle turnover driven by progenitor cells such as satellite cells, contributes to the maintenance of muscle integrity in the context of organ development and injury-repair cycles. Injurious events crucially occur in COPD patients’ skeletal muscles in the setting of exacerbations and infections which lead to acute decompensations for limited periods of time after which, patients typically fail to recover the baseline status they had before the acute event. Autophagy, which is dysregulated in muscles from COPD patients, is a key regulator of satellite cells activation and myogenesis, yet very little research has so far investigated the mechanistic role of autophagy dysregulation in COPD muscles. Using a genetically inducible murine model of COPD-driven muscle dysfunction and confirmed with a second genetic animal model, we found a significant myogenic dysfunction associated with a reduced proliferative capacity of freshly isolated satellite cells. Transplantation experiments followed by lineage tracing suggest that an intrinsic defect in satellite cells, and not in the COPD environment, plays a dominant role in the observed myogenic dysfunction. RNA sequencing analysis of freshly isolated satellite cells suggests cell cycle and autophagy dysregulation, which is confirmed by a direct observation of COPD mice satellite cells fluorescent-tracked autophagosome formation. Moreover, spermidine-induced autophagy stimulation leads to improved satellite cells autophagosome turnover, replication rate and myogenesis. Our data suggests that pulmonary emphysema causes a disrupted myogenesis, which could be improved with stimulation of autophagy and satellite cells activation, leading to an attenuated muscle dysfunction in this context.

overall_design: Differential expression of genes from isolated muscle satellite cells between wild-type mice and IL13TG (COPD) mice.

first: Joseph

last: Balnis


title: siRNA knockdown of C1GALT1 in SAS cells

status: Public on Jun 28 2021

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

summary: To determine the C1GALT1 regulated gene expression profile  in SAS cells

overall_design: SAS cells were transfected with non-targeting or C1GALT1 specific siRNAs for 72 hours and total RNA were extracted


title: Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds

status: Public on Apr 07 2021

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm

status: Public on Apr 06 2021

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

summary: This dataset includes the RNA sequencing of five replicates of the undifferentiated hESC subline VUB03_S2, which shows impaired mesendoderm induction, and 14 WT samples from GSE116372.

overall_design: Comparison of 5 replicates of VUB03_S2 vs. 14 wild-type samples.

first: C

last: Markouli

first: E

last: Couvreu de Deckersberg


title: Targeting the metabolic vulnerability of acute myeloid leukemia blasts with a combination of venetoclax and 8-chloro-adenosine

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary:
Purpose: To show that 8-Cl-Ado can target FAO and synergizes with VEN to significantly decrease the oxygen consumption rate (OCR) and in turn OXPHOS in CD34-enriched AML cells.
Methods: Using AML cell lines and LSC-enriched blast cells from pre-treatment AML patients, we evaluated the effects of 8-Cl-Ado, VEN and the 8-Cl-Ado/VEN combination on fatty acid metabolism, glycolysis and OXPHOS using liquid scintillation counting, a Seahorse XF Analyzer and gene set enrichment analysis (GSEA).
Results: We here report that VEN and 8-Cl-Ado synergistically inhibited in vitro growth of AML cells. Furthermore, immunodeficient mice engrafted with MV4-11-Luc AML cells and treated with the combination of VEN plus 8-Cl-Ado had a significantly longer survival than mice treated with either drugs alone (p≤0.006).
Conclusion: Taken together, the results suggest that 8-Cl-Ado enhances the antileukemic activity of VEN and that this combination represents a promising therapeutic regimen for treatment of AML.

overall_design:
We treated MV4-11 AML cells with 250 nM 8-chloro-adenosine, 10 nM venetoclax, combination of both or control, for 4h, 12 h and 24h, all in duplicates. combination of both or control, for 12 h and 24h, all in duplicates.
We also treated KG-1a AML cells  with 500 nM 8-chloro-adenosine, 10 nM venetoclax, combination of both or control, for 12 h and 24h, all in duplicates.
Finally, we treated primary AML blasts from 2 different patients (14269-HTB19-005, and 14269-HTB20-006) with 500 nM 8-chloro-adenosine, 10 nM venetoclax, combination of both or control, for 24h

first: Ralf

last: Buettner

first: Steven

last: Rosen

first: Le

last: Xuan

first: Truong

last: Nguyen

first: James

last: Sanchez

first: Guido

last: Marcucci

first: Xiwei

first: Min-Hsun

last: Chen


title: Profiling astrocyte transcriptional signatures in response to neurons and neuroactive compounds [RNA-seq]

summary: The goal of the study is to profile molecular signature of astrocytes in response to neuronal contact and neuroactive chemicals. We performed RNA-seq on (1) mouse embryonic stem cell derived astrocytes (mES_astrocytes) from different time points of culture to determine transcriptomic changes as astrocytes mature over time in culture, (2) mES_astrocytes cocultured with human neurons to determine how neurons affect astrocyte gene expression and (3) mES_astrocytes cultured in presence of neuroactive chemicals (glutamate, gamma-aminobutyric acid, acetylcholine, noradrenaline, and serotonin) to determine transcriptomic changes induced by different types of neuronal signaling.

overall_design: mES_astrocytes were collected (1) in duplicate on day 7, day 14, day 21, and day 35 in culture, (2) in triplicate at selective timepoints day 21 and day 35, (3) in duplicate after co-culture with neurons at day 35, and (4) in triplicate after induction with each neuroactive chemical at day 35 for profiling using RNA-seq.

first: Debosmita

last: Sardar

first: Benjamin

last: Deneen


title: The dynamic immune cell landscape in the lungs of Pneumocystis infected mice

status: Public on Mar 26 2021

city: Beijing

first: Zhaohui

last: Tong

state: Beijing

address: NO. 8, Gong Ti South Road

department: Department of Respiratory and Critical Care Medicine

country: China

institute: Beijing Chaoyang Hospital

summary: Pneumocystis pneumonia is an opportunistic pneumonia that has been increasing in non-HIV patients in recent years. To obtain a better understanding of the cellular and molecular mechanisms involved in disease pathogenesis, we profile the transcriptomes of mouse lungs with Pneumocystis pneumonia and from uninfected control subjects using single-cell RNA sequencing, yielding multiple populations of myeloid cells, T cells and B cells. We uncover a PCP-associated TREM2+ subpopulation of interstitial macrophages, which expands in PCP, differentiates from Ly6C+ monocytes. We also define the subsets of effector CD4+ T cells that expand after the infection of Pneumocystis. Finally, intercellular crosstalk between interstitial macrophages and effector CD4+ T cells via multiple ligand and receptor interactions reveals several anti-pneumocystis pathways. Our work dissects unanticipated aspects of the cellular and molecular basis of Pneumocystis pneumonia at a single-cell level, and provides a conceptual framework for the discovery of rational therapeutic targets in Pneumocystis pneumonia.

overall_design: Single-cell RNA profiles of wild type (WT) and mices  infected with Pneumocystis 1-4 weeks.

first: Zhao-Hui

first: Kan

last: Zhai

first: Hu-qin

last: Yang

first: Han

last: Sun


title: Decoding gene regulation in the fly brain

status: Public on Aug 10 2021

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

institute: KULeuven/VIB

summary:
The Drosophila brain is a work horse in neuroscience.
Single-cell transcriptome analysis, 3D morphological classification, and detailed mapping of the connectome have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly.
The developmental trajectories of each of these cell types, from neuroblast to mature neuron or glial cell, as well as their maintenance and plasticity in the adult brain, are controlled by gene regulatory networks (GRNs)
In this study, we profiled chromatin accessibility of 240,000 single cells, spanning nine developmental time points from larval, pupal, and adult brains, and integrated this data with single-cell transcriptomes.
This atlas reveals the regulatory connections between genomic enhancers and the single-cell transcriptomes for more than 80 cell types in the fly brain.
Each cell type is characterized by a unique chromatin accessibility landscape, with thousands of specific regulatory regions, summing to a total of 95,931 regulatory regions that are used in the brain.
Exploiting this resource, we find that the combination of expressed transcription factors is reflected by their respective motif architecture within cell type-specific enhancers.

overall_design: snATAC-seq (10x Genomics CHROMIUM Single Cell ATAC Library & Gel Bead Kit v1) of fresh brains across development (2 replicates per time point for larvae and pupa, 7 replicates for adult including 2 central brain only) from genotype mixed Drosophila melanogaster (DGRP-551, DGRP-409, DGRP-502 and DGRP-639)

first: J

last: Janssens

first: S

last: Aibar

first: I

middle: I

last: Taskiran


title: BRD1/2/13 are new core subunits of Arabidopsis SWI/SNF complexes

status: Public on Mar 22 2021

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

sample_organism:
Arabidopsis
Arabidopsis thaliana

platform_organism:
Arabidopsis
Arabidopsis thaliana


title: Production of Cloned-like Chicken by Allogeneic Transplantation of Somatic Cells Induced Primordial Germ Cells

status: Public on Mar 16 2021

city: Yangzhou City

first: Xia

last: Yuan

state: Jiangsu Province

address: 88 South University Ave

institute: Yangzhou university, Yangzhou, China

summary: Generation of genetically uniformed individuals from somatic cells is an effective approach for large-scale reproduction of elite varieties and a powerful tool for restoration of endangered species. However, this technique has never been realized in avian due to their oviparous reproduction pattern. In this study, we produced cloned-like chicken by allogeneic transplantation of somatic cells induced primordial germ cells (PGCs). Oct4, Sox2, Nanog and Lin28A (OSNL) factors were employed to reprogram primary chicken embryo fibroblasts (CEF) to pluripotent stem cells (iPS), in which DNA demethylation and histone acetylation were found to increase the efficiency to 13.00%. The obtained iPS presented embryonic stem cell like characters and were further induced to PGCs by BMP4/BMP8b/EGF, in which histone acetylation and glycolysis inhibition elevated the induction rate to 17.30% and 16.41%, respectively. With the optimized system, we induced Black Langshan Chicken (Gallus domestiaus, black feather) donated CEF to PGCs and transplanted them into the Recessive White Chicken (white feather) embryos. The transplanted cells migrated into the genital ridges and produced functional sperm or oocytes. The sexual matured recipients were self-crossed, with 189/509 (37.13%) cloned-like chicken produced. Microsatellite analysis confirmed their DNA inheritance from the black donor chicken. Thus, we demonstrated, for the first time, the feasibility of avian cloning from somatic cells.

overall_design:
mRNA profiles of chicken iPGC induced by different systems in vitro and primary PGCs
mRNA profiles of chicken iPS cells induced by different systems in vitro and primary ESCs

first: Bichun

last: Li

first: Ruifeng

last: Zhao

first: Qisheng

last: Zuo


title: mRNA expression profiling of BLM-Induced pulmonary fibrosis in rat

status: Public on Mar 05 2021

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Pulmonary fibrosis includes a variety of underlying causes of fibrosing interstitial lung diseases (ILDs). Pulmonary fibrosis is usually considered to be related to chronic inflammation of lung tissue and excessive proliferation of fibroblasts, however, the mechanism is complex and unclear.To study the underlying molecular mechanisms, we further applied high-throughput sequencing to analyze the differentially expressed genes in rat lung tissues induced by Bleomycin.

overall_design: Lung tissue mRNA profiles of  rats with and without Bleomycin injection

first: Hui

last: Yi

first: Xinyan

last: Huang

first: Gengpeng

last: Lin

first: Yukun

last: Kuang

first: Yubiao

last: Guo

first: Canmao

last: Xie


title: TNFα-induced alterations in stromal progenitors in CML BM result in enhanced LSC growth via CXCL1-CXCR2 signaling

status: Public on Jun 16 2021

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

summary: Leukemia stem cells (LSC) are not eradicated in chronic myeloid leukemia (CML) patients responding to tyrosine kinase inhibitor treatment. Bone marrow (BM) mesenchymal niches play an essential role in hematopoietic stem cell (HSC) maintenance. Here, we examined leukemia-induced alterations in mesenchymal progenitor populations using a murine CML model. 6C3+ stroma-forming progenitors were increased in CML BM, and demonstrated enhanced LSC but reduced HSC support compared to their normal counterparts. CML 6C3 cells showed enhanced TNFa-related gene signatures, and upregulated CXCL1 expression. TNFα signaling contributed to expansion and increased CXCL1 expression by 6C3 cells in CML BM. The CXCL1 receptor CXCR2 was upregulated in in LSC, and CXCR2 inhibition significantly reduced LSC growth both in vitro and in vivo. In conclusion, TNFα-induced alterations in stromal progenitors in CML BM result in enhanced CML LSC growth via CXCL1-CXCR2 signaling. Targeting this axis represents a novel therapeutic strategy to inhibit BM niche-protected LSC.

overall_design: Various esenchymal progenitors and long-term hematopoietic stem cells were sorted from the bone marrow of wild-type healthy adult (Normal) and SCL-tTA-BCR-ABL CML mice (CML) directly into RLT buffer and RNA prepared, with four biological replicates from each group.

first: Puneet

last: Agarwal


title: Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in Caldicellulosiruptor bescii

status: Public on Feb 23 2021

city: Athens

first: Michael

last: Adams

state: Georgia

address: 220 South Jackson Street

department: Department of Biochemistry and Molecular Biology

institute: University of Georgia

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

overall_design: Refer to individual Series


title: Single cell RNA-seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]

status: Public on Apr 27 2021

city: Aurora

first: Kathryn

middle: Fay

last: Scott

state: Colorado

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so, we sorted fluorescently marked pMN cells obtained from Tg(olig2:EGFP) zebrafish embryos at 24, 36 and 48 hours post fertilization and performed 10X Chromium single cell RNA-seq.

overall_design: Three samples obtained from wild-type zebrafish embryos at three developmental timepoints were analyzed.

first: Bruce

last: Appel

first: Kayt

first: Rebecca

last: O'Rourke

first: Austin

last: Gillen


title: Next Generation Sequencing Facilitates Quantitative Analysis of  in 14-day-old wt, brm-1, brd1,2,13 and brm-1 brd1,2,13  seedlings

first: yaoguang

last: yu

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: RNA from 14-day-old seedlings of wild-type, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150).
Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Examination of global RNA expression in 14-day-old wt, wt, brm-1, brd1,2,13 and brm-1 brd1,2,13 seedlings.

first: Yaoguang

last: Yu

first: Chenlong

last: Li


title: Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in Caldicellulosiruptor bescii [RNA-Seq]

summary: Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade various polysaccharide components of plant cell walls. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species C. saccharolyticus and C.bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to fourteen Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose.

overall_design: Five different growth substrates were used (glucose, cellobiose, crystalline cellulose (Avicel), xylose, birchwood xylan (Sigma), 5 g/L each). Growth experiments were performed in triplicate at 78°C as closed cultures without pH control (400 mL volume, shaken at 150 rpm).   Cells were harvested in mid-to-late exponential growth stage (0.5−1.5 × 108 cells mL−1). Cells were pelleted by centrifugation at 6,000 × g for 5 minutes, supernatant was decanted, and cell pellets were frozen in liquid nitrogen.

first: Steven

middle: D

last: Brown

first: Charlotte

last: Wilson

first: Mirko

last: Basen

first: Dawn

middle: M

last: Klingeman


title: Estrogen-induced cell cycle arrest as an unexpected outcome of aromatase inhibitor-resistance: Insights from single-cell analysis of a patient-derived xenograft model

status: Public on Feb 21 2021

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: We performed the single-cell analysis to reveal the mechanism of estrogen-induced cell cycle arrest using an Aromatase inhibitor-resistant patient-derived xenograft model (named GS3).

overall_design:
Following a treatment that lasted 7 days using Placebo, estradiol (E2) (1mg), and dihydrotestosterone (DHT) (12.5mg) pellet, GS3-PDX tumors were harvested and digested into a single-cell suspension. Cells isolated from two biological replicates were analyzed together.

>>> Raw data are not available due to patient privacy concerns<<<

first: Hitomi

last: Mori


title: Comprehensive approach to study DNA methylation changes in AML patients

status: Public on Jan 26 2021

city: Prague

first: Sarka

last: Sestakova

address: U Nemocnice 2094/1

department: Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

type: Methylation profiling by high throughput sequencing

summary: Many researchers have reported the prognostic significance of various DNA methylation changes in patients with acute myeloid leukemia (AML). We aimed for a comprehensive evaluation of these epigenetic aberrations that would refine the AML prognostication. We designed a sequencing panel targeting 239 regions described in literature as having a prognostic impact or being commonly associated with AML pathogenesis and analyzed 178 diagnostic samples of AML patients divided into test (n=128) and validation cohort (n=50).

overall_design: A comprehensive analysis of prognostically significant DNA methylation changes in 178 AML patients

first: Hana

last: Remesova

first: Cyril

last: Salek


title: Histone variant macroH2A1.1 enhances non-homologous end joining-dependent DNA double-strand-break repair and reprogramming efficiency of human iPSC

status: Public on Jan 08 2021

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

summary: Here we used RNA-Seq to gain deep mechanistic insight into the effects of  macroH2A1 splicing isoforms macroH2A1.1 and macroH2A1.2 on Human Umbelical Vein Endothelial Cells (HUVEC) undergoing cell reprogramming. The process was triggered using an episome construct carrying the reprogramming factors Oct4, Sox2, Klf4, L-Myc and Lin28. RNA-seq analysis was performed on the fourth day of the reprogramming process, to investigate the role. Heatmap anlysis of top 44 differently expressed genes (DEG) revealed that macroH2A1.1, but not macroH2A1.2,increased the expression of genes involved in DNA repair response (DDR) and cell reprogramming in HUVEC. Genes exhibiting absolute fold-change values >2 and p-values <0.05 were considered differentially expressed between contrasts. Statistical differences in gene expression were assessed by the ANOVA test. Correction for multiple test was achieved by the Benjamini-Hochberg procedure. The significance threshold was set to 0.05. Ingenuity pathway analysis (IPA) identified differences in evaluating top 44 DEG involved in DDR and top 12 DEG involved in cell reprogramming showed that macroH2A1.1 verexpression enhances several pathways involved in DNa repair and acquisition of cell pluripotency.

overall_design: Profiling the transcriptome of HUVEC reprogrammed to iPSC with overexpression of macroH2A1.1 or macroH2A1.2

first: Manlio

last: Vinciguerra


title: EPN1/2 potentiate NFkB signaling

status: Public on Jan 06 2021

city: Plainsboro

first: Yong

last: Wei

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: The transcriptome changes upon shRNA mediated knockdown of EPN1/2 were examined in human breast cancer cell line MDA-MB-231 cells

overall_design: Duplicate of pair comparison between vector control and shRNA knockdown of EPN1/2 in MDA-MB-231 cells

first: Xiaofeng

last: Cai


title: RNA-seq analysis of two genealogically linked South African Diuraphis noxia biotypes

status: Public on Dec 31 2020

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

summary: RNA was extracted from all instar (insect developmental) stages for both D. noxia biotypes SA1 and SAM with the purpose to capture as many expressed transcripts as possible. South African D. noxia biotype SA1 is known to be the least virulent aphid, while its offspring, the South African D. noxia biotype SAM is the most virulent. The overall purpose of the experiment was to establish a baseline availability of transcripts to the aphids as well as help improve on current genome assemblies. Three biological replicates of 100 aphids each was collected from both biotypes SA1 and SAM that were respectively reared on preference host cultivars. Whole aphids were flash frozen in liquid nitrogen, ground to a powder with micro pistils and RNA was extracted making use of a Qiagen RNeasy kit. Library preparation for sequencing was performed using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol. The replicate samples from the SAM biotype yielded between 120 – 140 million 100bp PE reads and the replicate samples from the SA1 biotype yielded between 113 – 137 million 100bp PE reads (with a Q20 phred score above 98% for all replicates) after sequencing on the NovaSeq6000 system. De novoassembly was performed making use of the Trinity package.

overall_design: Assessing and comparing transcripts produced from 2 genealogically linked Diuraphis noxia biotypes that greatly differ in their virulence to resistant wheat cultivars. 3 individual replicates from each biotype (SA1 and SAM) were collected (total of 6 samples) each consisting of 100 aphids of varying instar growth stages.

last: Botha-Obertholster

first: Francois

middle: V

last: Burger


title: Ovarian Cancer Ascites Inhibits Transcriptional Activation of Natural Killer Cells partly through MUC16

status: Public on Jan 01 2021

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Purpose:To investigate the effect of ascites of ovary cancer on human NK cells at the genome-wide level.

overall_design: Patient ascites NK cells were purified directly from ascites of human ovary cancer patients. Human peripheral blood NK cells were isolated from freshly prepared PBMCs taken from healthy donors. Cells were treated with either medium or human ascites of overy cancer for 24 hrs. Cells were lysed in RLT lysis buffer and total RNA extracted using the RNeasy micro kit for RNAseq.

first: Bin

last: Jia


title: Molecular characterization of DLBCL

status: Public on Jan 21 2021

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary: Transcriptomics and genetic characterization of Diffuse large B-cell lymphoma (DLBCL) have increased the understanding of the pathogenesis of the disease and provided potential novel therapeutic targets. This dataset collects transcriptomic and methylation assays for 168 DLBCL tissue samples.

overall_design:
RNA and DNA methylation profiles of DLBCL tissue samples were generated by Illumina sequencing

The logCPM_Normalized_human_PDX.csv includes primary and early passage PDX data, normalized together with the additional 20 intermediate passage samples (GSM8113583-GSM8113602).

first: Giorgio

last: Inghirami

first: Leandro

last: Cerchietti


title: DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders [Bisulfite-Seq]

status: Public on Nov 13 2020

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

summary: Mutations in DNA methyltransferase 3A (DNMT3A) have been detected in autism and related disorders, but how these mutations disrupt nervous system function is unknown. Here we define the effects of neurodevelopmental disease-associated DNMT3A mutations. We show that diverse mutations affect different aspects of protein activity yet lead to shared deficiencies in neuronal DNA methylation. Heterozygous DNMT3A knockout mice mimicking DNMT3A disruption in disease display growth and behavioral alterations consistent with human phenotypes. Strikingly, in these mice we detect global disruption of neuron-enriched non-CG DNA methylation, a binding site for the Rett syndrome protein MeCP2. Loss of this methylation leads to enhancer and gene dysregulation that overlaps with models of Rett syndrome and autism. These findings define effects of DNMT3A haploinsufficiency in the brain and uncover disruption of the non-CG methylation pathway as a convergence point across neurodevelopmental disorders.

overall_design: Total Bisulfite-seq from the brains of DNMT3A heterozygous KO and WT mice.

first: Diana

middle: L

last: Christian

first: Dennis

middle: Y

last: Wu


title: DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders [RNA-Seq]

overall_design: Total RNA-seq from the brains of DNMT3A heterozygous KO and WT mice

middle: W


title: Embryonic lethality and defective mammary gland development in activator function impaired conditional knock-in ErbB3V943R mice

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: ERBB3, a pseudo-kinase domain containing human epidermal growth factor receptor (ERBB/HER) family member, plays a key role in multiple cellular processes and is required for normal embryonic development. Following ligand binding, ERBB3 heterodimerizes preferentially with ERBB2, leading to allosteric kinase activation and signaling. ERBB3 has been shown to function primarily as an activator kinase that activates the receiver kinase in the asymmetric dimer activation complex. Structural studies of the activator-receiver interface have identified V943 as a key residue required for ERBB3 mediated activation of ERBB2. Here we report the generation of a knock-in mouse model where the endogenous ErbB3 allele was modified to allow tissue-specific conditional expression of ErbB3V943R (ErbB3CKI-V943R). Activation of ErbB3V943R expression during development resulted in embryonic lethality at around E12.0. Analysis of the embryos reveals thinning of the myocardium and reduced mesenchyme within the endocardial cushion of the heart, reminiscent of ErbB3 knockout mice. Tissue specific expression of ErbB3V943R in the epithelial cells of the mammary gland using an MMTV-Cre driver results in delayed elongation of the ductal network during puberty. Consistent with this, single cell RNA-seq analysis showed a reduction in a specific subset of fibrinogen-producing luminal epithelial cells. Our studies establish the importance in vivo of the allosteric interface in activation of the ERBB family and also provides an important tool that can be used to understand the role of ERBB3 in cancer development.

overall_design: Single-cell RNA sequencing of luminal epithelial cells from 6-week old wild-type or ErbB3 V943R conditional mutant mammary glands

first: Kate

last: Senger

first: Wenlin

last: Yuan

first: Meredith

last: Sagolla

first: Jonas

last: Doerr

first: Brad

last: Bolon

first: James

last: Ziai

first: Kai-Hui

last: Sun

first: Soren

last: Warming

first: Merone

last: Roose-Girma

last: Zhang

first: Lucinda

last: Tam

first: Robert

last: Newman

first: Subhra

last: Chaudhuri

first: Aju

last: Antony

first: Steffen

last: Durinck

first: Bijay

last: Jaiswal

first: Daniel

last: Lafkas

first: Zora

last: Modrusan

first: Somasekar

last: Seshagiri


title: BRD1, BRD2 and BRD13 are core subunits of Arabidopsis SWI/SNF complexes [ChIP-seq]

first: yaoguang

last: yu

summary:
Switch defective/sucrose non-fermentable chromatin remodeling complexes are multi-subunit machines that play vital roles in regulating chromatin structure and gene expression. However, how SWI/SNF complexes recognize target loci is still not fully understood. Here, we show that Arabidopsis bromodomain-containing homologous proteins, BRD1, BRD2 and BRD13, are core subunits of SWI/SNF complexes that are required for SWI/SNF genomic targeting. The three BRDs directly interact with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit. Phenotypic and transcriptome analysis of the brd1 brd2 brd13 triple mutants showed that the BRDs act in large redundancy to control developmental processes and gene expression that are also regulated by BRM. BRDs extensively co-localize with BRM on chromatin. brd1 brd2 brd13 mutation results in the reduced BRM protein levels and genome-wide targeting on chromatin. Finally, we demonstrate that the bromodomain of BRD2 is essential for genomic targeting of BRD2, highlighting the role of this reader domain in the recruitment of BRM-containing SWI/SNF complexes to target sites in plants.

SWI/SNF chromatin remodeling complexes are evolutionarily conserved and is confirmed to use the energy derived from hydrolysis of ATP to alter the density or the position of nucleosomes on the DNA or the composition of histone octamer. Bromodomain, an acetylated histone interaction module, was found in chromatin remodeling factors. During the 29 Arabidopsis bromodomain-containing protein, like GCN5 and GTE4/6, their function has been reported. Here, we reported three BRM-interacting bromodomain-containing protein, BRD1, BRD2 and BRD13 are new core subunits of Arabidopsis SWI/SNF complexes. brd1/2/13 displayed a similar phenotype like brm, such as down-ward curled leaves, reduced fertility, shorter silique and root. Moreover, brm brd1/2/13 shows more serious phenotype just like brm-1. Y2H, Co-IP, RNA-seq and ChIP-seq assay reveal that BRDs interact with BRM at both protein and chromatin level. Future more, BRDs are required for BRM genome-wide occupancy and BRM might bind to chromatin via BRDs bromodomain by interacting with their BBC domain.

overall_design:
Examination of
BRM occupancy in 14-day-old brm-1 and brd1/2/13 seedlings
BRD1 occupancy in 14-day-old brd1 seedlings
BRD2 occupancy in 14-day-old brd2 seedlings
global RNA expression in 14-day-old wt, brm-1, brd1/2/13 and brm-1 brd1/2/13 seedlings
H4K5ac and H4K8ac in 14-day-old WT and brd1/2/13 seedlings

first: Yaoguang

last: Yu

first: Chenlong

last: Li


title: RNA sequencing analysis of rupture-prone intracranial aneurysms and the remaining circle of Willis in rats

status: Public on Nov 09 2020

city: Suita City

first: Mika

last: Kushamae

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Molecular Pharmacology

country: Japan

institute: Research Institute, National Cerebral and Cardiovascular Center

summary: Comprehensive gene expression profile was obtained by RNA sequencing analysis using total RAN purified from intracranial aneurysm lesions and remaining circle of Willis in rats.

overall_design: Comparison of gene expression profile between an intracranial aneurysm lesion and the remaining circle of Willis from the same animal by RNA sequencing analysis of 3 rats.

first: Haruka

last: Miyata

first: Manabu

last: Shirai

first: Tomohiro

last: Aoki


title: The Transcriptional Repressors VAL1 and VAL2 Recruit PRC2 for Genome-wide Polycomb Silencing in Arabidopsis

status: Public on Nov 06 2020

city: guangzhou

first: Liang

middle: Bing

last: Yuan

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

summary: The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1 and VAL2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2–RY regulatory system is largely independent of the TRB–Telobox and BPC1–GA/AZF1–Telobox modules for Polycomb silencing in plants. Taken together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.

overall_design: 14-day-old seedling of VAL1 and VAL2 ChIP-seq, and 14-day-old seedling of H3K27me3 ChIP-seq of WT and val1val2.

middle: B

first: Chen


title: Transcriptional screen in the target region of sprouting hindlimb corticospinal fibers after thoracic spinal cord injury in rats

status: Public on Jan 31 2021

city: Zuerich

first: Natalie

last: Russi

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich and ETH Zurich

summary:
Depending on the severity of a CNS injury, in humans as well as in experimental animal models certain degrees of functional recovery are observed. Rodent studies have provided much evidence for underlying anatomical changes involving neurite outgrowth of both spared and axotomized fiber tracts, also referred to as sprouting.
Following a thoracic spinal cord injury (SCI) in adult rats, axotomized fibers of the hindlimb corticospinal tract (CST) were found to sprout into the cervical spinal cord at different rostrocaudal levels. Anterograde tracings showed that these new collaterals of motor cortical hindlimb fibers project into the intermediate laminae of the cervical grey matter, particularly pronounced at the level of cervical segment three (C3). The molecular cues which induce the growth and guide these sprouts of hindlimb CST fibers are unknown.
We hypothesize that sectreted factors and guidance and adhesion molecules are specifically expressed in the intermediate laminae of the cervical spinal cord to direct and target the ingrowth of the sprouting hindlimb CST fibers. To test our hypothesis the transcription profile of the target region of sprouts was investigated with RNA sequencing of total RNA extracted from the intermediate laminae (IV-VII) of the spinal gray matter at cervical level C3. Four major comparisons were performed, which were then again compared to each other. The first comparison was between samples of animals with an SCI sacrificed at four different time points after injury (1, 3, 6, 12 weeks after injury). The second and third comparison was between samples of rats with a SCI compared to their sham controls sacrificed at the same time point after surgery (1 week or 12 weeks respectively). The fourth comparison was between samples from animals of the two control groups, rats with a sham surgery which were either sacrificed at one or at twelve weeks after injury. We found that most changes in gene expression ocurred at one week after SCI and least changes occured at twelve weeks after SCI, suggesting that the largest effects on a global level of gene expression occur during early time points after injury. Interestingly, also we also found changes in gene expression when comparing the samples from the two control groups, which suggests that sham surgery consisting of a laminectomy is sufficient to induce transcriptional changes in the spinal cord. This is the first study to provide insight into transcriptional changes in the target region of sprouts investigating the role of the cervical spinal cord (target region) for sprouting of hindlimb CST fibers.

overall_design: Experiments were started with a total of 67 adult female Long Evans rats (250-300 g, obtained from Charles River Germany), which were housed in groups of four in a 12:12 hours light/dark cycle. Food and water were available ad libitum. Animals were given at least one week to acclimatize before the experimentation began. All experiments were performed during the light cycle. All animal procedures were conducted in accordance with the Veterinary Office of Canton Zurich, Zurich, Switzerland. Animals were stratified based on their baseline performance on the Montoya staircase test and then randomly assigned to 6 groups: n=10 in the control group euthanized at 1 week after sham surgery, n=10 in the control group euthanized at 12 weeks after sham surgery, n=10 in the SCI group euthanized at 1 week after injury (1 week group), n=10 in the SCI group euthanized at 3 weeks after injury (3 weeks group). n=11 in the SCI group euthanized at 6 weeks after injury (6 weeks group), and 6) n=16 in the SCI group euthanized at 12 weeks after injury (12 weeks group). Due to inadequate lesion size five animals were excluded. Based on RNA quality and quantity five samples per group were chosen for RNA sequencing (total  sample size= 30, 5 biological replicates/condition).

first: Anna-Sophie

last: Hofer

first: Anne

last: Engmann

first: Stefan

last: Imobersteg

first: Regula

last: Schneider

first: Jennifer

last: Heldner

first: Luca

last: Truscello

first: Kai

last: Fricke

first: Martin

middle: E

last: Schwab


title: DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders [ChIP-seq]

first: Harrison

last: Gabel

overall_design: Total ChIP-seq from the brains of DNMT3A heterozygous KO and WT mice

first: Diana

last: Christian

first: Dennis

last: Wu


title: Transcriptomic and metabolomic Profiling reveal the protective effect of Acanthopanax senticosus (Rupr. & Maxim.) Harms combined with Gastrodia elata Blume on cerebral ischemia-reperfusion injury

status: Public on Oct 31 2020

city: Nanchang

first: zhifeng

last: li

address: 56 Yangming road

institute: Jiangxi University of Traditional Chinese Medicine

summary: In this work, we discussed the effects Acanthopanax senticosus Harms (ASE) combined with Gastrodia elata Blume (GEB) in the treatment of CIR injury. In pharmacodynamic studies, found that co-administration of ASE and GEB may improve neuronal injury and prevent neuronal apoptosis by reducing oxidative stress and inflammation, and also help prevent CIR injury. On the basis of our hypothesis, we combined the results of transcriptomic and metabonomic analyses and found that ASE and GEB could prevent cerebral ischemia-reperfusion injury induced by middle cerebral artery occlusion by targeting phenylalanine, pyrimidine, methionine, and sphingolipid metabolism. This study provides the basis for the compatibility and efficacy of ASE and GEB.

overall_design: Brain mRNA profiles of adult male Wistar rats

first: Bingfeng

last: Lin

first: Renhao

last: Chen

first: Qi

last: Wang

first: Zhifeng

last: Li

first: ShiLin

last: Yang

first: YuLin

last: Feng


title: A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

status: Public on Nov 20 2020

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

summary: To understand intestinal cell-specific responses to host commensal bacteria, we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single-cell RNA-seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue, and describe distinct microbial responses in each cell type.

overall_design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single-cell suspension for sequencing on the 10X Genomics platform.

first: Reegan

last: Willms

first: Lena

last: Ocampo Jones

last: Hocking


title: Cisplatin-induced rat model of kidney injury: physiological, functional, histological and gene expression profile evaluations

status: Public on Feb 15 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Cisplatin is a chemotherapeutic drug used for the treatment of solid tumors and hematological malignancies and it is considered as a gold standard therapy in oncology. Its nephrotoxic effect has been largely investigated in vivo but a comprehensive overview that illustrates the effect of cisplatin not only in kidney but also on the entire organism at the same time is still missing. Here we established a stable model of cisplatin-induced acute renal injury in immune competent Sprague Dawley (SD) rats and described the systemic effects of the aforementioned drug. A broad panel of plasma and urine parameters was checked, the histology of different organs was evaluated and the assessment of renal function was measured by using an innovative transcutaneous device. Additionally gene expression profiling with RNAseq technology was performed. Changes in renal injury markers, such as plasma creatinine and urea and urinary albumin, were detected already 2 days after cisplatin administration. Renal function was seriously compromised and so the cytoarchitecture of the kidney. Inflammation was found in liver, lungs and heart. Gene expression profiling of renal tissue revealed 6333 significant differentially expressed genes, 49 pathways and 14 miRNAs.

overall_design: SD rats were treated with 7mg/kgBW cispaltin or Saline Solution (Ctrl) and sacrificed 15 days after.

first: Cristina

last: Daniele

first: Norbert

last: Gretz


title: The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4/UL5 Transcripts

status: Public on Feb 01 2021

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the influence of the RNA binding protein ZAP (ZC3HAV1) on the CMV gene expression cascade

overall_design:
PolyA RNA-sequencing and 4su-RNA-seq was performed from CMV infected primary human foreskin fibroblasts and controls, with and without ZAP (ZC3HAV1) knockout, as well as ZAP eCLIP

UPDATE: [Feb 22, 2024] The treatment times were corrected from 8hpi to 24hpi in the following Samples: GSM4848747, GSM4848748, GSM4848757, GSM4848758, GSM4848767, GSM4848768, GSM4848777, and GSM4848778.

first: Ana

middle: C

last: Gonzalez-Perez

first: Markus

last: Stempel

first: Christian

last: Urban

first: Antonio

last: Piras

first: Thomas

last: Hennig

first: Sabina

last: Ganskih

first: Yuanjie

last: Wei

first: Albert

last: Heim

last: Landthaler

first: Andreas

last: Pichlmaier

first: Lars

last: Dolken

first: Mathias

last: Munschauer

first: Florian

last: Erhard

first: Melanie

last: Brinkmann


title: Modulating Androgen Receptor-driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors [SLAM-seq]

status: Public on Oct 05 2020

city: Houston

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Castration resistant prostate cancers (CRPCs) lose sensitivity to androgen deprivation therapies but frequently remain dependent on oncogenic transcription driven by androgen receptor (AR) and its splice variants. To discover novel modulators of AR variant activity, we used a lysate-based small molecule microarray (SMM) assay and identified KI-ARv-03 as an AR variant complex binder that reduces AR-driven transcription and proliferation in prostate cancer cells. We deduced KI-ARv-03 to be a potent, selective inhibitor of CDK9, an important cofactor for AR, MYC, and other oncogenic transcription factors. Further optimization resulted in KB-0742 , an orally bioavailable, selective CDK9 inhibitor with potent anti-tumor activity in CRPC models. In 22Rv1 cells, KB-0742 rapidly downregulates nascent transcription, preferentially depleting short half-life transcripts and AR-driven oncogenic programs. In vivo , oral administration of KB-0742 significantly reduced tumor growth in CRPC, supporting CDK9 inhibition as a promising therapeutic strategy to target AR dependence in CRPC.

overall_design: SLAM-seq in 22Rv1 castration resistant prostate cancer cells

first: André

last: Richters

first: Shleby

middle: K

last: Doyle

first: Angela

middle: N

last: Koehler


title: Modulating Androgen Receptor-driven Transcription in Prostate Cancer with Selective CDK9 InhibitorsModulating Androgen Receptor-driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors

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

overall_design: Refer to individual Series


title: Modulating Androgen Receptor-driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors [ATAC-seq]

overall_design: 22Rv1 castration resistant prostate cancer cells

first: Jost

last: Koren


title: Single cell transcriptome profiling for hidradenitis suppurativa

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Hidradenitis Suppurativa (HS) is a debilitating chronic inflammatory disease characterized by chronic abscess formation and development of multiple draining sinus tracts in the groin, axillae, and perineum.  Through the use of transcriptomic approaches, we characterize the inflammatory responses in HS in depth, revealing the cell types and immune responses involved.

overall_design: We conducted scRNA-seq on lesional skin from HS patients, and investigated the different disease pathways, including Hippo signaling.

first: Johann

last: Gudjonsson


title: Inositol Trisphosphate Receptor Mediated Ca2+ Signalling Stimulates Mitochondrial Function and Gene Expression in Core Myopathy Patients [Human arrays]

status: Public on Sep 15 2020

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Elevated inositol trisphosphate receptor (IP3R) levels have been previously reported in skeletal muscle myotubes derived from patients with ryanodine receptor 1 (RyR1) mutation related core myopathies. However, the functional relevance and the relationship of IP3R mediated Ca2+ signalling with the pathophysiology of the disease is unclear. It has also been suggested that mitochondrial dysfunction underlies the development of central and diffuse multi-mini-cores, devoid of mitochondrial activity, a key pathological consequence of RyR1 mutations. Here we used muscle biopsies of central core and multi-minicore disease patients with RyR1 mutations, as well as cellular and in vivo mouse models of the disease to characterise whole genome and mitochondrial gene expression to assess if remodeling of skeletal muscle following loss of functional RyR1 mediates bioenergetic adaptation.

overall_design: 8 Samples were analyzed, with 3/4 technical replicates, 3 Controls and 5 Patients

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Gyorgy

last: Szabadkai

first: Matteo

last: Suman


title: DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders

first: Harrison

last: Gabel


title: Inositol Trisphosphate Receptor Mediated Ca2+ Signalling Stimulates Mitochondrial Function and Gene Expression in Core Myopathy Patients [Mouse arrays]

overall_design: 6 Samples were analyzed, with 3  biological replicates, 3 Controls and 5 Transgenic mice


title: Modulating Androgen Receptor-driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors [ChIP-seq]

overall_design: H3K27ac and FOXA1 ChIP-seq (chipmentation) in 22Rv1 castration resistant prostate cancer cells


title: Single-cell transcriptomics reveals temporal dynamics of critical regulators of germ cell fate during mouse sex determination

status: Public on Nov 30 2020

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

institute: UNIGE

summary: Despite the importance of germ cell differentiation for sexual reproduction, gene networks underlying their fate remain unclear. Here, we describe a comprehensive characterization of gene expression dynamics during sex determination based on single-cell RNA sequencing on 14,750 XX and XY mouse germ cells between embryonic days 10.5 and 16.5. By computational gene regulation inference analysis, we identified sex-specific, sequential waves of master regulator genes during germ cells differentiation and unveiled that the meiotic initiator Stra8 is regulated by positive and negative master regulators acting in an antagonistic fashion. Consistent with the importance of the somatic environment, we found that rare adrenal germ cells exhibit delayed meiosis and display altered expression of master genes controlling the female and male genetic programs. Our study provides a molecular roadmap of germ cell sex determination at single-cell resolution will serve as a valuable resource for future studies of gonad development, function and disease.

overall_design: This dataset contains primordial germ cells data from 28 10x single cell RNAseq captures on whole organs.  Urogenital ridges and adrenal glands were enzymatically dissociated at 37ºC for 20 and 40 minutes, respectively, using the Papain dissociation system (Worthington #LK003150). Cells were resuspended in DMEM 2%FBS, filtered through a 70 μm cell strainer and stained with the dead cell marker Draq7™ (Beckman Coulter, #B25595). Viable single cells were collected on a BD FACS Aria II by excluding debris (side scatter vs. forward scatter), dead cells (side scatter vs. Draq7 staining), and doublets (height vs. width). Testes and ovaries (from E12.5 to E16.5) were enzymatically dissociated at 37ºC during 15 minutes in Trypsin-EDTA 0.05% (Gibco #25300054), resuspended in DMEM 2%FBS and filtered through a 70 μm cell strainer. After counting, 3000 to 7000 single cells were loaded on a 10x Chromium instrument (10x Genomics). Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Each condition (organ, sex and developmental stage) was performed in two biological independent replicates. Library quantification was performed using the Qubit fluorometric assay with dsDNA HS Assay Kit (Invitrogen). Library quality assessment was performed using a Bioanalyzer Agilent 2100 with a High Sensitivity DNA chip (Agilent Genomics). Libraries were diluted, pooled and sequenced on an Illumina HiSeq4000 using paired-end 26 + 98 bp as the sequencing mode. Libraries were sequenced at a targeted depth of 100 000 to 150 000 total reads per cell. Sequencing was performed at the Health 2030 Genome Center, Geneva.

first: Chloé

last: Mayère

first: Yasmine

last: Neirijnck

first: Pauline

last: Sararols

first: Isabelle

last: Stévant

first: Françoise

last: Kühne

first: Anne

middle: A

last: Chassot

first: Marie-Christine

last: Chaboissier

first: Emmanouil

middle: T

last: Dermitzakis

first: Serge

last: Nef


title: Stress-induced RNA–chromatin interactions promote endothelial dysfunction (RNA-seq)

status: Public on Aug 17 2020

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

summary: Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.

overall_design: Performing polyA-enriched RNA-seq in HUVECs with LINC00607 knockdown by two different LNAs under high glucose and TNFa treatment.

first: Riccardo

last: Calandrelli

first: Lixia

last: Xu

first: Yingjun

last: Luo

first: Weixin

last: Wu

first: Xiaochen

last: Fan

first: Tri

last: Nguyen

first: Chien-Ju

last: Chen

first: Kiran

last: Sriram

first: Rama

last: Natarajan

first: Zhen

last: Bouman-Chen


title: Total RNA sequencing of KIR+ and KIR- NK cells from patients experiencing or not a Cytomegalovirus reactivation after haploidentical hematopoietic stem cell transplantation

status: Public on Oct 29 2020

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

institute: Humanitas Clinical and Research Center

summary:
AIM: To investigate the adaptive properties of NK cells, by comparing the expression profiles of FACS-sorted KIR+ (CD158b1b2j) and KIR- NK cells from patients experiencing or not a Cytomegalovirus (HCMV) reactivation after haploidentical hematopoietic stem cell transplantation (h-HSCT).
RESULTS: Our flow cytometry data demonstrate that KIR+ NK cells are expanded in h-HSCT patients upon HCMV reactivation, thus suggesting that these cells could be important in controlling the viral infection and could be endowed with adaptive features.
By comparing the expression profiles of KIR+ and KIR- NK cells from reacivated patients, we demonstrated a cytokine receptor unbalance, a prevalence of pathways associated to mitochondrial respiration and consequent ATP synthesis, a downregulation of genes involved in epigenetic reprogramming, all properties attributable adaptive NK cells.
By comparing the molecular fingerprint of KIR+ NK cells between patients experiencing a HCMV reactivation and not reactivated patients, we observed in reactivated group an upregulation of INFG expression and in genes involved in Signaling receptor activity and MHC class II antigen presentation , thus strengthens the hypothesis that our KIR+ NK cells in reactevated h-HSCT patients are able to produce IFN-γ driving specific responses upon re-stimulation.   However, the enrichment in PD-1 signaling, let us speculate that KIR+ NK cells from reactivated h-HSCT patients have impaired effector-functions.

overall_design: Total mRNA profils of KIR+ and KIR- NK cells after h-HSCT

first: Elisa

last: Zaghi

first: Simone

last: Puccio

first: Clara

last: Di Vito

first: Domenico

last: Mavilio


title: Analysis of Circulating Breast Cancer Cell Heterogeneity and Interactions with Peripheral Blood Mononuclear Cells.

status: Public on Aug 25 2020

city: Aurora

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

summary:
Purpose: To infer interactions between circulating breast cancer cells and peripheral mononuclear cells using bioinformatics analysis of single cell RNA-sequencing.
Methods: Filter based method for capturing single cells from 7.5mL of blood from patients with breast cancer, followed by single cell RNA-sequencing.
Results: Transcriptomes predicted for two CTC populations with distinct expression profiles and interactions with peripheral blood mononuclear cells.

overall_design: 10 samples from breast cancer patients (9 with metastatic breast cancer and 1 with stage 2 local breast cancer). A total of 7.5 mL of blood from each sample was used to capture single cells for single cell RNA-sequencing.

first: Peter

last: Kabos

first: Heather

last: Brechbuhl

last: Paul

first: Austin

last: Gillen


title: Stress-induced RNA–chromatin interactions promote endothelial dysfunction (iMARGI)

first: Sheng

last: Zhong

overall_design: Map RNA-DNA interactions in HUVEC human cell lines using iMARGI technique in three samples: control (no treatment) and after 3 and 7 days of treatment to mimic endothelial to mesenchymal transition.

first: Riccardo

last: Calandrelli

first: Lixia

last: Xu

last: Luo

last: Wu


title: Single Cell RNA Sequencing of neonatal and juvenile mice skin (wound and unwounded)

status: Public on Jul 01 2020

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

summary: We perform 10X Genomics scRNA-Seq on P2, P21, P2 + 7 days post wound, P21 + 7 days post wound, with 3 bioreplicates for each condition. Fastq files and output folders were generated from Cellranger pipeline. Loom files were generated using Velocyto.py for downstream analysis. Chemistry: V2

overall_design: scRNA-Seq on P2, P21, P2 7 days post wound, P21 7 days post wound, with 3 bioreplicates for each condition

middle: R

first: Quan

last: Phan


title: Stress-induced RNA–chromatin interactions promote endothelial dysfunction (scRNA-seq)

overall_design: Performing single-cell RNA-seq in HUVEC human cell lines in three samples: control (no treatment) and after 3 and 7 days of treatment to mimic endothelial to mesenchymal transition.

first: Yingjun

first: Weixin

first: Xiaochen

last: Fan

first: Tri

last: Nguyen

first: Chien-Ju

last: Chen

last: Sriram

last: Natarajan

last: Bouman-Chen


title: 4U-DMS-MaP probing of nascent ribosomes

status: Public on Aug 28 2020

city: Baltimore

first: Yumeng

last: Hao

state: Maryland

address: 3400 N. Charles Street, Jenkins 408

department: Biophysics

institute: Johns Hopkins University

summary: Probe rRNA structural changes during assembly with dimethyl sulfate

overall_design: Nascent transcripts were metabolically pulse-labelled with 4-thio-urdine and rifampicin, then treated with dimentyl sulfate to probe structural changes

last: Hulscher

first: Boris

last: Zinshteyn

first: Sarah

last: Woodson


title: Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for 24 hours (collected at 120 hpf)

status: Public on Jun 23 2020

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from 96-120 hours post fertilization (hpf).

overall_design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum (tg(fabp10a: ER-tdTomato) specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:(fabp10:ER-tdTomato) and WT-ABNYU and larvae were exposed from 96-120 hpf to 0,  175 and 350 mM ethanol. We collected livers from 20-35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 (Illumina).

first: Anjana

last: Ramdas Nair

first: Chi

last: Zhang

last: Sadler (Edepli)


title: RNA sequencing analysis of human omental metastatic ovarian cancer from FFPE samples

status: Public on Jun 30 2020

city: Los Angeles

first: Sandra

last: Orsulic

state: CA

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

summary: To investigate the differential gene expression pattern across a large panel of omental metastatic ovarian cancers

overall_design: Examination of gene expression using RNA sequencing in 130 omental metastatic ovarian cancers

first: Barbie

last: Taylor-Harding

first: Ye

last: Hu


title: Stress-induced RNA–chromatin interactions promote endothelial dysfunction (Hi-C)

first: Sheng

last: Zhong

overall_design: Map chromatin interactions in HUVEC human cell lines using Hi-C technique in three samples: control (no treatment) and after 3 and 7 days of treatment to mimic endothelial to mesenchymal transition.

first: Riccardo

last: Calandrelli

first: Lixia

last: Xu

last: Luo

last: Wu

last: Fan

first: Kiran

first: Rama

first: Zhen


title: Disruption of TFIIH activities generates a transcriptional stress gene expression response and reveals possible new targets against cancer

status: Public on Jul 08 2020

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: UNAM

summary: The global effect on transcription between cancer cells and their progenitors and investigating how these compounds affect TFIIH integrity. Here, we used an oncogenesis model to compare the effect of TFIIH inhibitors: TPL and THZ1 between transformed cells and their progenitors. RNA-seq and RNAPII-ChIP-seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy

overall_design: RNAseq in cells MCF10A-Er-Src with TPL 4h-125 nM and RNAPII-ChIP-seq with TPL 4h-125 nM

first: Maritere

last: Uriostegui-Arcos


title: The methylomic landscape of fallopian tube lesions associated with ovarian high grade serous carcinoma

status: Public on Jul 29 2020

first: Thomas

last: Pisanic

state: MD

address: Shaffer Hall 200D, 3400 N Charles St

department: Institute for NanoBioTechnology

type: Methylation profiling by genome tiling array

summary: The current paradigm in the development of high-grade serous carcinomas (HGSCs) proposes that the majority of HGSCs arise from precursor serous tubal intraepithelial carcinoma (STIC) lesions of the fallopian tube. The goal of this study is to identify genomic regions that exhibit high-specificity differential hypermethylation for potential use as biomarkers for detecting STIC and HGSC at stages when curative intervention likely remains feasible.

overall_design: We used MethylationEPIC platform to compare genome-wide methylation among 12 STICs along with respective adjacent-normal epithelia, one p53 signature lesion and 2 samples of concurrent HGSC. The resulting methylomic data were analyzed by unsupervised hierarchical clustering and multidimensional analysis. Regions of high-confidence STIC-specific differential hypermethylation were identified using selective bioinformatic criteria and compared with published MethylationEPIC data (GSE155760) from 23 HGSC tumors and 11 healthy fallopian tube mucosae.

last: Pisanic II

first: Yeh

last: Wang

first: Hanru

last: Sun

first: Michael

last: Considine

first: Lihong

last: Li

first: Tian-Li

first: Ie-Ming

last: Shih


title: Next Generation Sequencing Facilitates Quantitative Analysis of  in 14-day-old wt, brm-1,  brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

status: Public on Jun 21 2020

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: RNA from 14-day-old seedlings of wild-type, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150).
Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Examination of global RNA expression in 14-day-old wt, brm-1,  brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

first: Yaoguang

last: Yu

first: Chenlong


title: BRIP1/2 are core members of SWI/SNF complex

overall_design: Refer to individual Series


title: Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis

summary: SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.

overall_design: Examination of BRM occupancy in 14-day-old brm-1 and brip1 brip2 seedlings. Examination of BRIP1 occupancy in 14-day-old brip1 seedlings. Examination of BRIP2 occupancy in 14-day-old brip2 seedlings.


title: Inositol Trisphosphate Receptor Mediated Ca2+ Signalling Stimulates Mitochondrial Function and Gene Expression in Core Myopathy Patients

first: Gerolamo

last: Lanfranchi


title: Single cell 3' RNA sequencing of 23 Korean colorectal cancer patients

status: Public on Apr 04 2020

city: Seoul

first: Yourae

last: Hong

address: 81, Irwon-ro

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

summary: For the understanding intrinsic cancer cell signatures and the surrounding microenviroment, we provide single-cell 3' RNA sequencing dataon 63,689 cells from 23 CRC patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analysis of primary colorectal cancer and normal mucosa samples depicts a comprehensive cellular landscape of colorectal cancer and potential cellular interaction, which would be a valuable resource for the development of therapeutic strategies.

overall_design:
Single-cell 3' mRNA sequencing data were obtained from 23 patients in 23 primary colorectal cancer and 10 matched normal mucosa. To remove low-quality cells, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes. 67,296 cells have passed the criteria. To eliminate cells of an ambiguous identity, we combined the Seurat multiCCA and RCA pipelines for initial clustering and cell type identification, and removed discordant cells from 2 methods. After defining the global cell type, cells with a number of genes exceeding the outliers were removed to eliminate potential doublets. 63,689 cells have passed the final criteria.

**Raw data not provided due to patient privacy concerns**

first: Hae-Ock

last: Lee

first: Yong

last: Cho

first: Woong-Yang

last: Park


title: Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8+ T cell stemness and antitumor immunity

status: Public on Feb 13 2020

city: Bethesda

first: Peng

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

summary: Interleukin (IL)-2 and IL-21 dichotomously shape CD8+ T cell differentiation. IL-2 drives terminal differentiation, generating cells that are poorly effective against tumors, whereas IL-21 promotes stem cell memory T cells (TSCM) and antitumor responses. Here we investigated the role of metabolic programming in the developmental differences induced by these cytokines. IL-2 promoted effector-like metabolism and aerobic glycolysis, robustly inducing lactate dehydrogenase (LDH) and lactate production, whereas IL-21 maintained a metabolically quiescent state dependent on oxidative phosphorylation. LDH inhibition rewired IL-2–induced effects, promoting pyruvate entry into the tricarboxylic acid cycle and inhibiting terminal effector and exhaustion programs, including mRNA expression of members of the NR4A family of nuclear receptors, as well as Prdm1 and Xbp1. While deletion of Ldha prevented development of cells with antitumor effector function, transient LDH inhibition enhanced the generation of memory cells capable of triggering robust antitumor responses after adoptive transfer. LDH inhibition did not significantly affect IL-21–induced metabolism but caused major transcriptomic changes, including the suppression of IL-21–induced exhaustion markers LAG3, PD1, 2B4, and TIM3. LDH inhibition combined with IL-21 increased the formation of TSCM cells, resulting in more profound antitumor responses and prolonged host survival. These findings indicate a pivotal role for LDH in modulating cytokine-mediated T cell differentiation and underscore the therapeutic potential of transiently inhibiting LDH during adoptive T cell-based immunotherapy, with an unanticipated cooperative antitumor effect of LDH inhibition and IL-21.

overall_design: RNA-Seq analyses using TCR pre-activated CD8+ T cells that were treated with either no cytokine, or with IL-2, IL-21, IL-2 + LDHi, IL-21 + LDHi.

first: Dalton

last: Hermans

first: Sanjivan

last: Gautam

first: Juan

last: García-Cañaveras

first: Daniel

last: Gromer

first: Suman

last: Mitra

first: Rosanne

last: Spolski

first: Stephen

last: Christensen

first: Rosa

last: Nguyen

first: Jian-Xin

last: Lin

first: Jangsuk

last: Oh

first: Ning

last: Du

first: Sharon

last: Veenbergen

first: Jessica

last: Fioravanti

first: Risa

last: Ebina-Shibuya

first: Christopher

last: Bleck

first: Leonard

middle: M

last: Neckers

first: Joshua

last: Rabinowitz

first: Luca

last: Gattinoni

first: Warren

middle: J

last: Leonard


title: The Obese Adipocyte

status: Public on Mar 19 2020

city: Boston

last: Farmer

address: 72 E Concord St.

department: Biochemistry

institute: Boston University School of Medicine

summary: We report the application of high-throughput sequencing to study the changes in the transcriptional profile of visceral white adipocytes during a setting of chronic high fat diet.

overall_design: Three RNAsequencing experiments at various time points throughout a high fat diet regimen (8-week / 20-week / 34-week and    CHOW / HFD).

last: Jones

first: Nabil

last: Rabhi

first: Joseph

last: Orofino

first: Ramya

last: Gamini

first: Valentina

last: Perissi

first: Cecile

last: Vernochet


title: Transcriptome profiling of SUM159 and derivatives with different metastasis capability

status: Public on Jan 13 2021

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary:
Triple negative breast cancer cell line SUM159 labeled with triple reporter (TR, TK-GFP-fLUC) injected into Nude mice via mammary fat pad and tail vein injection. Tumor progression is monitored by in vivo bioluminescent imaging.
Tumors from mammary and lung were isolated and cultured. These derivatives cells are further tested for their capability to develop mammary primary tumor and metastasis in lung and bone in mice.
The total RNA samples are extracted from the panel of SUM159 and derivatives and the transcriptome profiles are determined by microarray. The correlation of transcriptome of the cells to metastasis capability indicated candidate genes and regulatory pathways of metastasis of TNBC.

overall_design: Transcriptome correlation to metastasis capability of a panel of 7 cells from SUM159 origin.

first: Mark

last: Esposito