title: Cellular Damage in the Target and Out-of-Field Peripheral Organs during VMAT SBRT Prostate Radiotherapy: An In Vitro Phantom-Based Study

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

institute: Poznan University of Medical Science

summary:
New developments show that patients with prostate cancer can benefit from radiotherapy deliv-ered with a hypo-fractionated regimen. The aim of our study was to investigate the effect of hy-po-fractionated stereotactic body radiation therapy (SBRT) of prostate cancer on out-of-field organs. We used a humanoid phantom to irradiate prostate cells in conditions similar to patient therapy, using SBRT planning. Our results show that radiation doses in the location of the intes-tine and lung resulted in significantly higher radiation doses than the further locations.
We observed a high radiotoxic effect in the cells irradiated in the prostate, and a small increase in DNA damage and cell killing in the intestine location. Gene expression analysis revealed significant enrichment of the biological processes related to the radiation response in the prostate. In the lung and thyroid, the enrichment of several gene groups was revealed, however the processes were not clearly related to the response to radiation. Our study provides extensive data on out-of-field safety of prostate SBRT.

overall_design: The PNT1A cells were placed and irradiated in a quasi-humanoid phantom under conditions similar to those of real-life radiotherapy. The phantom was made with water-equivalent poly(methyl methacrylate) (PMMA) slices in the coronal plane to simulate the torso, head, and neck. The slices included natural cork and gypsum inhomogeneities in the lung and head locations to simulate lung tissue and bones, respectively. The layer for cell irradiation was equipped with a water container to allow for the placement of five flasks with the cells.   A radiation treatment plan was created for the T-25 culture flask containing PNT1A cells in the prostate location, which was delineated as the gross tumour volume (GTV). The flask was considered the clinical target volume (CTV). To create the planning target volume (PTV), a margin of 3 mm was added around the CTV, following the usual clinical practice to ensure that the PTV received the prescribed dose. The other four flasks were placed in the water containers in the following locations at various distances from the axial plane: intestine (transverse colon) (15 cm from the axial plane; lung (35 cm); thyroid (52 cm); and brain (74 cm). Figure 1 shows the VMAT plan for these organs at risk.  We used a 6 MV photon beam with a flattening filter to deliver the total dose of 70 Gy to the cells in the prostate, delivered in seven consecutive fractions of 10 Gy each (the highest fraction dose delivered for prostate SBRT). This approach is known as dose scaling (see AAPM Report 158). The 10 Gy SBRT fraction was used for planning (instead of 2 Gy, which is used for conventional fractionations, to a total dose of 70 Gy) because we wanted to assure the same scheme of collimator leaves’ movement (a different scheme is used for different doses per fraction during arc therapies). Treatment plans were prepared for the RapidArc VMAT technique using three co-planar arcs, with the first, second, and third arcs delivered, respectively, counterclockwise (gantry angles from 140° to 220°), clockwise (181° to 179°), and counterclockwise (179° to 181°), and with a 0.5 cm multi-leaf collimator

first: Igor

last: Piotrowski

first: Katarzyna

last: Kulcenty

first: Wiktoria

last: Suchorska

first: Karol

last: Jopek

first: Marta

last: Kruszyna-Mochalska

first: Agnieszka

last: Skrobala

first: Piotr

last: Romanski

first: Adam

last: Ryczkowski

first: Dorota

last: Borowicz

first: Natalia

last: Matuszak

first: Julian

last: Malicki


title: Progesterone signaling in endometrial epithelial organoids

status: Public on May 26 2022

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

country: USA

institute: NIEHS

summary: 3D chromatin structure of endometrial organoids and PRKO and Sox17cKO mouse uterus

overall_design: HiC of endometrial orgaoids treated with estrogen and progesterone and ovariectomized uterus from progesterone receptor-null (PRKO) and PR-CrexSox17-flox mice 1 hour after treatment with V or progesterone

first: Sylvia

middle: C

last: Hewitt

first: San-pin

last: Wu

first: Sara

last: Grimm

first: Tianyuan

last: Wang

first: Artiom

last: Gruzdev

first: Mita

last: Ray

first: Marja

last: Brolinson

first: Steven

middle: L

last: Young

first: Thomas

middle: E

last: Spencer

first: Alan

last: DeCherney

first: Francesco

middle: J

last: DeMayo


title: Isolating metastatic cell populations from zebrafish

status: Public on May 30 2022

city: Washington

first: Jerry

last: Xiao

state: DC

address: 3900 Reservoir Rd NW, PCS Bldg, Room GR10C

department: Tumor Biology

institute: Georgetown University

type: Expression profiling by high throughput sequencing

summary: The zebrafish-tumor-metastasis (ZTM) model is a robust method for the isolation of metastatic cells and is uniquely suited to facilitate study of cancer metastasis and metastasis-preventing therapies.

overall_design: Two parental populations of MDA-MB-231 cells (P15 and P18) were sequenced, along with two serially isolated and propagated populations that had undergone the ZTM model (F1 and F2).

first: J

middle: R

last: McGill

first: A

last: Lekan

first: D

last: Wilkins

first: S

last: Choudhury

first: E

last: Glasgow

first: R

last: Schlegel

last: Agarwal


title: The estrogen receptor α cistrome of human endometrium and epithelial organoids and progesterone receptor cistrome in epithelial organoids

first: Franco

last: Demayo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The ESR1 Cistrome in human endometrial biopsies was characterized and compared to gene regulations between the proliferative and mid-secretory pahses to infer estrogen target genes. ESR1 and PGR cistromes and 3D-cjromatin structures in cultured endometrial biopsies were characterized and compared to gene regulations induced by estrogen or progesterone in comparison to the whole endometrium.

overall_design: ESR1 ChIPseq of endometrial biopsies from proliferative or mid-secretory phases and ESR1 and PGR ChIPseq of human endometrial epithelial cells grown in culture organoid cultures and treated with estradiol and medroxyprogesterone acetate

first: Sylvia

last: Hewitt

first: San-pin

last: Wu


title: The effect of dietary fibre exposure on gene expression profiles in Caco-2 and THP-1 cells

city: Wageningen

first: Coen

last: Govers

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen Food & Biobased Research

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

overall_design: Refer to individual Series


title: Global Stable-isotope Tracing Metabolomics Reveals System-wide Metabolic Alternations in Aging Drosophila

status: Public on May 29 2022

city: Shanghai

first: Ruohong

last: Wang

state: Not in US

address: 100 Haike Road, 13th building

department: IRCBC

country: China

institute: Chinese Academy of Sciences

summary: System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. Using Drosophila as an aging model organism, we probe the in vivo tracing kinetics with quantitative information on labeling patterns, extents and rates on a metabolome-wide scale. We curate a system-wide metabolic network to characterize metabolic homeostasis and disclose a system-wide loss of metabolic coordinations that impacts both intra- and inter-tissue metabolic homeostasis significantly during Drosophila aging. Importantly, we reveal an unappreciated metabolic diversion from glycolysis to serine metabolism and purine metabolism as Drosophila aging. The developed technology facilitates a system-level understanding of metabolic regulation in living organisms.

overall_design: mRNA-seq of total RNAs from 3d and 30d flies, in triplicates, using Illumina Miseq.

first: Jingshu

last: Li

last: Liu

first: Zheng-Jiang

last: Zhu


title: Single cell transcriptomic profiling of gill cells of zebrafish (Danio rerio) exposed to normoxia and hypoxia

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors, neuroepithelial cells (NECs). Although the structure, function and development of the gill have been studied extensively, transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology, we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish, acclimated to 14 days of normoxia and hypoxia. Overall, approximately 13,000 cells were sequenced with an average depth of 27,000 reads per cell. We identified 16 cell clusters in the gill, including NECs, neurons, pavement cells, endothelial cells and mitochondrion-rich cells. NECs were identified through expression of vmat2, encoding vesicular monoamine transporter, and showed highly differential expressions of tph1a, sv2, and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills.

overall_design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.

first: Wen

last: Pan

first: Michael

last: Jonz


title: Tumour-derived exosomes regulate apoptosis of CD45+EpCAM+ cells in lung cancer

city: Qingdao

first: Zhen

last: Sun

address: Room 808, Block D, Haike Business Center Qingdao Oceantec Valley Jimo

institute: QINGDAO SINO-CELL BIOMED CO., LTD.

type: Non-coding RNA profiling by high throughput sequencing

summary: Cancer-derived exosomes can deliver nucleic acids, proteins, and lipids to neighboring or distant cells and subsequently modulate recipient cells. Recently, high levels of microRNAs (miRNAs) have been identified in cancer-derived exosomes, which provide a favorable microenvironment that contribute to tumorigenesis, tumor metastasis, angiogenesis, chemoresistance, and immune escape. Howerer, the mechanism of the cancer-derived exosomes regulating CD45+EpCAM+ cell apoptosis remains unclear.

overall_design: Exosomes (1 samples per group) were collected from HCC827 cell culture supernatant on 48h. Then the total RNAs were extracted and subjected to miRNA sequencing.

first: B


title: Gene expression data from human breast cancer MCF-7 cells treated with siRNAs targeting SCFD2

status: Public on May 28 2022

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

summary: To examine the role of SCFD2 in breast cancer, MCF-7 cells were treated with siRNAs targeting SCFD2 (siSCFD2) or control siRNA (siControl). SCFD2 silencing represses expressions of anti-apoptotic genes which are positively associated with shorter relapse-free survival in ER-positive breast cancer patients. These results reveal the clinical and functional significance of SCFD2 and its targets in hormone-dependent breast cancer. SCFD2 may be applied to the cancer management as a promising diagnostic and therapeutic target.

overall_design: Total RNA was extracted from MCF-7 cells treated with siRNAs targeting SCFD2 (siSCFD2 #A and #B) or control siRNA (siControl) and then used for Affymetrix microarrays analysis.

first: Toshihiko

last: Takeiwa

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Elevated Extracellular Purine Nucleotides Impair Muscle Regeneration in Diabetic Mice by Suppressing Early Activation of Muscle Satellite Cells

city: Hong Kong

first: Lifang

last: HAN

address: 6202D, Clear Water Bay

department: LIFS

institute: HKUST

summary: Chronic diabetic patients often exhibit defective tissue repair. Similarly, injury-induced muscle regeneration was also found to be defective in diabetic mice. However, the underlying mechanisms remain obscure. Here, we found that quiescent muscle satellite cells (MuSC) from db/db diabetic mice, a mouse model for obesity-induced type 2 diabetes, failed to re-enter the cell cycle upon activation in vivo but not in culture, suggesting the involvement of certain niche factors. Elevated extracellular AMP (eAMP) and adenosine (eAdo) were detected in both muscle tissues and blood of diabetic patients and mice. Unexpectedly, we found that eAMP and eAdo potently inhibited cell cycle re-entry of MuSC, and consequently impaired injury-induced muscle regeneration. Mechanistically, we demonstrated that eAMP and eAdo impaired the functions of MuSC via a signaling axis of equilibrative Ado transporter (ENT)-Ado kinase (ADK)-AMPK, which in turn inhibited an mTORC1-dependent cell growth checkpoint and subsequent cell cycle re-entry. Moreover, eAdo also inhibited early activation of quiescent fibroadipogenic progenitors and human MuSC by the same mechanism. Importantly, treatment of db/db diabetic mice with an ADK inhibitor not only reduced plasma glucose level but also partially restored the regenerative functions of MuSC in vivo. Collectively, our study suggests that both ENT and ADK are promising therapeutic targets for the treatment of diabetes and for restoring the regenerative functions of tissue stem cells.

overall_design: mRNA profiles of muscle satellite cells treated with or without 0.05mM adenosine for 24 hours

last: Han

first: Zhenguo


title: Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle.

status: Public on May 27 2022

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

institute: University of tsukuba

summary:
Gene expression profile was investigated using zebrafish muscle unger  fasting-refeeding conditions.
This study revealed fasting-refeeding responsive genes in zebrafish muscle.

overall_design: Zebrafish muscle under the fasting (for 24 hours) or refeeding (after 3 or 8 hours) conditions were analysed using mRNA-sequencing.

first: Takehito

last: Sugasawa

first: Ritsuko

last: Komine


title: C. elegans small RNA-seq profiling of a null mutant with a deletion of the entire lotr-1 coding sequence

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: Proteins containing LOTUS and Tudor domains have critical roles in the germline, including in small RNA biology. LOTR-1 is the only protein expressed in the germline of C. elegans which has LOTUS and Tudor domains. Here, to understand the influence of LOTR-1 in small RNA biology, we sequenced small RNAs of wild-type and lotr-1 mutant animals.

overall_design: Small RNA-seq profiling of wild-type and lotr-1 mutant worms in triplicates. The mutant analysed in this experiment has a deletion of the entire lotr-1 coding sequence. RNA was treated with RppH prior to library preparation.

first: Ida

last: Isolehto

first: Miguel

middle: V

last: Almeida

first: René

middle: F

last: Ketting


title: Cigarette smoke extract disturbs mitochondria-regulated airway epithelial cell responses to pneumococci

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

summary: Chronic obstructive pulmonary disease (COPD) is a heterogenous respiratory disease mainly caused by smoking. Respiratory infections constitute a major risk factor for acute worsening of COPD symptoms or COPD exacerbation. Mitochondrial functionality, which is crucial for the execution of physiologic functions of metabolically active cells, is impaired in airway epithelial cells (AECs) of COPD patients as well as smokers. However, the potential contribution of mitochondrial dysfunction in AECs to progression of COPD, infection-triggered exacerbations in AECs and a potential mechanistic link between mitochondrial and epithelial barrier dysfunction is unknown to date. In this study, we used an in vitro COPD exacerbation model based on AECs exposed to cigarette smoke extract (CSE) followed by infection with Streptococcus pneumoniae (Sp). The levels of oxidative stress, as an indicator of mitochondrial stress were quantified upon CSE and Sp. The expression of proteins associated with mitophagy, mitochondrial content and biogenesis as well as mitochondrial fission and fusion was quantified upon CSE and Sp. Transcriptional AEC profiling was performed to identify the potential changes in innate immune pathways and correlate them with mitochondrial function. We found that CSE exposure substantially altered mitochondrial function in AECs by suppressing mitochondrial complex protein levels, reducing mitochondrial membrane potential and increasing mitochondrial stress and mitophagy. Moreover, CSE-induced mitochondrial dysfunction correlated with reduced enrichment of genes involved in apical junctions and innate immune responses to Sp, particularly type I interferon responses. Together, our results demonstrated that CSE-induced mitochondrial dysfunction may contribute to impaired innate immune responses to Sp and may thus trigger COPD exacerbation.

overall_design:
16HBE14o- Human Bronchial Epithelial Cell Line was treated in vitro with 9 treatment conditions with two replicates per condition. In total 18 samples were analyzed.
1.) untreated: medium negative control
2.) FCCP: positive control, incubation with 50 µM FCCP for 4 h
3.) CSE: 15 % cigarette smoke extract for 28 h
4.) CSE + FCCP: 15 % cigarette smoke extract for 24 h, then  addition of 50 µM FCCP for 4 h
5.) CSE cessation: 15 % cigarette smoke extract for 24 h, then medium replacement for 4 h
6.) 10 MOI: Streptococcus pneumonia infection with 10 MOI for 4 h
7.) 20 MOI: Streptococcus pneumonia infection with 20 MOI for 4 h
8.) CSE + 10 MOI: 15 % cigarette smoke extract for 24 h, then Streptococcus pneumonia infection with 10 MOI for 4 h
9.) CSE + 20 MOI: 15 % cigarette smoke extract for 24 h, then Streptococcus pneumonia infection with 20 MOI for 4 h

first: Mahyar

last: Aghapour

first: Christy

last: Tulen

first: Mohsen

middle: A

last: Sarabi

first: Sönke

last: Weinert

first: Mathias

last: Müsken

first: Borna

last: Relja

first: Frederik-Jan

last: Schooten

first: Alexander

middle: H

last: Remels

first: Rüdiger

last: Braun-Dullaeus

first: Dunja

last: Bruder


title: SMCHD1 variants induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome. [RNA-Seq]

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: Determination of SMCHD1 epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS).

overall_design: By combining RNA Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers.

first: Magdinier

last: Frédérique

first: Laberthonnière

last: Camille

first: Chevalier

last: Raphael

first: Dion


title: C. elegans small RNA-seq profiling of three different lotr-1 mutant alleles

first: Emil

last: Karaulanov

overall_design: Small RNA-seq profiling of wild-type and lotr-1 mutant worms. The three mutants analysed in this experiment have different deletions in the lotr-1 gene (details are described in the associated paper). RNA was treated with RppH prior to library preparation.

first: Miguel

last: Almeida

first: René


title: MicroRNAs and other small RNAs in Aedes aegypti saliva and salivary glands following chikungunya virus infection

city: Rome

first: Bruno

last: Arca

address: P.le Aldo Moro 5

department: Public Health and Infectious Diseases

country: Italy

institute: Sapienza University

summary: Mosquito saliva facilitates blood feeding through the anti-haemostatic, anti-inflammatory and immunomodulatory properties of its proteins. However, the potential contribution of non-coding RNAs to host manipulation is still poorly understood. We analysed small RNAs from Aedes aegypti saliva and salivary glands and show here that chikungunya virus-infection triggers both the siRNA and piRNA antiviral pathways with limited effects on miRNA expression profiles. Saliva appears enriched in specific miRNA subsets and its miRNA content is well conserved among mosquitoes and ticks, clearly pointing to a non-random sorting and occurrence. Finally, we provide evidence that miRNAs from Ae. aegypti saliva may target human immune and inflammatory pathways, as indicated by prediction analysis and searching for experimentally validated targets of identical human miRNAs. Overall, we believe these observations convincingly support a scenario where both proteins and miRNAs from mosquito saliva are injected into vertebrates during blood feeding and contribute to the complex vector-host-pathogen interactions.

overall_design: Small RNAs from saliva and salivary glands of uninfected and chikungunya virus infected Aedes aegypti mosquitoes were analyzed by RNAseq. All samples were analyzed in triplicate.


title: Transcriptome sequencing of the hepatic samples in antibiotic-treated mice under normal light-dark cycle and short-day

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

summary: Intestinal microbiota dysbiosis is related to many metabolic diseases in human health. Meanwhile, as an irregular environmental light-dark cycle, short-day (SD) may induce host circadian rhythms disturbances and worsen the risks of gut dysbiosis. Herein, we investigated how LD cycles regulate intestinal metabolism upon the destruction of gut microbes with antibiotic treatments. The transcriptome data indicated that SD have some negative effects on hepatic metabolism, endocrine, digestive, and diseases processes compared with normal light-dark cycle (NLD).The SD induced epithelial and hepatic purine metabolism pathway imbalance in ABX mice, the gut microbes, and their metabolites, all of which could contribute to host metabolism and digestion, endocrine system disorders, and may even cause diseases in the host.

overall_design: The antibiotic-treated mice were managed under alternating photoperiods of normal light-dark cycle (NLD, 12-hour light /12-hour dark, n=3) and short day (SD, 8-hour light / 16-hour dark, n=3). Mice were then anesthetizedwith ether andeuthanizedby spinal dislocation, the liver samples were collected for transcriptome sequencing.


title: Transcriptional profile of human endometrial epithelial cells grown as organoids and treated with hormones

first: Franco

last: Demayo

summary: Endometrial epithelial cells were cultured as organoids and transcriptional profiles of vehicle, E2 or E2+MPA treated cultures were compared.

overall_design: gene responses of organoids isolated from 2 donors were grown and treated with E2, E2+MPA and  or vehicle

first: Sylvia

last: Hewitt

first: San-pin

last: Wu

first: Sara

last: Grimm

first: Tianyuan

last: Wang

first: Artiom

last: Gruzdev

first: Mita

last: Ray

first: Marja

last: Brolinson

first: Steven

last: Young

first: Thomas

last: Spencer

first: Alan

last: DeCherney

first: Francesco

last: DeMayo


title: Next generation sequencing analysis of transcript abundance during growth mycelia in the rice false smut fungus Ustilaginoidea virens

status: Public on May 25 2022

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: Epigenetic modification is important for cellular functions. Trimethylation of histone H3 lysine 4 (H3K4me3), which associates with transcriptional activation, is one of the important epigenetic modifications. In this study, the biological functions of UvKmt2-mediated H3K4me3 modification were characterized in Ustilaginoidea virens, which is the causal agent of the false smut disease, one of the most destructive diseases in rice. Phenotypic analyses of the ΔUvkmt2 mutant revealed that UvKMT2 is necessary for growth, conidiation, secondary spore formation, and virulence in U. virens. RNA-seq analysis demonstrated that UvKmt2-mediated H3K4me3 acts as an important role in transcriptional activation. In particular, H3K4me3 modification involves in the transcriptional regulation of conidiation-related and pathogenic genes. The down-regulation of UvHOG1 and UvPMK1 genes may be one of the main reasons for the reduced pathogenicity and stresses adaptability of the ∆Uvkmt2 mutant. Overall, H3K4me3, established by histone methyltransferase UvKMT2, contributes to fungal development, secondary spore formation, virulence, and various stresses response through transcriptional regulation in U. virens.

overall_design: Examination of mRNA expression of WT and ΔUvkmt2 mutant strain in Ustilaginoidea virens strain

first: Yanjun

last: Kou

first: Zeng

last: Tao


title: Genome-wide mapping of H3K4 tri-methylation in ΔUvkmt2 mutant strain of Ustilaginoidea virens

summary: Epigenetic modification is important for cellular functions. Trimethylation of histone H3 lysine 4 (H3K4me3), which associates with transcriptional activation, is one of the important epigenetic modifications. In this study, the biological functions of UvKmt2-mediated H3K4me3 modification were characterized in Ustilaginoidea virens, which is the causal agent of the false smut disease, one of the most destructive diseases in rice. Phenotypic analyses of the ΔUvkmt2 mutant revealed that UvKMT2 is necessary for growth, conidiation, secondary spore formation, and virulence in U. virens. Immunoblotting and chromatin immunoprecipitation assay followed by sequencing (ChIP-seq) showed that UvKMT2 is required for the establishment of H3K4me3, which covers 1729 genes of the genome in U. virens. In particular, H3K4me3 modification involves in the transcriptional regulation of conidiation-related and pathogenic genes. The down-regulation of UvHOG1 and UvPMK1 genes may be one of the main reasons for the reduced pathogenicity and stresses adaptability of the ∆Uvkmt2 mutant. Overall, H3K4me3, established by histone methyltransferase UvKMT2, contributes to fungal development, secondary spore formation, virulence, and various stresses response through transcriptional regulation in U. virens.

overall_design: Examination of H3K4 tri-methylation of ΔUvkmt2 mutant strain of Ustilaginoidea virens. Two biological replicates were performed.


title: LOTR-1 interacts with ZNFX-1 to balance epigenetic signals in the C. elegans germline

first: Emil

last: Karaulanov

summary:
Proteins containing LOTUS and Tudor domains have critical roles in the germline, including in small RNA biology. LOTR-1 is the only protein expressed in the germline of C. elegans which has LOTUS and Tudor domains. Here, to understand the influence of LOTR-1 in small RNA biology, we sequenced small RNAs of wild-type and lotr-1 mutant animals.

This SuperSeries is composed of the SubSeries listed below.


title: I-SPY2-990 mRNA/RPPA Data Resource

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

institute: University of California, San Francisco

type:
Expression profiling by array
Protein profiling by protein array

summary:
The I-SPY2-990 mRNA/RPPA data resource contains gene expression, protein/phosphoprotein and clinical data for ~990 patients from the first 10 completed arms of the I-SPY 2 platform trial for aggressive, early stage breast cancer.  Experimental treatments include pan-HER2 inhibitors and anti-HER2 agents, PARP inhibitor/DNA damaging agent combinations, an AKT inhibitor, immunotherapy, and ANG1/2, IGF1R and HSP90 inhibitors added to standard of care chemotherapy.  All patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. 736 patients (all arms except ganitumab and ganetespib) have normalized LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm.

This SuperSeries is composed of the mRNA and RPPA SubSeries listed below.

overall_design: For details, please see individual series GSE19404 (mRNA) and GSE196093 (RPPA)


title: Divergent transcription from lentiviral gene editing of cancer cells

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

summary: We explored a gene editing approach to depleting ephrinB2 from colorectal cancer cells using an inducible lentiviral vector encoding a short hairpin (sh) RNA for ephrinB2 silencing via RNA interference. We discovered that lentiviral integration in the host DNA frequently drives divergent gene transcription generating antisense reads by forcing splicing and read-through into the host DNA resulting in expression of chimeric vector/host transcripts.

overall_design: Examination of RNA expression in HT-29 derived cell clones (596 clones).

first: Giovanna

last: Tosato

first: Taekyu

last: Ha

first: Vishal

last: Koparde

first: Parthav

last: Jailwala


title: Molecular signatures predictive of response to mecasermin in  children with Rett syndrome

city: Dublin 8

first: Daniela

last: Tropea

address: TRINITY SCIENCES CENTRE SAINT JAMES'S HOSPITAL JAMES'S STREET

department: Psychiatry

country: Ireland

institute: Trinity College Dublin

summary:
Purpose: Rett syndrome (RTT) is a devastating neurodevelopmental disorder without effective treatments. Attempts at developing targeted therapies have been relatively unsuccessful, at least in part, because the genotypical and phenotypical variability of the disorder. Therefore, identification of biomarkers of response and surrogate endpoints is a high priority.
Methods: We used RNA sequencing to measure differential gene expression in whole blood samples of participants patients (n=9) were analysed from phase I mecasermin trial
Results: When all patients (n=9) were analysed, gene expression was unchanged during the study (baseline vs. end of treatment).
Conclusions: Our preliminary analyses revealed gene expression profiles associated with differential breathing phenotype response to mecasermin in RTT.

overall_design:
Whole blood mRNA profiles of patients with RTT and MRD

Timepoint 0 = baseline
Timepoint 1 = after multiple ascending dose phase
Timepoint 2 = washout period
Timepoint 3 = after open label extension phase

first: Stephen

last: Shovlin

first: Chloe

last: Delepine

first: Lindsay

last: Swanson

first: Snow

last: Bach

first: Mustafa

last: Sahin

first: Mriganka

last: Sur

first: Walter

last: Kaufmann


title: Induction of mouse totipotent stem cells by a defined chemical cocktail [RRBS]

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

type: Methylation profiling by high throughput sequencing

summary: We demonstrate induction and long-term maintenance of totipotent stem cells (TotiSCs) from mouse pluripotent stem cells (PSCs) by a combination of three small molecules, TTNPB, 1-Azakenpaullone, and WS6. These cells, which we designated as ciTotiSCs (chemically induced totipotent stem cells), resembled mouse totipotent 2C-embryo stage cells at both transcriptome and epigenome level.

overall_design: RRBS-seq of ciTotiSC with two replicates.

first: Yanyan

last: Hu

first: Yuanyuan

last: Yang

first: Yuxia

last: Zhang

first: Jiawei

last: Yu

first: Xin

first: Zeran

last: Jia

first: Dan

last: Wang

first: Yinqing

last: Li

first: Tianhua

last: Ma

first: Kang

last: Liu

first: Sheng

last: Ding


title: I-SPY2-990 mRNA/RPPA Data Resource: mRNA component

first: Denise

last: Wolf

summary: The I-SPY2-990 mRNA/RPPA Data Resource contains gene expression and clinical data for 987 patients from 10 arms of the neoadjuvant I-SPY2 TRIAL for aggressive early stage breast cancer [210 Control (Ctr); 71 veliparib/carboplatin (VC); 114 neratinib (N); 93 MK2206; 106 ganitumab; 93 ganetespib; 134 trebananib; 52 TDM1/pertuzumab(P); 44 H/P; 69 pembrolizumab (pembro)]. All 987 patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. The ISPY2-990 mRNA/RPPA Data Resource also includes normalized pre-treatment LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer for 736 patients (see companion GEO record GSE196093 for data and details).

overall_design:
Fresh-frozen pre-treatment breast cancer tumors (n=987) from 10 arms of the neoadjuvant ISPY2 trial for high risk, early-stage breast cancer were assayed using two Agilent 44K expression arrays: (1) Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] or (2) Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)]; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.

The sample characteristics and their values represent:
HER2: the status of the HER2 gene
1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors
1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR)
1 = complete response; 0 = failed complete response
MP: MammaPrint status
0 = MammaPrint high risk 1 (MP1); 1 = MammaPrint (ultra) high risk 2 (MP2)
Arm: arm of the trial per patient:
Paclitaxil (Control arm: HER2- subset); Paclitaxil + Trastuzumab (Control arm: HER2+ subset); Paclitaxel + ABT-888 (veliparib) + Carboplatin; Paclitaxel + AMG-386 (AMG-386 arm: HER2- subset); Paclitaxel + AMG-386 + Trastuzumab (AMG-386 arm: HER2+ subset); Paclitaxel + MK-2206 (MK-2206 arm: HER2- subset); Paclitaxel + MK-2206 + Trastuzumab (MK-2206 arm: HER2+ subset); Paclitaxel + Neratinib; Paclitaxel + Ganetespib; Paclitaxel + Ganitumab; Paclitaxel + Pembrolizumab; Paclitaxel + Pertuzumab + Trastuzumab; or T-DM1 + Pertuzumab. All patients also received subsequent doxorubicin + cyclophosphamide.

A ComBat batch correction process was applied to the raw data on a group of patients (~800). Linear adjustment factors from this group were derived so they could be applied to the remaining group of ~100 patients. The ISPY2_LinearFit_forCombiningExp<GPLXXXXX> files contain linear adjustments to go from raw to batch corrected data.

For fully normalized and batch corrected data on the gene level, please use "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt", provided in the supplementary files. For biomarkers/signatures used in the manuscript, please see supplemental data file in the manuscript.

first: Christina

last: Yau

first: Laura

last: van 't Veer


title: I-SPY2-990 mRNA/RPPA Data Resource: RPPA component

summary: The RPPA component of the I-SPY2-990 mRNA/RPPA Data Resource contains protein/phosphoprotein data from pre-treatment laser capture microdissected (LCM) tumor biopsies for 139 key signaling proteins/phosphoproteins in cancer for 736 patients from 8 arms of the neoadjuvant I-SPY2 TRIAL (NCT01042379) for aggressive early stage breast cancer [194 Control (Ctr); 63 veliparib/carboplatin (VC); 105 neratinib (N); 87 MK2206; 128 trebananib; 49 TDM1/pertuzumab(P); 43 H/P; and 67 pembrolizumab (pembro)].   This record also contains clinical data for these patients, including HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. RPPA endpoints assayed are from hormone receptor (n=4), HER family (n=14), cell cycle/proliferation (n=20), immune (n=18), DNA repair deficiency (DDR; n=15), AKT/mTOR/PI3K (n=7), apoptosis/autophagy (n=10), IGF1R (n=6), TIE/ANG (n=4), growth/survival/metabolism (n=22) and RTK (n=19) pathways.  For gene expresson data for all 736 patients with RPPA data, plus an additional 150 patients for a total 987 patients from 10 arms of  I-SPY2 (mRNA component of the I-SPY2-990 Data Resource), see the companion GEO record/subseries GSE194040.

overall_design:
Reverse phase protein array (RPPA) array run on isolates from pre-treatment breast cancer biopsy samples that were first LCM-enriched for epithelial cells.
The sample characteristics and their values represent:
HER2: the status of the HER2 gene. 1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response
Arm: arm of the trial per patient, detailing treatment during taxol-phase of protocol:
Paclitaxil (Control arm: HER2- subset); Paclitaxil + Trastuzumab (Control arm: HER2+ subset); Paclitaxel + ABT-888 (veliparib) + Carboplatin; Paclitaxel + AMG-386 (AMG-386 arm: HER2- subset); Paclitaxel + AMG-386 + Trastuzumab (AMG-386 arm: HER2+ subset); Paclitaxel + MK-2206 (MK-2206 arm: HER2- subset); Paclitaxel + MK-2206 + Trastuzumab (MK-2206 arm: HER2+ subset); Paclitaxel + Neratinib;  Paclitaxel + Pembrolizumab; Paclitaxel + Pertuzumab + Trastuzumab; or T-DM1 + Pertuzumab.  All patients also received subsequent doxorubicin + cyclophosphamide.
Arm (short name): abbreviated name of treatment arm in the trial per patient (n=8 arms) - Control, VC, AMG-386, MK-2206, N, Pembro, Pertuzumab, TDM1/P
RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.

first: Julia

last: Wulfkuhle

first: Emanuel

last: Petricoin III

last: van ‘t Veer


title: Induction of mouse totipotent stem cells by a defined chemical cocktail [ATAC-seq]

first: Pengcheng

last: Tan

overall_design: ATAC-seq of ciTotiSC and mESC. Each has two replicates.


title: HOX epi-mutations, driven by maternal SMCHD1 or LRIF1 haploinsufficiency, trigger homeotic transformations in genetically wildtype offspring

city: Singapore

first: Shifeng

last: Xue

address: 14 Science Drive 4

country: Singapore

institute: National University of Singapore

summary: The body plan of animals is laid out by an evolutionary-conserved HOX code which is colinearly transcribed after zygotic genome activation (ZGA). Here we report that SMCHD1, a chromatin-modifying enzyme needed for X-inactivation in mammals, is maternally required for timely HOX expression. Using zebrafish and mouse Smchd1 knockout animals, we demonstrate that Smchd1 haplo-insufficiency brings about precocious and ectopic HOX transcription during oogenesis and embryogenesis. Unexpectedly, wild-type offspring born to heterozygous knockout zebrafish smchd1 mothers exhibited patent vertebrate patterning defects. The loss of maternal Smchd1 was accompanied by HOX epi-mutations driven by aberrant DNA methylation. We further show that this regulation is mediated by Lrif1, a direct interacting partner of Smchd1, whose knockout in zebrafish phenocopies that of Smchd1.  Rather than being a short-lived maternal effect, HOX mis-regulation is stably inherited through cell divisions and persists in cultured fibroblasts derived from patients haploinsufficient for SMCHD1. We conclude that maternal Smchd1/Lrif1 sets up an epigenetic state in the HOX loci that can only be reset in the germline. Such an unusual inter-generational inheritance, whereby a phenotype can be one generation removed from its genotype, casts a new light on how unresolved Mendelian diseases may be interpreted.

overall_design: RNA-seq of wt and smchd1 maternal zygotic null zebrafish embryos at 4-cell and sphere stages

first: Thanh Thao Nguyen

last: Ly

first: Raunak

middle: S

last: Vijayakar

first: Jingyi

last: Chen

first: Joel

last: Ng

first: Ajay

last: Mathuru

first: Frederique

last: Magdinier

first: Bruno

last: Reversade


title: Expression data on lungs from Atf4wt/wt and Atf4D/D mice

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Expression data on isolated lung fibroblasts from Atf4wt/wt (LFBwt/wt) and Atf4D/D (LFBD/D) mice.

summary:
To identify the impact of ATF4 deletion on the expression of collagen-associated and fibroblast activation genes.
We used microarrays to detail the gene expression profile on lung fibroblasts post ATF4 deletion. Many genes to be differentially expressed, with a profound reduction in expression of collagen-associated and fibroblast activation genes in LFBD/D. We identified that ECM organization/degradation and collagen biosynthesis pathways to be the most impaired in LFBD/D.

overall_design: Lung fibroblasts were isolated from Atf4wt/wt (LFBwt/wt) and Atf4D/D (LFBD/D) mice and cultured until passage 2, for RNA extraction and hybridization on Affymetrix microarrays.

first: Ioannis

middle: I

last: Verginadis

first: Harris

last: Avgousti

first: Frank

last: Chinga

first: John

middle: W

last: Tobias


title: Landscape of open chromatin regions in Rice upon exposure to abiotic stresses

status: Public on May 24 2022

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

summary: The goal of the study is to illustrate how various abiotic stresses reshape the chromatin architecture of the Rice genome to fine tune gene expression.

overall_design: Oryza sativa L. Japonica nipponbare was grown in a plant growth chamber (Conviron®) at 28°C under a photoperiod of 16 h/8 h. 14-day old seedlings were subjected to heat (42°C for 30 min and 3 h), cold (4°C for 12 h and 24 h), and salt (250 mM NaCl for 2 h and 6 h) stress. The 14-day old seedlings grown at 28°C were taken as the control sample. Open chromatin was extracted using Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE-seq) from two biological replicates. RNA-seq was performed on two biological replicates

middle: K

first: Somya

last: Singh

first: Manu

last: Agarwal

first: Karel

last: Riha


title: Bone marrow-derived macrophages from a murine model of Sjögren's syndrome demonstrate an aberrant, inflammatory response to apoptotic cells

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

summary: We report that bone marrow derived macrophages from our Sjögren's syndrome mouse model exhibit an elevated inflammatory response to both apoptotic cells and TLR stimuli according to RNA-Seq data and pathway anyalysis

overall_design: Bone marrow derived macrophages from our Sjögren's syndrome model and B6 controls were treated with apoptotic cells or CpG and changes in transcriptome were reported

first: Richard

last: Witas

first: Yiran

last: Shen


title: Expression data on freshly isolated lungs from Atf4wt/wt and Atf4D/D mice.

summary:
Since acute deletion of host ATF4 caused a significant tumor-inhibitory phenotype, and since activated CAFs also play a critical role in the establishment of the metastatic niche we speculated that ATF4 deficiency could also result in an inhibitory effect on lung metastasis. Thus, we examined the impact of host ATF4 deletion in the pre-metastatic niche by analyzing  gene expression changes on lungs from Atf4wt/wt and Atf4D/D mice at 4 weeks post tamoxifen treatment.
Genome-wide microarray analysis identified 21 genes to be significantly downregulated in Atf4D/D lungs, including collagen-associated genes. Also, pathway analysis on the most dysregulated genes revealed defects on collagen formation, extracellular matrix organization and integrin cell surface interactions pathways.

overall_design: Lungs were isolated from Atf4wt/wt and Atf4D/D mice for RNA extraction and hybridization on Affymetrix microarrays.


title: AhR in the amelioration of Autoimmune Hepatitis

status: Public on May 23 2022

city: Columbia

first: Alkeiver

last: Cannon

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary: 10X Genomics Chromium Next GEM Single cell V(D)J reagent kits v1.1 was used to process single cell suspensions from Naïve or Concanavalin A exposed mice treated with vehicle, TCDD, or FICZ. The V(D)J enrichment was omitted.

overall_design: Single cell suspensions were isolated from liver mononuclear cells 24 hours after ConA exposure. Libraries were constructed and sequenced from either Naïve mice or those exposed to Concanavalin A and subsequently treated with vehicle, TCDD, or FICZ.

first: Bryan

last: Holloman

first: Kiesha

last: Wilson

first: Kathryn

last: Miranda

first: Prakash

last: Nagarkatti

first: Mitzi


title: Expression data from shVDAC1 in Huh7

city: Nantong

first: Yu

last: Zhang

address: Xisi road 20th

institute: Affiliated hospital of Nantong University

summary:
Our previous study has shown that the expression of voltage-dependent anion channel 1 (VDAC1) is closely related to the tumorigenesis and progression of HCC.Nevertheless, tumorigenesis and progression of HCC are complex processes, and the specific mechanism of VDAC1 affecting the proliferation and invasion of HCC has not yet been elucidated.
To further study the role of downstream related molecules of VDAC1, we utilized the Affymetrix GeneChip system to analyze the downstream gene expression profile of VDAC1

overall_design: There were  two groups, normal cell line group (NC) and VDAC1 knockdown group (KD). 3 samples per group.

first: Zhong

last: Chen


title: Lung epithelial CYP1 activity regulates aryl hydrocarbon receptor dependent allergic airway inflammation

city: Munich

first: Ulrich

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

summary: Transcriptional analysis of human lung epithelial cells indicates a functional link of AhR to barrier protection/inflammatory mediator signaling upon allergen challenge.

overall_design: Primary normal bronchial epithelial cells (NHBEs) were incubated eihter medium or AhR inhibitor CH223191 (1µM/mL) for 2 hours, afterwards with IL-4 (50ng/mL)  and house dust mite extract (40µg/mL)  for 6 hours.

first: F

last: Alessandrini

first: R

last: de Jong

first: M

last: Wimmer

first: A-M

last: Maier

first: I

last: Fernandez

last: Hils

first: J

last: Buters

first: T

last: Biedermann

first: U

first: C

last: Hoffmann

last: Esser-von Bieren

middle: B

last: Schmidt-Weber

last: Ohnmacht


title: High-throughput RNA Sequencing of BMDM of Mus musculus stimulated by C. auris or C. albicans

status: Public on May 21 2022

city: Shanghai

first: chen

middle: xiao

last: qing

state: 上海

address: Life Science Laboratory Building, 320 Yueyang Road, Xuhui District,

department: Institut Pasteur of Shanghai ,CAS

institute: Pathogenic Fungal Infection and Host Immunity Research Group

summary: Candida auris has been globally recognized as a multidrug-resistant human fungal pathogen that contributes for the worldwide occurrence of nosocomial outbreaks. It has been reported that C. auris was able to avoid neutrophil attack, suggestive of an impaired innate immune response. Whether C. auris evades the innate immune recognition of BMDM (bone marrow derived macrophage) remains poorly understood, and as for well-known Candida species -C. albicans, it can trigger immune response. To determine whether occurs difference between immune response stimulated by C. auris or C. albicans, we performed mRNA-seq of BMDM stimulated by C. auris or C. albicans.

overall_design: RNAsequencing profiles of  BMDMs stimulated for 3h and 6h with live C. albicans (SC5314), C. auris (BJCA001), and PBS control.

first: D

last: Zhou

first: Y

last: Wang

last: Zou


title: Generation of specialized blood vessels via lymphatic transdifferentiation

status: Public on May 19 2022

city: Rehovot

first: Yaara

last: Tevet

state: Israel

address: Hertzel 234

department: Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the  vascular system, endothelial cells (ECs) of blood and lymphatic vessels (LVs) differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins , lymphatic ECs (LECs) themselves are not known to generate other cell - types . Here, we  u s e recurrent imaging and lineage - tracing of ECs in zebrafish anal fins (AF) from early development  through adulthood , to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover, we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs, uncovering a link between cell ontogeny and  functionality. We further use scRNA - seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally, we show that akin to its normal  development, the vasculature is re - derived from lymphatics during AF regeneration,  demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall, our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation, and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs

overall_design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells

first: Rudra

middle: N

last: Das

first: Stav

last: Safriel

first: Yanchao

last: Han

first: Noga

last: Moshe

first: Giuseppina

last: Lambiase

first: Ivan

last: Bassi

first: Julian

last: Nicenboim

first: Matthias

last: Bruckner

first: Dana

last: Hirsch

first: Raya

last: Eilam-Altstadter

first: Weibke

last: Herzog

first: Roi

last: Avraham

first: Kenneth

middle: D

last: Poss

first: Karina

last: Yaniv


title: High throughput, label-free isolation of circulating tumor cell clusters in meshed microwells

city: Atlanta

first: A. Fatih

last: Sarioglu

state: GA

address: 315 Ferst Dr. NW

department: Electrical and Computer Engineering

institute: Georgia Institute of Technology

summary: Extremely rare circulating tumor cell (CTC) clusters are both increasingly appreciated as highly metastatic precursors and virtually unexplored. Technologies are primarily designed to detect single CTCs and often fail to account for the fragility of clusters or to leverage cluster-specific markers for higher sensitivity. Meanwhile, the few technologies targeting CTC clusters lack scalability. Here, we introduce the Cluster-Wells, which combines the speed and practicality of membrane filtration with the sensitive and deterministic screening afforded by microfluidic chips. The >100,000 microwells in the Cluster-Wells physically arrest CTC clusters in unprocessed whole blood, gently isolating virtually all clusters at a throughput of >25 mL/h, and allow viable clusters to be retrieved from the device. Using the Cluster-Wells, we isolated CTC clusters ranging from 2–100+ cells from prostate and ovarian cancer patients and analyzed a subset using RNA sequencing. Routine isolation of CTC clusters will democratize research on their utility in managing cancer.

overall_design: Gene expression profiling of circulating tumor cell clusters isolated from two metastatic prostate cancer patients, LNCaP and PC-3 prostate tumor cell lines, and white blood cells of heatlhy donors.

first: Mert

last: Boya

first: Tevhide

last: Ozkaya-Ahmadov

first: Brandi

middle: E

last: Swain

first: Chia-Heng

last: Chu

first: Norh

last: Asmare

first: Ozgun

last: Civelekoglu

first: Ruxiu

last: Liu

first: Dohwan

last: Lee

first: Sherry

last: Tobia

first: Shweta

last: Biliya

first: L

last: McDonald

first: Bassel

last: Nazha

first: Omer

last: Kucuk

first: Martin

middle: G

last: Sanda

first: Benedict

last: Benigno

first: Carlos

last: Moreno

first: Mehmet

last: Bilen

first: John

first: A


title: Expression data from shSMPDL3A in Huh7

first: Yu

last: Zhang

summary:
Our previous study has shown that the expression of SMPDL3A is closely related to the tumorigenesis and progression of HCC.Nevertheless, tumorigenesis and progression of HCC are complex processes, and the specific mechanism of SMPDL3A affecting the proliferation and invasion of HCC has not yet been elucidated.
To further study the role of downstream related molecules of SMPDL3A, we utilized the Affymetrix GeneChip system to analyze the downstream gene expression profile of SMPDL3A

overall_design: There were  two groups, normal cell line group (NC) and SMPDL3A knockdown group (KD). 3 samples per group.

first: Zhong

last: Chen


title: Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Alcohol induced increases in sperm Histone H3 lysine 4 trimethylation correlate with increased placental CTCF occupancy and altered developmental programming

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

summary: Using a mouse model, studies by our group reveal that paternal preconception alcohol intake affects offspring fetal-placental growth, with long-lasting consequences on adult metabolism. Here, we tested the hypothesis that chronic preconception male alcohol exposure impacts histone enrichment in sperm and that these changes are associated with altered developmental programming in the placenta. Using chromatin immunoprecipitation, we find alcohol-induced increases in sperm histone H3 lysine 4 trimethylation (H3K4me3) that map to promoters and presumptive enhancer regions enriched in genes driving neurogenesis and craniofacial development. Given the colocalization of H3K4me3 with the chromatin binding factor CTCF across both sperm and embryos, we next examined CTCF localization in the placenta. We find global changes in CTCF binding within placentae derived from the male offspring of alcohol-exposed sires. Furthermore, altered CTCF localization correlates with dysregulated gene expression across multiple gene clusters; however, these transcriptional changes only occur in male offspring. Finally, we identified a correlation between genomic regions exhibiting alcohol-induced increases in sperm H3K4me3 and increased CTCF binding in male placentae. Collectively, our analysis demonstrates that the chromatin landscape of sperm is sensitive to chronic alcohol exposure and that a subset of these affected regions exhibits increased placental CTCF enrichment.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H3K4me3 in alcohol-exposed mouse sperm and chromatin binding factor CTCF in placentae of male offspring at GD14.5

first: Yudhishtar

last: Bedi

first: Haiqing

last: Wang

first: Kara

last: Thomas

first: Alison

last: Basel

first: Julien

last: Prunier

first: Claude

last: Robert

first: Michael

middle: C

last: Golding


title: Gene expression in human breast cancer T47D cells associated with expression of PTH-AS, a lncRNA downstream of parathyroid hormone

city: Itabashi-ku

first: Miho

last: Akimoto

state: Tokyo

department: Department of Biochemistry

institute: Teikyo University

summary: To comprehensively analyze the effect of PTH-AS on gene expression, microarray analysis was performed using human breast cancer T47D cells expressing PTH-AS. The gene expression levels of full-length PTH-AS expressing T47D cells (T47D-PA6) and vector control (T47D-VC1) or incomplete PTH-AS expressing T47D cells (T47D-PA5) were compared. As a result, 1453 genes were differentially expressed in his T47D-PA6 compared to T47D-VC1. Except for genes whose expression was altered in T47D-PA5 cells expressing incomplete PTH-AS, PTH-AS expression in T47D cells upregulated 914 genes and downregulated 600 genes. Many of the altered genes have been classified as immune-related biological processes. Particularly striking was the significant upregulation of JAK-STAT pathway-related genes, including the interferon-related DNA damage resistance signature (IRDS) that promotes cancer.

overall_design: To eliminate artifacts from extracellular gene transfer, full-length PTH-AS-expressing T47D cells (T47D-PA6) were compared with vector control (T47D-VC1) as well as T47D cells expressing incomplete PTH-AS (T47D-PA5) .

first: Tomoki

last: Okazaki


title: RNA seq after RNA pol III manipulation by Brf1 and Maf1 knockdown, Maf1 overexpression and ML60218 treatment in ST2 cells before, and during differentiation into osteoblasts

status: Public on May 20 2022

city: Houston

first: Ellen

last: Busschers

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Maf1, a key repressor of RNA polymerase III-mediated transcription, has been shown to promote mesoderm formation in vitro. Here, we show, for the first time, that Maf1 plays a critical role in the regulation of osteoblast differentiation. We also found that, in contrast to MAF1 overexpression, other perturbations that repress RNA pol III transcription, including Brf1 knockdown and the chemical inhibition of RNA pol III by ML-60218, inhibited osteoblast differentiation. RNA-seq was used to determine the basis for these opposing actions on osteoblast differentiation. RNA polymerase III-dependent transcription was manipulated in ST2 stromal cells by Brf1 or Maf1 knockdown, ML-60218 treatment and MAF1 overexpression. The ST2 cells were then tested for their capacity to differentiate into osteoblasts. RNA-seq was performed on day 0, before differentiation and day 4 after differentiation medium was added. The modalities used to perturb RNA pol III transcription resulted in distinct changes gene expression, indicating that this transcription process is highly sensitive and triggers diverse gene expression programs and phenotypic outcomes. Specifically, Maf1 induced genes in ST2 cells known to promote osteoblast differentiation. Furthermore, genes that are induced during osteoblast differentiation displayed codon bias.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ST2 cells before (d0), and during (d4) osteoblast differentiation. cells were manipulated by shBrf1 (=shBr) or SCRB control, shMaf1(=shMA) or SCRM control, pinducer20-MAF1 (=MAF1) or pInducer20-empty control (=pInd), 40uM ML-60218 treatment (=ML) or DMSO control. each condition has 3 replicates

last: Phillips

first: Naseer

last: Ahmad

first: Li

last: Sun

first: James

last: Iben

first: Christopher

middle: J

last: Walkey

first: Aleksandra

last: Rusin

first: Tony

last: Yuen

first: Clifford

last: Rosen

first: Ian

last: Willis

first: Mone

last: Zaidi

first: Deborah

middle: L

last: Johnson


title: Comparison of different T cell extracellular vesicles derived from activated, and expanded primary CD4+ and CD8+ human T cells.

city: Oxford

first: Ashwin

last: Jainarayanan

address: Roosevelt Dr, Headington, Oxford OX3 7FY

department: KIR, NDORMS

institute: University of Oxford

summary: The present dataset contains small non-coding RNA sequencing data from extracellular vesicles steadily released by donor matched, cultured human CD4+ and CD8+ T cells and from extracellular vesicles released within the immunological synapse. The dataset includes RNA sequencing files collected within two independent sequencing facilities. Control samples (S0) are included to correct the sequencing data from noise in the case of EVs released in the synapse (S1).

overall_design: Side-by-side comparison of microRNA concealed in steadily released EVs and EVs released within the immunological synapse of donor matched, syngeneic, activated, and expanded primary CD4+ and CD8+ human T cells.

first: Pablo

middle: F

last: Céspedes

first: Lola

last: Fernández-Messina

first: Francisco

last: Sanchez-Madrid

last: Dustin


title: Effect of bile duct ligation on growth factors expression from mouse whole extrahepatic bile duct (EHBD) tissue and cultured mouse neonatal fibroblasts and bile duct organoids

city: Ann Arbor

first: Nureen Hanisah

last: Mohamad Zaki

state: Michigan

address: 109 Zina Pitcher Pl, RM2438

department: Internal Medicine, GI

institute: University of Michigan

summary: Dynamic changes in growth factor expression is observed after bile duct ligation at different time points compared to sham-treated mice, corresponding to increase in biliary cell proliferation and repair

overall_design: One sample is analyzed for every sham and bile duct ligation groups after 12, 24, and 48 hours of ligation, and one sample each for mouse bile duct organoid and neonatal fibroblasts culture. All samples were obtained from wildtype C57/BL6 mice.

first: Nataliya

last: Razumilava

first: Nureen

last: Hanisah

first: Mohamad

last: Zaki


title: Anchor-Based Bisulfite Sequencing determines genome-wide DNA methylation

city: Carlsbad

first: Benjamin

last: Delatte

address: 1914 Palomar Oaks Way STE 150

department: Advanced Research

institute: Active Motif

summary: Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling; however, WGBS is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). We show that ABBS captures accurate DNA methylation information in Escherichia coli and mammalian cells, while requiring approximately 20 times fewer sequencing reads than WGBS. The ABBS protocol is simple and can be performed in a single day.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: WGBS and ABBS on E. coli and K562 cells


title: Arylhydrocarbon receptor and the cytochrome P450 enzyme CYP1B1 prevent exacerbation of allergic airway inflammation

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

institute: Helmholtz Center Munich

summary: Signaling via the arylhydrocarbon receptor (AhR) is thought to contribute to exacerbation of allergic asthma by anthropogenic pollution. The physiological role of AhR and its downstream targets CYP1 family members upon exposure to aeroallergens remain unknown. We seek to characterize the role of the AhR pathway for the regulation of allergic airway inflammation (AAI). We employed knockout animals of the AhR and its downstream target cytochrome P450 enzymes CYP1A1, CYP1A2 and CYP1B1 and subjected them to preclinical allergic asthma models (ragweed and house dust mite) to assess the role of AhR and CYP1 family members in allergic airway inflammation. Histological, transcriptional and functional assays were used to uncover relevant cell types and mechanistic insights. In the ragweed model, AhRKO/KO and CYP1B1KO/KO but not CYP1A2 KO/KO or CYP1A2KO/KO animals showed exacerbation of AAI including elevated infiltration of cells in the bronchoalveolar lavage fluid and increased serum levels of IgE and allergen-specific IgG1. AhR KO/KO and CYP1B1KO/KO animals showed also more severe reactions in HDM-induced allergic AAI. Bone marrow chimeras as well as qPCR analysis and immune fluorescence histology indicate that expression of CYP1B1 in non-hematopoietic cells – presumably lung epithelial cells – is necessary to prevent exacerbation of HDM-induced AAI. Mechanistically, we show that CYP1B1 deficiency leads to enhanced expression and activity of CYP1A1 in lung epithelial cells and thus potentially to deprivation from endogenous AhR ligands. Transcriptional analysis of primary lung epithelial cells indicates a functional link of the AhR to regulation of circadian clock genes at baseline and massive alteration of gene expression upon allergen exposure.

overall_design: mRNA profiles of FACS-purified single alive CD45-EpCAM+ lung epithelial cells of wildtype, AhR-KO/KO and CYP1B1-KO/KO mice at steady state or after houst dust mite allergy

first: Renske

last: de Jong

first: Ann-Marie

last: Maier

first: Christian

last: Hoffmann


title: Distinct cellular tools of mild hyperthermia-induced acquired stress tolerance in Chinese Hamster Ovary cells

status: Public on May 18 2022

city: Szeged

first: Zsolt

last: Torok

address: Temesvari krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

summary: Mild stress could help cells to survive more severe environmental or pathophysiological conditions. In the current study, we investigated the cellular mechanisms which contribute to the development of stress tolerance upon a prolonged (0-12h) fever-like (40 °C) or a moderate (42.5 °C) hyperthermia in mammalian CHO cells. Our results indicate that mild heat triggers a distinct, dose dependent remodeling of the cellular lipidome followed by the expression of heat shock proteins only at higher heat dosages. A significant elevation in the relative concentration of sat-urated membrane lipid species, specific lysophosphatidylinositol and sphingolipid species sug-gests prompt membrane microdomain reorganization and an overall membrane rigidification in response to the fluidizing heat in a time dependent manner. RNAseq experiments reveal that mild heat initiate endoplasmic reticulum stress-related signaling cascades resulting in lipid re-arrangement and ultimately in an elevated resistance against membrane fluidization by benzyl alcohol. To protect cells against lethal, protein denaturing high temperatures the classical heat shock protein response was required. The different layers of stress response elicited by different heat dosages highlights the capability of cells to utilize multiple tools to gain resistance against or to survive lethal stress conditions.

overall_design: CHO cells were seeded on culture plates for 24h prior to heat treatments which included 4 bio-logical repeats of 4 sample groups (37 °C, 40 °C for 1 h, 6 h and 42.5 °C for 1 h)

first: Ádám

last: Tiszlavicz

first: Imre

last: Gombos

first: Mária

last: Péter

first: Zoltán

last: Hegedűs

first: Ákos

last: Hunya

first: Barbara

last: Dukic

first: István

last: Nagy

first: Begüm

last: Peksel

first: Gábor

last: Balogh

first: Ibolya

last: Horváth

first: László

last: Vígh

last: Török


title: Activity of Estrogen Receptor β Agonists in Therapy-Resistant Estrogen Receptor-Positive Breast Cancer

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: We found by RNA seq analysis that the expression of the cyclin D1 gene, the classic target of estrogen-stimulated transcription through an AP1 response element, negatively correlated with that of ERβ/ESR2 as measured using Spearman correlation coefficient (rho = -0.45, p = 0.005). ERβ/ESR2 expression was also negatively correlated with that of ERα/ESR1 (rho = -0.35, p = 0.033). However, ERβ/ESR2 mRNA expression positively correlated with that of IGFBP4 (rho = 0.58, p < 0.001) and CXCL12 (rho = 0.54, p < 0.001). The univariate Cox proportional hazards estimate for overall survival by ESR2 expression was 0.54 (95% CI 0.06, 5.22), suggesting a positive trend that did not reach statistical significance in this numerically limited cohort .

overall_design: Thirty-seven patients with metastatic ERα+/HER2- breast cancer were included in this study. All the patients in this cohort were female with a median age of 56 years (range 27-78). The patients were predominantly Caucasian (35, 95%) and most women were postmenopausal (23, 66%). The objective was to determine the mRNA expression levels of the genes which are targets of ER-AP1 mediated transcription and AP1 independent ER mediated transcription including CCND1, MYC, IGF-1, Bcl-2, MMP-1, FN1, IGFBP-4, E2F4, CXCL12, PGR, EBAG9, and TRIM25 and correlated with ESR1 and ESR2.

first: Mathew

last: Cherian


title: mRNA, ncRNA-seq and miRNA-seq of AGS cellline and AGS cellline with neutrophil extracellular traps

city: Harbin

first: Yanan

last: Jiang

address: 157 Baojian Road

department: Pharmacology

institute: Harbin Medical University

overall_design: ncRNA-seq and miRNA-seq of AGS cellline (3 replicates as control)  and AGS cellline with neutrophil extracellular traps(3 replicates as treatment).

first: Changjian

last: Li


title: Nanchangmycin exerts antifibrotic activity by inhibiting collagen production, migration, and proliferation of hepatic stellate cells

city: Boston

first: Alan

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: We report the RNA sequencing results of human primary hepatic stellate cells (HSCs) treated with DMSO or 1 µM nanchangmycin (NCMC) for 48 hours. We find that multiple HSC activity and liver fibrosis related gene signatures, including ECM-related gene signatures, are negatively enriched in nanchangmycin treated HSCs.

overall_design: Examination of mRNA expression by RNA sequencing in DMSO or nanchangmycin treated hepatic stellate cells.

first: Wenyang

first: Raza-Ur

last: Rahman

first: Sean

last: Moran


title: RBM33

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: RBM33 eCLIP

summary: Enhanced UV crosslinking immunoprecipitation (eCLIP) was performed to identify direct RNA targets of RBM33

overall_design: 20 million HCT116 or HEK293T cells were seeded in a 15 cm dish and reverse transfected with 40 µg pLJM1-EV or pLJM1-FH-RBM33 plasmid using Fugene HD (Promega). Media was changed 24 hours later. 48 hours after transfection, UV crosslinking was performed on ice at 250 nm (400 mJ/cm2) in a Spectrolinker XL-1500 (Spectronics). Cells were scraped in PBS, pelleted, snap-frozen in liquid nitrogen and stored at -80ºC until needed. Monoclonal FLAG M2 antibody (F1804, Sigma) conjugated to Dynabeads Protein G (Invitrogen) was used to immunoprecipitate FH-RBM33. For each cell line, duplicate size-matched input and IP samples were prepared and sequenced.

first: Anu

last: Thomas

first: Frederick

last: Rehfeld

first: He

last: Zhang

first: Mohammad

last: Goodarzi

middle: T


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation

status: Public on May 17 2022

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation [CHi-C]

summary: The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. We used Hoxd genes and their biphasic regulation during limb development as a paradigm, since they are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced at the time when the neighboring TAD starts to activate its enhancers in distal limb cells. We introduced a strong distal limb enhancer into the ‘proximal limb TAD’ and found that its new context strongly suppresses its distal specificity, even though it continues to be bound by HOX13 transcription factors, which normally are responsible for this activity. Using local genetic alterations and chromatin conformation measurements, we see that the enhancer is capable of interacting with target genes, with a pattern comparable to its adoptive neighborhood of enhancers. Its activity in distal limb cells can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the local chromatin context, which can exert a dominant control over its activity.

overall_design: wild type (wt) and mutant (542) tissue samples were collected from E12.5 mouse embryos. Proximal limb, distal limb, and forebrain domains were collected and processed as described in Buenrostro 2013.

first: Christopher

last: Bolt

first: Aurélie

last: Hintermann

first: Bénédicte

last: Mascrez

first: Antonella

last: Rauseo

first: Guillaume

last: Andrey

first: Denis

last: Duboule


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation [CUT&RUN]


title: The role of CTH in the innate immune response to H. pylori

city: Nashville

first: Keith

last: Wilson

state: TN

address: 2215B Garland Ave., 1015B MRB IV

institute: Vanderbilt University Medical Center

summary: RNA sequencing by Illumina NovaSeq6000 was performed on F4/80 positive cells isolated from the gastric tissue of mice infected or not with H. pylori SS1 for 16 weeks to determine the role of CTH in the innate immune response in the stomach.

overall_design: Gastric macrophages were isolated from 5 infected mice per genotype and the controls were a pool of 10 uninfected mice per genotype

first: Yvonne

last: Latour

first: Alain

middle: P

last: Gobert


title: The expression levels of mRNAs between miR-124-3p knockdown group and negative control group in mouse retina at postnatal day 9

city: Guangzhou

first: YISHEN

last: WANG

address: No.54 Xianlie South Road, Yuexiu District

institute: State Key Laboratory of Ophthalmology, Image Reading Center, Zhongshan Ophthalmic Center, Sun Yat-Sen University

summary: Although the miR-124a-3p knockdown mouse exhibited neuronal dysfunction and dysmaturation by disinhibition of Lhx2, its downstream responses in mouse retinal development after birth were still relatively deficient at the transcriptome level. In our previous study, miR-124-3p exhibited a significantly increasing trend after birth, and its related pathways predicted by bioinformatics analysis were associated with biological processes that may play crucial roles in mouse retinal development. To gain insight into its downstream processes, RNA-Seq was used to obtain the expression profile of mRNA transcripts after the knockdown of miR-124-3p.

overall_design: Retinal mRNA profiles of 6-day old miR-124-3p knockdown (anti-miR-124) and negative control (NC) mice

first: Y

last: Wang


title: Spaceflight analogue culture enhances the host-pathogen interaction between Salmonella and a 3-D biomimetic intestinal co-culture model

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

summary: Physical forces associated with spaceflight and spaceflight analogue culture regulate a wide range of physiological responses by both bacterial and mammalian cells that can impact infection. However, our mechanistic understanding of how these environments regulate host-pathogen interactions in humans is poorly understood. Using a spaceflight analogue low fluid shear culture system, we investigated the effect of Low Shear Modeled Microgravity (LSMMG) culture on the colonization of Salmonella Typhimurium in a 3-D biomimetic model of human colonic epithelium containing macrophages. RNA-seq profiling of stationary phase wild type and hfq mutant bacteria alone indicated that LSMMG culture induced global changes in gene expression in both strains and that the RNA-binding protein Hfq played a significant role in regulating the transcriptional response of the pathogen to LSMMG culture. However, a core set of genes important for adhesion, invasion, and motility were commonly induced in both strains. LSMMG culture enhanced the colonization (adherence, invasion and intracellular survival) of Salmonella in this advanced model of intestinal epithelium using a mechanism that was independent of Hfq. Although S. Typhimurium hfq mutants are normally defective for invasion when grown as conventional shaking cultures, LSMMG conditions unexpectedly enabled high levels of colonization by an isogenic hfq mutant. In response to infection with either the wild type or mutant, host cells upregulated transcripts involved in inflammation, tissue remodeling, and wound healing during intracellular survival. Interestingly, infection by the hfq mutant led to fewer transcriptional differences between LSMMG- and control-infected host cells relative to infection with the wild type strain. This is the first study to investigate the effect of LSMMG culture on the interaction between S. Typhimurium and a 3-D model of human intestinal tissue. These findings advance our understanding of how physical forces can impact the early stages of human enteric salmonellosis.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Wild type (WT) Salmonella enterica serovar Typhimurium (S. Typhimurium) and an isogenic hfq deletion mutant (hfq) were grown to stationary phase in Rotating Wall Vessel (RWV) bioreactors positioned in the Low Shear Modeled Microgravity (LSMMG - sample names contain the term LFS) or control orientation. A subset of the samples analyzed in this dataset are triplicate samples of these bacteria alone (no host cells) that were fixed just prior to infection and analyzed using the Illumina NexSeq platform. Comparisons were made between the LSMMG cultures of each strain to the same strain grown as a re-oreinted control. Comparisons were also made between wild type and mutant bacteria under the LSMMG culture condition only or the control culture condition only. The second set of samples in the dataset are the host transcriptional responses to infection with these RWV-cultured strains during adherence (30 minutes post-infection), invasion (3 hours post-infection) and survival (24 hours post-infection). The model host in this study was an RWV-derived, three-dimensional (3-D) intestinal co-culture model comprised of colonic epithelial cells (HT-29) and macrophages (U937).

first: Jiseon

last: Yang

first: Karla

last: Franco

first: Shanshan

first: Trenton

last: Davis

first: Bruce

last: Aronow

first: Heather

last: Bean

first: Richard

middle: R

first: Rebecca

last: Forsyth

first: C

middle: M

last: Ott

first: Sandhya

last: Gangaraju

first: Bianca

last: Kang

first: Brian

last: Hanratty

first: Seth

last: Nydam

first: Wei

last: Kong

first: Jason

last: Steel

first: Cheryl

middle: A

last: Nickerson

first: Eric

last: Nauman

first: Kristina

last: Buss


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation [nCATS]

first: Lucille

last: Lopez-Delisle

first: Christopher

last: Bolt

first: Aurélie

last: Hintermann

first: Bénédicte

last: Mascrez

first: Antonella

last: Rauseo

first: Guillaume

last: Andrey

first: Denis

last: Duboule


title: Gene expression profile at single cell level of whole Drosophila melanogaster embryos at three developmental stages

status: Public on May 16 2022

city: Eugene

first: Austin

last: Seroka

state: Oregon

address: 1440 Franklin Blvd

department: Institute of Neuroscience

institute: University of Oregon

summary: Embryonic development results in the production of distinct tissue types, and different cell types within each tissue. A major goal of developmental biology is to uncover the “parts list” of cell types that comprise each organ. Here we perform single cell RNA sequencing (scRNA-seq) of the Drosophila embryo to identify the genes that characterize different cell and tissue types during development. We assay three different timepoints, revealing a coordinated change in gene expression within each tissue. Interestingly, we find that the elav and mhc genes, whose protein products are widely used as markers for neurons and muscles, respectively, show broad pan-embryonic expression, indicating the importance of post-transcriptional regulation. We next focus on the central nervous system (CNS), where we identify genes characterizing each stage of neuronal differentiation: from neural progenitors, called neuroblasts, to their immediate progeny ganglion mother cells (GMCs), followed by new-born neurons, young neurons, and the most mature neurons. Finally, we ask whether the clonal progeny of a single neuroblast (NB7-1) share a similar transcriptional identity. Surprisingly, we find that clonal identity does not lead to transcriptional clustering, showing that neurons within a lineage are diverse, and that neurons with a similar transcriptional profile (e.g. motor neurons, glia) are distributed among multiple neuroblast lineages. Although each lineage consists of diverse progeny, we were able to identify a previously uncharacterized gene, Fer3, as an excellent marker for the NB7-1 lineage. Within the NB7-1 lineage, transcriptional clusters are identifiable in neuroblasts and neurons, and each cluster is composed of current temporal transcription factor (e.g. Hunchback, Kruppel, Pdm, and Castor), novel temporal factors, and/or targets of the temporal transcription factors. In conclusion, we have characterized the embryonic transcriptome for all major tissue types and for three stages of development, as well as the first transcriptomic analysis of a single, identified neuroblast lineage, finding a lineage-enriched transcription factor.

overall_design:
Whole embryos were staged according to developmental windows of interest, dissociated and run through the 10X 3' mRNA seq pipeline
Please note that processed data was generated from both Lane 1&2 samples and is linked to the corresponding *Lane 1* sample records.

first: Sen-Lin

last: Lai

first: Chris

middle: Q

last: Doe


title: Cell cycle states of pluripotent cells dictate lineage decisions

city: jerusalem

first: Muhammad

last: Awawdy

address: The Hebrew University, The Edmond J. Safra Campus - Givat Ram

institute: Hebrew university of jerusalem

summary: Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling, to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based differentiation protocol we show that only cells in the G2/M phase are capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Mechanistically, we show that Esrrb is a potent XEN state inducer as it is predominantly upregulated during G2/M phase, and cells engineered to overexpress Esrrb during G1 phase forced the cells to become XENs. Interestingly, this phenomenon is unique to the pluripotency ground state as sorting cells after 48 hours of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between cell-cycle states of pluripotent cells and lineage decisions, emphasizing the regulatory role of cell cycle during exit from pluripotency and can be further expand our understanding of early differentiation events.

overall_design: We used R1 mESC line, each experiment includes technical duplicats.we established R1 clones with Fucci, sorted according to cell cycle stage at 0, 2 , 4 days of RA differentiation - then bulk or single cell analysis. We also used R1-fucci-Over expression ESRRB cells and zhbtc4 esrrb KO cells and preformes single cell analysis on them.

first: Sapir

last: Herchcovici Levy

first: Lee

last: Arnon

first: Sharon

last: Feldman

first: Adi

last: Alajem

first: Shlomtzion

last: Lahav

first: Danny

last: Bavli

first: Xue

last: Sun

first: Yossi

last: Buganim

first: Oren

last: Ram


title: RNA expression changes after tRF-3004b over-expression in HEK293T

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

summary: We compared gene expression after human tRF-3004b (from tRNA-Gln, naming based on tRFdb: http://genome.bioch.virginia.edu/trfdb/) over-expression.

overall_design: HEK293T Ctrl non-targeting RNA and tRF-3004b overexpression

first: Shekhar

last: Saha

first: Briana

last: Wilson

first: Rohan

last: Parikh

first: Anindya

last: Dutta


title: RNA-fractionation sequencing

first: Joshua

last: Mendell

summary: To identify potential RBM33 substrates, we performed whole transcriptome sequencing (RNA-seq) on nuclear and cytoplasmic RNA from RBM33 wild-type and knockout cells

overall_design: 400 000 WT, RBM33 KO-1, or RBM33 KO-2 HCT116 cells were seeded in 6-well plates. For each replicate, 48 hours later, one well was subjected to total RNA extraction and one well to nuclear-cytoplasmic fractionationFractionation was performed as described previously (Lee et al., 2016). Briefly, cells were collected by trypsinization and lysed in 175 µL RLN1 buffer [50 mM Tris-HCl pH 8, 140 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, and 1:1000 SUPERase In RNase inhibitor (Thermo Fisher Scientific)]. Following a 5-minute incubation on ice, the sample was centrifuged at 300 g for 2 minutes. The supernatant, representing the cytoplasmic fraction, was collected and centrifuged at 16000 g for 5 minutes to clear debris. The initial pellet, representing the nuclear fraction, was gently resuspended in 500 µL RLN1 and centrifuged at 1000 g for 5 minutes to wash. The pellet was then resuspended in 175 µL RLN2 buffer [50 mM Tris-HCl pH 8, 500 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, and 1:1000 SUPERase In RNase inhibitor (Thermo Fisher Scientific)]. RNA was extracted from each of these fractions by Trizol in combination with the miRNeasy mini kit (Qiagen) with an on-column DNase digestion.

first: Anu

last: Thomas

first: Frederick

last: Rehfeld

first: He

last: Zhang

first: Mohammad

last: Goodarzi


title: The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intra-cellular communication after learning

first: Johannes

last: Gräff

state: Vaud

address: Rte Cantonale

institute: École Polytechnique Fédérale de Lausanne


title: MicroRNA-21 Promotes Pancreatic β cell Function through Modulating Glucose Uptake

city: Qingdao

first: Bin

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: Pancreatic β cell dysfunction greatly contributes to the pathogenesis of type 2 diabetes. MiR-21 has been shown to be induced in the islets of glucose intolerant patients and type 2 diabetic mice. However, the role of miR-21 in the regulation of pancreatic β cell function remains largely elusive. In the current study, we studied the pathway by which miR-21 regulates glucose-stimulated insulin secretion utilizing mice lacking miR-21 in their β cells (miR-21βKO). We found that miR-21βKO mice developed glucose intolerance due to impaired glucose-stimulated insulin secretion. Mechanistic studies revealed that miR-21 enhances glucose uptake and subsequently promotes insulin secretion by up-regulating Glut2 expression in a miR-21-Pdcd4-AP-1 dependent pathway. Over-expression of Glut2 in knockout islets resulted in rescue of the impaired glucose-stimulated insulin secretion. Furthermore, we demonstrated that delivery of miR-21 into the pancreas of type 2 diabetic db/db mice is able to promote Glut2 expression and significantly reduce blood glucose level. Taking together, our results reveal that miR-21 in islet β cell promotes insulin secretion and support a role for miR-21 in the adaptation of pancreatic β cell function in type 2 diabetes.

overall_design: Examination  RNA expression  in WT&miR-21βKO  islet

first: Qingguo

last: Ruan

first: Ruiling

last: Liu


title: The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intra-cellular communication after learning [ChIP-seq]

summary: Long-term memory formation relies on synaptic plasticity, activity-dependent transcription and epigenetic modifications. Multiple studies have shown that HDAC inhibitor (HDACi) treatments can enhance individual aspects of these processes, and thereby act as putative cognitive enhancers. However, their mode of action is not fully understood. In particular, it is unclear how systemic application of HDACis, which are devoid of substrate specificity, can target pathways that promote memory formation. In this study, we explore the electrophysiological, transcriptional and epigenetic responses that are induced by CI-994, a class I HDAC inhibitor, combined with contextual fear conditioning (CFC) in mice. We show that CI-994-mediated improvement of memory formation is accompanied by enhanced long-term potentiation in the hippocampus, a brain region recruited by CFC, but not in the striatum, a brain region not primarily implicated in contextual memory formation. Furthermore, using a combination of bulk and single cell RNA sequencing, we find that synaptic plasticity-promoting gene expression cascades are more strongly engaged in the hippocampus than in the striatum, but only when HDACi treatment co-occurred with CFC, and not by either treatment alone. Lastly, using ChIP-sequencing, we show that the combined action of HDACi application and conditioning is required to elicit enhancer histone acetylation in pathways that may underlie improved memory performance. Together, our results indicate that systemic HDACi administration amplifies brain-region specific processes that are naturally induced by learning. These findings shed light onto the mode of action of HDACis as cognitive enhancers.

overall_design: We used ChIP-sequencing to determine the H3K27ac changes induced by HDACi paired with either context or CFC exposure. . There are 3 treatments within each brain region and each treatment has 4 replicates. Each replicate consists of genomic DNA of the H3K27ac ChIPed samples or the corresponding input.

first: Allison

last: Burns

first: Mélissa

last: Farinelli-Scharly

first: Sandrine

last: Hugues-Ascery

first: Jose

middle: V

last: Sanchez-Mut

first: Giulia

last: Santoni


title: Genome-wide CRISPR screen for export factors of NORAD lncRNA

summary: Fluorescence based genome-wide screening strategy in which the endogenous NORAD transcript was tagged with an IRES-GFP cassette that could only be translated after successful transport to the cytoplasm. Infection of these cells with a genome-wide lentiviral CRISPR library followed by the identification of sgRNAs that were enriched in cells with diminished fluorescence

overall_design: Brunello lentiCRISPR_v2 library (Addgene #73179) was used. The two independent reporter cell lines served as biological replicates. In each replicate, 19 million cells were seeded into seven 15 cm dishes each, in media containing 8 µg/mL of polybrene (Millipore) and lentiviral library at a multiplicity of infection of ~0.5. Two days post-transduction, cells were seeded into media containing 1 µg/mL puromycin (Thermo Fisher Scientific). Cells were selected in puromycin containing media for the next ten days, during which they were passaged every two days. On day 10 in puromycin, the dimmest 0.5% cells were sorted to collect at least 200 000 cells per replicate in addition to 50 million unsorted cells per replicate.


title: The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intra-cellular communication after learning [RNA-seq]

overall_design: We were interested in determining the transcriptional differences in two brain regions, the hippocampus and the striatum, after HDACi treatment paired with CFC. Each library consists of the total RNA from one brain region (either hippocampus or striatum) taken from a single mouse one hour after behavioral paradigm. There are 4 treatments within each brain region and each treatment has 4 replicates.


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation [ATAC-seq]

first: Lucille

last: Lopez-Delisle

first: Christopher

last: Bolt

first: Aurélie

last: Hintermann

first: Bénédicte

last: Mascrez

first: Antonella

last: Rauseo

first: Guillaume

last: Andrey

first: Denis

last: Duboule


title: Context-dependent enhancer function revealed by targeted inter-TAD relocation [ChIP-seq]


title: The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intra-cellular communication after learning [scRNA-seq]

overall_design: We were interested in determining the HDACi-mediated transcriptional differences in the cell types of the hippocampus after CFC. To do so we performed single nuclear RNA-sequencing by extracting nuclei from the hippocampi of 5 pooled mice per sample.  Each group (Veh-CFC and HDACi-CFC) has two replicates.  Nuclei then underwent 10x library preparation and sequencing.


title: Analysis of transcriptional changes induced in TSLP in CD4+ T cells

status: Public on May 15 2022

first: Margherita

last: Boieri

address: 55 Fruit Street

institute: Masachusetts General Hospital

summary: TSLP-stimulated CD4+ T cells block the promotion of breats tumor in mice. In this experiment, we analyze the differences in gene expression profiles of CD4+ T cells in PyMT mice in presence or absence of TSLP-stimulated CD4+ T cell

overall_design: Analysis of differentially regulated genes in test group versus control

first: Shadmehr

last: Demehri

first: Anna

last: Maliksevic


title: Analysis of transcriptional changes induced in PyMT breast tumor by TSLP stimulated CD4+ T cells

summary: TSLP-stimulated CD4+ T cells block the promotion of breats tumor in mice. In this experiment, we analyze the differences in gene expression profiles of PyMT breast tumors in presence or absence of TSLP-stimulated CD4+ T cell


title: Glucocorticoid receptor maintains vasopressin responses in kidney collecting duct cells

city: Taipei

first: Ming-Jiun

last: Yu

address: No. 1 Jen-Ai Road Sec. 1, Rm 816

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University

summary: Water permeability of the kidney collecting ducts is regulated in part by the amount of the molecular water channel protein aquaporin-2 (AQP2), whose expression, in turn, is regulated by the pituitary peptide hormone vasopressin. We previously showed that stable glucocorticoid receptor knockdown diminished the vasopressin-induced Aqp2 gene expression in the collecting duct cell model mpkCCD. Here, we investigated the pathways regulated by the glucocorticoid receptor by comparing transcriptomes of the mpkCCD cells with or without stable glucocorticoid receptor knockdown. Glucocorticoid receptor knockdown downregulated 5,394 transcripts associated with 55 KEGG pathways including “vasopressin-regulated water reabsorption,” indicative of positive regulatory roles of these pathways in the vasopressin-induced Aqp2 gene expression. Quantitative RT-PCR confirmed the downregulation of the vasopressin V2 receptor transcript upon glucocorticoid receptor knockdown. Glucocorticoid receptor knockdown upregulated 3,785 transcripts associated with 42 KEGG pathways including the “TNF signaling pathway” and “TGFβ signaling pathway,” suggesting the negative regulatory roles of these pathways in the vasopressin-induced Aqp2 gene expression. Quantitative RT-PCR confirmed the upregulation of TNF and TGFβ receptor transcripts upon glucocorticoid receptor knockdown. TNF or TGFβ inhibitor alone, in the absence of vasopressin, did not induce Aqp2 gene transcription. However, TNF or TGFβ blunted the vasopressin-induced Aqp2 gene expression. In particular, TGFβ reduced vasopressin-induced increases in Akt phosphorylation without inducing epithelial-to-mesenchymal transition or interfering with vasopressin-induced apical AQP2 trafficking. In summary, our RNA-seq transcriptomic comparison revealed positive and negative regulatory pathways maintained by the glucocorticoid receptor for the vasopressin-induced Aqp2 gene expression.

overall_design: RNA-seq transcriptomic comparison between control and stable glucocorticoid receptor knockdown mpkCCD cells

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last: Yang

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last: Lin