title: Tissue disaggregation and isolation of specific cell types from transgenic Xenopus appendages for transcriptional analysis by FACS

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

summary: Xenopus embryos and tadpoles are versatile models for embryological, cell biological, and regenerative studies. Genomic and transcriptomic approaches have been increasingly employed in these frogs. Most of these genome-wide analyses have profiled tissues in bulk, but there are many scenarios where isolation of single cells may be advantageous, including isolation of a preferred cell type, or generation of a single-cell suspension for applications such as scRNA-Seq. Here we present a protocol for the disaggregation of complex tail and limb bud tissue, and use cell type-specific fluorescence in transgenic X. tropicalis appendages to isolate specific cell populations using fluorescence activated cell sorting (FACS). Our protocol addresses a specific challenge in Xenopus embryos and tadpoles: the storage of maternal yolk platelets in each cell, which can introduce light scatter and thereby false positives into FACS analysis. Here we gate against both non-transgenic and ubiquitously transgenic animals to reduce both false positives and false negatives. We use the Xtr.Tg(pax6:GFP;cryga:RFP;actc1:RFP)Papal transgenic line as a test case to demonstrate that nucleic acid preparations made from sorted cells are high quality and specific. We anticipate this method will be adaptable to study various cell types that have transgenic reporter lines to better profile cell types of interest.

overall_design: The posterior third of an anestitized tadpole tail was amputated at NF stage 41. Tadpoles were replaced in media without anesthetiz and allowed to regenerated until desired collection timepoint. The regenerated tail was isolated from the tadpole and cells were dissociated into single cell suspension using Liberase, washed in PBS and sorted for fluoresence through an Aria III cell sorter.

first: Alex

last: Chitsazan


title: RNA analysis of Nr4a1 and Nr4a1-knockout mammary tumor cells from MMTV-PyVT transgenic mice

status: Public on Oct 01 2020

city: xiamen

first: yang

last: pengbo

address: xiangan

country: China

institute: xiamen university

type: Expression profiling by high throughput sequencing

summary: MMTV-PyVT Mammary tumors were harvested from PyVT-wild-type (WT), PyVT-Nr4a1 knockout (KO)  littermates on a congenic FVB/NJ background,minced and incubated with collagenase type I digestion solution .The digested Mammary tumor cells were collected and maintained in DMEM medium containing 10% FBS for 24 hour.

overall_design: Differential mRNA expression of Mammary tumor cells between PyVT-wild-type (WT) mice and age matched PyVT-Nr4a1 knockout (KO) mice was quantified by RNA-seq data analysis

first: Qiao

last: Wu

first: Hangzi

last: Chen

first: Pengbo

last: Yang


title: Neoplastic-stromal cell crosstalk regulates matrisome expression in pancreatic cancer

status: Public on Sep 30 2020

city: Boston

first: Kim

middle: Christin

last: Honselmann

address: 55 Fruit Street

department: Surgery

country: USA

institute: Massachusetts General Hospital & Harvard Medical School

summary:
Purpose: The goal of this study was to identify BET-dependent pathways in the PDAC stroma and the epithelial compartment.
Methods: Monocultures and Cocultures of a low passage PDAC cell line (MGH1319) and a cancer-associated fibroblast cell line (CAF-1) were treated with either BETi (CPI203) or CTRL for 24 hours. Each condition was done as a single experiment and all cells were subjected to FACS, RNA was isolated using the RNeasy Micro Kit (CAT No.74004) and sequenced at 75 bp Pair End on the NextSeq sequencer (Illumina). qRT–PCR validation was performed using TaqMan assays.
Results: In vitro co-cultures of PDAC and CAF cells demonstrated that matrisome expression was regulated by BET-dependent PDAC-CAF crosstalk.
Conclusions: PDAC matrisome expression is dependent on tumor-stroma crosstalk and regulated in parts by BET proteins.

overall_design: RNA profiles of monocultures and cocultures from PDAC and CAF cells treated with CPI203 (BET inhibitor) or CTRL for 24 hours were generated by pair end sequencing on the NextSeq sequencer (Illumina).

middle: C

first: Andrew

middle: S

last: Liss


title: Transcriptomic data of leaves from eight sunflower lines and their sixteen hybrids under water deficit

status: Public on Sep 22 2020

city: Castanet-Tolosan

first: Ludovic

last: Legrand

address: 24 Chemin de Borde Rouge

country: France

institute: INRA/CNRS

summary: Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower and included both inbred lines and their hybrids. Drought stress was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide transcriptomics data from sunflower leaves. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the transcriptomic basis of heterosis.

overall_design: Transcriptomic profiling of sunflower responses to drought including a large genetic variability

first: Louise

last: Gody

first: Harold

last: Duruflé

first: Nicolas

last: Blanchet

first: Clément

last: Carré

first: Baptiste

last: Mayjonade

first: Stéphane

last: Munos

first: Lise

last: Pomiès

first: Simon

last: de Givry

middle: B

last: Langlade

first: Brigitte

last: Mangin


title: Epigenetic subtypes of neuroblastoma [scRNA-seq SK-N-SH]

status: Public on Sep 17 2020

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

country: Germany

institute: University Heidelberg

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide single cell expression profiles (scRNA-seq MARS-seq) of SK-N-SH cells (n=1176)

overall_design: single-cell RNA-seq in SK-N-SH cell line (n=1176) under the following culture conditions:  RPMI1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.

first: Frank

last: Westermann


title: RNA-seq for hand-microdissected glomeruli from Immunoglobulin A nephropathy patients

city: Seoul

first: Sehoon

last: Park

address: Daehak-ro 101

country: South Korea

institute: Seoul National University Hospital

summary: We collected glomeruli from biopsy specimens from IgA nephropathy patients with relatively preserved kidney function (eGFR ≥ 60 mL/min/1.73 m2 and urine protein-to-creatinine ratio < 3 g/g) and from normal kidney cortices by hand microdissection and performed RNA-seq. The transcriptomic profiling of IgA nephropathy glomerulus provide insights for intraglomerular pathophysiology of IgAN before reaching profound kidney dysfunction.

overall_design: RNA-seq with 14 IgA nephropathy patients and 10 normal kidney cortices isolated for renal cell carcinoma patients

first: Hajeong

last: Lee

first: Jae Wook

first: Seung Hee


title: Drosophila voltage-gated sodium channels are only expressed in active neurons and are localized to distal axonal initial segment-like domains

status: Public on Sep 29 2020

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

summary: In multipolar vertebrate neurons, action potentials (AP) initiate close to the soma, at the axonal initial segment (AIS). Invertebrate neurons are typically unipolar with dendrites integrating directly into the axon. Where APs are initiated in the axons of invertebrate neurons is unclear. Voltage-gated sodium (NaV) channels are a functional hallmark of the AIS in vertebrates. We used an intronic MiMIC to determine the endogenous gene expression and subcellular localization of the sole NaV channel in both male and female Drosophila, para. Despite being the only NaV channel in the fly, we show that only 23 ±1% of neurons in the embryonic and larval CNS express para, while in the adult CNS para is broadly expressed. We generated a single-cell transcriptomic atlas of the whole 3rd instar larval brain to identify para expressing neurons and show that it positively correlates with markers of differentiated, actively firing neurons. Therefore only 23 ±1% of larval neurons may be capable of firing NaV-dependent APs. We then show that Para is enriched in an axonal segment, distal to the site of dendritic integration into the axon, which we named the Distal Axonal Segment (DAS). The DAS is present in multiple neuron classes in both the 3rd instar larval and adult CNS. Whole cell patch clamp electrophysiological recordings of adult CNS fly neurons are consistent with the interpretation that Nav-dependent APs originate in the DAS.  Identification of the distal NaV localization in fly neurons will enable more accurate interpretation of electrophysiological recordings in invertebrates.

overall_design: scRNA-seq (10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry) of fresh and fixed third instar larval brains from genotype mixed Drosophila melanogaster

first: Thomas

last: Ravenscroft

first: Jasper

last: Janssens

first: Hugo

last: Bellen


title: Selective activation of FZD7 in human pluripotent stem cells

status: Public on Sep 18 2020

city: La Jolla

first: Theresa

last: Gaasterland

state: CA

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

summary: Human pluripotent stem cells ( (H1/WA01/NIH stem cell registry number 0043) were treated with WNT3a protein, a FZD7-specific WNT mimetic, and a GSK3 inihibitor in time series to determine genes differentially upregulated and downregulated across all conditions or within one condition only.

overall_design: Comparison of gene expression in response to treatment in time series, with timepoint 0 hour as baseline.

first: Terry

first: Karl

last: Willert


title: Epigenetic subtypes of neuroblastoma [SK-N-BE(2)-C Ectopic HRASV12 induction]

status: Public on Sep 16 2020

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide single cell expression profiles (scRNA-seq 10x Genomics) of SK-N-BE(2)-C cells after induction of mutant HRASV12

overall_design: single-cell RNA-seq in SK-N-BE(2)-C cell line after ectopic induction of mutant HRASV12 and control


title: Two aldehyde clearance systems are essential to prevent lethal formaldehyde accumulation in mice and humans

status: Public on Sep 21 2020

city: Cambridge

first: Sam

last: Watcham

address: Jeffery Cheah Biomedical Centre

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: Reactive aldehydes arise as by-products of metabolism, and are normally cleared by multiple families of enzymes. We find that mice lacking two aldehyde detoxifying enzymes, mitochondrial ALDH2 and cytoplasmic ADH5, have greatly shortened lifespans and develop leukemia. Hematopoiesis is profoundly disrupted, with a reduction of hematopoietic stem cells and also common lymphoid progenitors causing a severely depleted acquired immune system. We show that formaldehyde is the common substrate of ALDH2 and ADH5, and establish methods to quantify elevated blood formaldehyde and formaldehyde-DNA adducts in tissues. Bone marrow derived progenitors actively engage DNA repair but also imprint a formaldehyde-driven mutation signature similar to ageing-associated human cancer mutation signatures. Furthermore, we identify analogous genetic defects in children causing a new inherited bone marrow failure and pre-leukemic syndrome. Endogenous formaldehyde clearance alone is therefore critical for hematopoiesis and in limiting mutagenesis in somatic tissues.

overall_design: LK (lin-c-Kit+) and lin-c-KitloSca1+ blood progenitor cells from WT, Aldh2-/-, Adh5-/- and Aldh2-/-Adh5-/- mice were sequenced by 10X Genomics (one mouse each) and compared across genotypes

first: Felix

last: Dingler

first: Meng

last: Wang

first: Nicola

last: Wilson

first: Berthold

last: Gottgens

first: KJ

last: Patel


title: Epigenetic subtypes of neuroblastoma [ATAC-Seq]

first: Carl

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide chromatin accessiblity profiles from ATAC-seq data in 2 neuroblastoma cell-lines.

overall_design: ATAC-seq chromatin accessibility profiles in 2 neuroblastoma cell-lines

first: Frank


title: Epigenetic subtypes of neuroblastoma [HiChIP]

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide 3D chromatin organization profiles using HiChIP in 2 neuroblastoma cell-lines.

overall_design: HiChIP 3D chromatin organization in 2 neuroblastoma cell-lines.


title: Single-cell mapping of progressive fetal-to-adult transition in human naïve T cells

status: Public on Sep 25 2020

city: San Francisco

first: Daniel

last: Bunis

state: California

address: 35 Medical Center Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Epigenetic subtypes of neuroblastoma

last: Herrmann


title: Spontaneous Cell Fusions as a Mechanism of Parasexual Recombination in Tumor Cell Populations.

status: Public on Sep 12 2020

city: TAMPA

first: Daria

last: Miroshnychenko

state: FL

address: 12902 USF Magnolia Drive

department: Cancer Physiology

institute: Moffitt Cancer Center

type: Genome variation profiling by genome tiling array

summary: Initiation and progression of cancers reflect the underlying process of somatic evolution, which follows a Darwinian logic, i.e., diversification of heritable phenotypes provides a substrate for natural selection, resulting in the outgrowth of the most fit subpopulations.  Although somatic evolution can tap into multiple sources of diversification, it is assumed to lack access to (para)sexual recombination – a key diversification mechanism throughout all strata of life. Based on observations of spontaneous fusions involving cancer cells, reported genetic instability of polypoid cells, and precedence of fusion-mediated parasexual recombination in fungi, we asked whether cell fusions could serve as a source of parasexual recombination in cancer cell populations. Using differentially labelled tumor cells, we found evidence of low-frequency, spontaneous cell fusions between carcinoma cells in multiple cell line models of breast cancer both in vitro and in vivo. While some hybrids remained polyploid, many displayed partial ploidy reduction, generating diverse progeny with heterogeneous inheritance of parental alleles, indicative of partial recombination. Hybrid cells also displayed elevated levels of phenotypic plasticity, which may further amplify the impact of cell fusions on the diversification of phenotypic traits. Using mathematical modeling, we demonstrated that the observed rates of spontaneous somatic cell fusions may enable populations of tumor cells to amplify clonal heterogeneity, thus facilitating the exploration of larger areas of the adaptive landscape, relative to strictly asexual populations, which may substantially accelerate a tumor’s ability to adapt to new selective pressures.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's protocol. DNA was extracted from frosen cell pellet using Quiagen DNAeasy kit. 12 samples were analysed: 3 subclones of hybrid between Hs578T and MDA231 cell lines, 2 subclones of hybrid between MCFDCIS and SUM159 cell lines. Parental cell lines, 2 replicates of each, except for MCFDCIS: Hs578T, MDA231, SUM159, MCFDCIS. Cell were grown in correcponding media before collecting the samples, no treatment was applied.


title: A novel TLX1 driven T-ALL zebrafish model: comparative genomic analysis with other leukemia models

city: Gent

first: Siebe

last: Loontiens

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

institute: Ghent University

summary: We generated a new rag2-TLX1 driven T-ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T-ALLs (sequencing performed in the Speleman lab). In addition, RNA sequencing was performed on various additional zebrafish T-ALL models (shrek, hulk, otg, hMYC, sequenced in the Frazer lab) to look at the molecular differences between the various existing T-ALL models.

overall_design: RNA sequencing data from TLX1, shrek, hulk, otg T-ALL samples, wild type thymocytes sequenced in the Speleman lab, wild type thymocytes sequenced in the Frazer lab. Shrek, otg, hulk, hMYC preleukemic thymocytes

first: Suzanne

last: Vanhauwaert

first: Lisa

last: Depestel

first: Givani

last: Dewyn

first: Wouter

last: Van Loocke

first: Finola

middle: E

last: Moore

first: Elaine

middle: G

last: Garcia

first: Lance

last: Batchelor

first: Chiara

last: Borga

first: Barbara

last: Squiban

first: Megan

last: Malone-Perez

first: Pieter-Jan

last: Volders

first: Volodimir

last: Olexiouk

first: Pieter

last: Van Vlierberghe

first: David

middle: M

last: Langenau

first: Kimble

middle: J

last: Frazer

first: Kaat

last: Durinck

last: Speleman


title: Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene expression programs in bladder cancer [RNA-seq]

status: Public on Sep 15 2020

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Bladder cancer prognosis is closely linked to the underlying differentiation state of the tumor, ranging from the less aggressive and most differentiated luminal tumors to the more aggressive and least differentiated basal tumors. Sequencing of bladder cancer has revealed that loss-of-function mutations in chromatin regulators and mutations that activate receptor tyrosine kinase (RTK) signaling frequently occur in bladder cancer. However, little is known as to whether and how these two types of mutations functionally interact or cooperate to regulate tumor growth and differentiation state. Here, we focus on loss of the histone demethylase UTX (also known as KDM6A) and activation of the RTK FGFR3, two events that commonly co-occur in muscle invasive bladder tumors. We show that UTX loss and FGFR3 activation cooperate to disrupt the balance of luminal and basal gene expression in bladder cells. UTX localized to enhancers surrounding many genes that are important for luminal cell fate, and supported the transcription of these genes in a catalytic-independent manner. In contrast to UTX, FGFR3 activation was associated with lower expression of luminal genes in tumors and FGFR inhibition increased transcription of these same genes in cell culture models. This suggests an antagonistic relationship between UTX and FGFR3. In support of this model, UTX loss-of-function potentiated FGFR3-dependent transcriptional effects and the presence of UTX blocked an FGFR3-mediated increase in the colony formation of bladder cells. Taken together, our study reveals how mutations in UTX and FGFR3 converge to disrupt bladder differentiation programs that could serve as a therapeutic target.

overall_design: Two separate RNA-seq experiments analyzing the effect of UTX expression in UMUC1 bladder cancer cells, which have a UTX loss of function mutation: 1) UTX expression in full/regular media (10% FBS) and tumorsphere media (B27, FGF2, EGF), and 2) UTX-expression with co-expression of either wild type or S249C FGFR3. Both experiments were done in triplicate.

first: Lijuan

last: Feng

first: Thomas

last: Carroll

first: C

middle: D

last: Allis


title: Transcriptomic profiling of the adaptive and innate immune responses of Atlantic salmon to Renibacterium salmoninarum infection

status: Public on Sep 24 2020

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify Atlantic salmon genes responsive to R. salmoninarum pathogen, fish were intraperitoneally injected with R. salmoninarum (BKD) or sterile KDM-2 medium (control). Head kidney samples were collected at 13 days post-infection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to different levels of R. salmoninarum infection.

overall_design:
Atlantic salmon (54 ± 6 g) in the BKD group were injected with live R. salmoninarum, whereas fish in the control group were injected with sterile KDM-2 medium. The head kidney samples were collected at 13 days post-infection. The infection level of samples was determined using a TaqMan qPCR assay, and fish (n=5) with no (Control), high (H-BKD) or low (L-BKD) infection level were subjected to microarray analyses. Test samples were labeled with Cy5, whereas the common reference (i.e. a RNA pool of all 15 samples included in microarray experiment) was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array (i.e. 15 arrays in total).
variable: Control: Control1, Control2, Control3, Control4, Control5.
variable: L-BKD: L-BKD1, L-BKD2, L-BKD3, L-BKD4, L-BKD5.
variable: H-BKD: H-BKD1, H-BKD2, H-BKD3, H-BKD4, H-BKD5.
biological replicate: Control: Control1, Control2, Control3, Control4, Control5.
biological replicate: L-BKD: L-BKD1, L-BKD2, L-BKD3, L-BKD4, L-BKD5.
biological replicate: H-BKD: H-BKD1, H-BKD2, H-BKD3, H-BKD4, H-BKD5.

first: Albert

last: Caballero-Solares

first: Sabrina

last: Inkpen

first: Mohamed

last: Emam

first: Surendra

last: Kumar

first: Camila

last: Bouniot

first: Ruben

last: Avendaño-Herrera

first: Eva

last: Jakob

first: Matthew

middle: L

last: Rise


title: Subacute toxicity study of nicotinamide mononucleotide via oral administration

status: Public on Sep 08 2020

city: Shanghai

first: yingnan

last: you

address: 26 Qiuyue Rd., Pudong

institute: Chinese Academy of Sciences

summary: To investigate genome-wide gene expression changes induced by 1340mg/kg/d or 2680mg/kg/d NMN adnimistration in mice using next-generation sequencing

overall_design: mRNA profiles of control (gavaged with water for 7d) and 1340mg/kg/d or 2680mg/kg/d NMN treated mice (gavaged with NMN for 7d)

first: Yingnan

last: You

last: Liu


title: Memory-like HCV-specific CD8+ T cells retain a chronic scar after cure of chronic HCV infection

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: Investigation of phenotypical changes between exhausted HCV-specific CD8+ T cells during chronic infection and after DAA-mediated cure investigation of heterogeneity withhin the HCV-specific CD8+ T cell population

overall_design: Single-cell RNA sequencing of HCV-specific CD8+ T cell subsets of 6 chronically infected patients during chronic HCV infection (n=6) and after DAA-mediated HCV cure targeting conserved (n=2).

first: Nina

last: Hensel

last: Sagar

first: Dominic

last: Gruen

first: Maike

last: Hofmann

first: Robert

last: Thimme


title: ERK1/2-RSK2 signaling is a developmental switch required for estrogen homeostasis

city: Nashville

first: Deborah

last: Lannigan

state: TN

address: 2220 Pierce Ave

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

summary: Transcriptomic analysis of the mature ER+ population in the mammary gland revealed enrichment for estrogen-responsive genes in the RSK2-KO compared to the wild type.

overall_design: Anlaysis of gene expresison from FACS sorted EpCam-hi_CD49f+lowSca+CD49b- cells from the mammary glands of 12wk RSK2(+/+) or RSK2(-/-) mice at estrous and diestrus stages.

middle: A

first: Katarzyna

last: Ludwik

first: Zachary

last: Sandusky


title: Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection

status: Public on Sep 07 2020

address: Hugstetterstr. 55

institute: UNIVERSITÄTSKLINIKUM FREIBURG

overall_design:
Low-input RNA sequencing of CD127/PD-1-based HCV-specific CD8+ T cell subsets of five chronically infected patients during chronic HCV infection and after DAA-mediated HCV cure targeting conserved (n=3) and variant (n=2) epitopes and of 3 patients after spontaneously resolved infection.

**Raw Data not provided**

first: Zuguang

last: Gu

first: Naveed

last: Ishaque


title: Dynamic Optima In Cell Sizes Enable Normal Gastrulation Movements In Zebrafish Embryos During Early Development

city: Mumbai

first: Sreelaja

last: Nair

state: Maharashtra

address: IIT Bombay campus, Powai

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Bombay

summary: Current knowledge of the mechanisms of cell migration is based on differentiated cells in culture where it is known that the actomyosin machinery drives migration via dynamic interactions with the extracellular matrix and adhesion complexes. However, unlike differentiated cells, cells in early metazoan embryos also dynamically change cell sizes as they migrate. The relevance of cell size to cell migration and embryonic development is not known. Here we investigate these phenomena in zebrafish embryos, a model system in which reductive cell divisions causes cell sizes to decrease naturally over time as cells migrate collectively to sculpt the embryonic body plan. Because mutations that can perturb cell sizes so early in development do not exist, we generate haploid and tetraploid zebrafish embryos and show that cell sizes in such embryos are smaller and larger than the diploid norm, respectively. Cells in embryos made of smaller or larger than normal cells migrate sub-optimally, leading to gastrulation defects. Multiple lines of evidence suggest that the observed defects originate from altered cell size, and not from pleotropic effects of altered ploidy. This interpretation is strengthened by finding that gastrulation defects are rescued by increasing cell sizes in embryos wherein cell sizes are smaller than normal. We show that the migration defects are cell-autonomous by live imaging migrating haploid and tetraploid cells during gastrulation in chimeric diploid embryos. Analysis of membrane protrusion dynamics in single cells shows that cells normally extend protrusions non-uniformly during migration, a phenomenon which is perturbed when cell sizes deviate from the norm. Thus, an optimal range of developmental stage-specific cell sizes appears necessary for collective cell migration to correctly position cells in space and time to shape an amorphous ball of blastoderm into an embryo.

overall_design: RNA sequencing analysis of diploid (control), haploid and tetraploid zebrafish embryos at 3 hours post fertilization (hpf) stage done as 3 experimental replicates for each condition

first: Triveni

last: Menon

first: Asfa

last: Sabrin

first: Rahul

last: Kumar


title: Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

city: Bellevue

first: Serena

state: Washington

department: Genome Sciences

institute: University of Washington

summary: Ctyokine-stimulated polarization and repolarization of murine bone marrow-derived macrophages (LPS + IFNγ, IL-4); bulk RNA-seq timecourse and bulk ATAC-seq for selected timepoints and conditions

overall_design: Bulk RNA-seq and bulk ATAC-seq was performed on mouse bone marrow-derived macrophages treated with either LPS + IFNγ or IL-4 at multiple timepoints after cytokine-induced polarization and repolarization. Unpolarized macrophages were used as a control. Three biological replicates were performed for all bulk experiments; one biological replicate was performed for the 10X experiment.

first: S

first: H

middle: H

last: Gustafson

first: D

last: Jackson

last: Pun

first: C

last: Trapnell


title: The effect of YAP/TAZ on the expression of the heat shock transcriptome

status: Public on Sep 05 2020

city: CHENGDU

first: Min

last: Luo

state: SICHUAN

address: NO.17, the third section of South Renmin Road

institute: SICHUAN UNIVERSITY

summary: We found that heat stress induces a strong and rapid YAP dephosphorylation and activation. To determin what is the physiological functions of YAP in response to heat stress, we performed RNA-SEQ analysis on siCon and siYAP/TAZ knockdown tumor cells with or without heat shock. Results indicated that 95% of heat inducible genes is blocked (83% completely and 12% partially) by YAP/TAZ knockdown in the B16-OVA melanoma cells whereas only 5% of heat inducible genes were unaffected, supporting a previously unrecognized prominent role of YAP/TAZ in the expression of the heat shock transcriptome and cell survival.

overall_design: siCon and siYAP/TAZ knockdown cells with or without heat shock, in triplicate.

first: Bin

last: Shao


title: Chemical Systems Biology Reveals Mechanisms of Dissociated Glucocorticoid Receptor Signaling

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Glucocorticoids display remarkable anti-inflammatory activity, but their use is limited by undesirable on-target effects including insulin resistance and skeletal muscle atrophy. We used a chemical systems biology approach called Ligand Class Analysis (LCA) to examine ligands designed to alter the receptor through distinct structural mechanisms. These ligands displayed a full range of activity profiles, providing the variance required to identify ligand-specific gene expression and transcriptional coregulator interaction patterns that were highly predictive of their effects on myocyte glucose disposal and protein balance. Anti-inflammatory effects were linked to inhibition of glucose disposal in skeletal muscle but not to muscle atrophy. This approach successfully predicted dissociated activity in vivo, identifying compounds that were muscle sparing or anabolic for protein balance and mitochondrial potential.  LCA defines the mechanistic links between the ligand-receptor interface and the physiological outcomes of the ligands, a general approach that can be applied to any ligand-regulated allosteric signaling system.

overall_design: Steroid-deprived C2C12 myotubes were compared by nascent RNA-seq after a 2-hour treatment with vehicle or Dexamethasone

first: Nelson

last: Bruno

first: Sathish

last: Srinivasan

first: Charles

last: Nettles

first: Douglas

last: Kojetin

first: Zhuang

last: Jin

first: Siddaraju

middle: V

last: Boregowda

first: Donald

last: Phinney

first: Jason

last: Nowak

first: Olivier

last: Elemento

first: René

last: Houtman

first: Diana

last: Stavreva

first: Gordon

last: Hager

first: Kamenecka

last: Theodore

first: Kendall

middle: W


title: Expression data from human osteoblast cultures

status: Public on Sep 03 2020

city: Auckland

first: Dorit

last: Naot

address: Private Bag 92019

department: Medicine

country: New Zealand

institute: University of Auckland

summary:
Studies in Aotearoa New Zealand found higher bone mineral density and lower rate of hip fracture in people of Polynesian ancestry compared to Europeans.
We hypothesised that differences in osteoblast gene expression contribute to the differences in bone properties between the two groups, and aimed to identify mechanisms that underlie the bone phenotype.

overall_design: Bone samples were obtained from people of Polynesian and European ancestry who had total joint replacement surgeries for osteoarthritis, and primary osteoblasts were cultured from bone fragments. RNA was extracted from the osteoblasts, and gene expression was compared between the two groups, using 10 samples from each.

first: Ally

last: Choi


title: Comparative gene expression profiling in livers of A1cf-transgenic and wild-type mice

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: Rationale: RNA binding protein Apobec1 Complementation Factor (A1CF) regulates posttranscriptional ApoB mRNA editing but the range of RNA targets and long-term impact of altered A1CF expression on liver function are unknown. Objective: We studied hepatocyte-specific A1cf transgenic (A1cf +/Tg), A1cf+/Tg Apobec1– /– and A1cf –/– mice fed chow or high fat/high fructose diets using RNA-Seq, RNA-CLIP Seq and tissue microarrays from human hepatocellular cancer (HCC). Findings: A1cf +/Tg mice exhibited increased hepatic proliferation and steatosis, with increased lipogenic gene expression (Mogat1, Mogat2, Cidea, Cd36) associated with shifts in polysomal RNA distribution. Aged A1cf +/Tg mice developed spontaneous fibrosis, dysplasia and HCC, which was accelerated on a high fat/fructose diet and independent of Apobec1. RNA-Seq revealed increased expression of mRNAs involved in oxidative stress (Gstm3, Gpx3, Cbr3), inflammatory response (Il19, Cxcl14, Tnfα, Ly6c), extracellular matrix organization (Mmp2, Col1a1, Col4a1), proliferation (Kif20a, Mcm2, Mcm4, Mcm6) with a subset of mRNAs (including Sox4, Sox9, Cdh1) identified in RNA CLIP-Seq. Increased A1CF expression in human HCC correlated with advanced fibrosis and with reduced survival in a subset with nonalcoholic fatty liver disease. Conclusions: Hepatic A1CF overexpression selectively alters polysomal distribution and mRNA expression, promoting lipogenic, proliferative and inflammatory pathways leading to HCC.

overall_design: Samples from A1cf-transgenic mice were compared to samples from age-matched wild-type C57BL/6NJ mice as a reference. For each genotype, pools were prepared containing RNAs from 3-4 separate mice, labeled, and hybridized to Agilent microarrays.

first: Valerie

last: Blanc

first: Saeed

last: Soleymanjahi

first: Joseph

last: Nadeau

first: ILKe

last: Nalbantoglu

first: Yan

last: Xie

first: Elizabeth

last: Molitor

first: Blair

last: Madison

last: Brunt

last: Mills

first: Deborah

last: Rubin

first: Irene

middle: O

last: Ng

first: Yeonjung

last: Ha

first: Lewis

middle: R

last: Roberts

first: Nicholas

last: Davidson


title: Epigenetic subtypes of neuroblastoma [cell lines]

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

institute: University Heidelberg

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 25 neuroblastoma cell-lines.

overall_design: H3K27ac histone modifications in 25 neuroblastoma cell-lines

first: Frank

last: Westermann


title: The transcription factor Fosl2 controls systemic autoimmunity by repressing FoxP3 during T cell development

status: Public on Sep 04 2020

city: Zurich

first: Oliver

last: Distler

address: Gloriastrasse 25

department: Department of Rheumatology

country: Switzerland

institute: University Hospital Zurich

summary:
Purpose: We aimed to charaterise the transfriptional effects of Fosl2 in T cells
Methods: We used wt, Fosl2 overexpressing (Fosl2tg) and Fosl2 knock-out (Fosl2ko) CD4+ naive T cells that we stimulated for 24 hours with anti-CD3 and anti-CD28. RNA-was extracted and sequenced using
Results: We identified a set of genes whose expression is regulated by Fosl2 in T cells, including Foxp3.

overall_design: RNA-sequencing from T cells with overexpression or knock-out of Fosl2.

first: Florian

last: Renoux


title: Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene expression programs in bladder cancer

first: Douglas

last: Barrows

overall_design: Refer to individual Series


title: Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene expression programs in bladder cancer [ChIP-seq]

overall_design: ChIP-seq for UTX, MLL4 and various histone post-translational modifications in UMUC1 bladder cancer cells.

first: Lijuan

last: Feng

first: Thomas

last: Carroll

first: C

last: Allis


title: An integrative multiomic network model links the canonical lipid metabolism pathway to glucose regulation in coronary artery disease

status: Public on Sep 01 2020

first: Daniel

middle: Michael

last: Jordan

address: 1 Gustave L Levy Place, box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Elevated plasma cholesterol and Type 2 Diabetes (T2D) are associated with Coronary Artery Disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explored the relationship between lipid and glucose control by constructing network models from the STARNET study with sequencing data from seven cardiometabolic tissues obtained from CAD patients during coronary artery by-pass grafting surgery. By integrating gene expression, genotype, metabolomic and clinical data, we identified a Glucose and Lipid Determining (GLD) regulatory network showing inverse relationships with lipid and glucose traits. Master regulators of the GLD network also impacted lipid and glucose levels in inverse directions. Experimental knockdown of one of the GLD network master regulators, Lanosterol Synthase (LSS), in mouse confirmed the inverse relationships to glucose and lipid levels as predicted by our model and provided mechanistic insights.

overall_design: RNAseq data from 6 mice fed BIBB-515 and 6 mice fed a control diet

first: Ariella

middle: T

last: Cohain

first: William

last: Barrington

first: Noam

last: Beckmann

first: Carmen

last: Argmann

first: Sander

last: Houten

first: Alexander

last: Charney

first: Raili

last: Ermel

first: Katyayani

last: Sukhavasi

first: Oscar

last: Franzen

first: Simon

last: Koplev

last: Whatling

first: Gillian

last: Belbin

first: Jialiang

last: Yang

first: Ke

last: Hao

first: Eimear

last: Kenny

first: Zhidong

last: Tu

first: Jun

last: Zhu

first: Li-Ming

last: Gan

first: Ron

last: Do

first: Chiara

last: Giannarelli

first: Jason

last: Kovacic

first: Arno

last: Ruusalepp

first: Aldons

last: Lusis

first: Johan

last: Bjorkegren

first: Eric

last: Schadt


title: GM-CSF-transduced proliferating myeloid cells represent cell cycle related gene signature

status: Public on Aug 31 2020

city: Tokyo

first: Minaho

last: Kawamura

address: BLICK GATE Suidobashi F2, Chiyodaku-kandamisakicho

country: Japan

summary: We previously established a method to generate myeloid lineage cells with proliferation capacity from induced pluripotent stem cells (iPSCs) (Zhang R. Cancer Immunol Res. 3: 668, 2015). In this study, we generated the GM-CSF-producing cells by genetic engineering of mouse iPSC-derived proliferation myeloid cells (iPSC-pMCs). Gene expression profiles revealed GM-CSF-transduced iPSC-pMCs (GM-pMCs) generated from C57BL/6 mice and 129Sv mice shared 180 up-regulated genes and 236 down-regulated genes compared with their corresponding iPSC-pMCs. Gene ontology analysis showed that the up-regulated gene signature shared by C57BL/6 GM-pMCs and 129Sv GM-pMCs was enriched for transcripts associate with cell cycle, cell cycle process, mitotic cell cycle and regulation of mitotic cell cycle.

overall_design: Gene expression profiles of C57BL/6  iPSC-pMCs, GM-CSF-transuduced C57BL/6 iPSC-pMCs, GM-CSF-treated C57BL/6 iPSC-pMCs, 129Sv   iPSC-pMCs, GM-CSF-transuduced 129Sv iPSC-pMCs, GM-CSF-treated 129Sv iPSC-pMCs

first: R

last: Zhang

first: H

last: Mahima


title: isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

city: Philadelphia

first: Yi

last: Xing

state: PA

address: 3615 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

summary: We report isoCirc, a long-read sequencing strategy coupled with an integrated computational pipeline to characterize full-length circular RNA (circRNA isoforms) using rolling circle amplification (RCA) followed by long-read sequencing. Applying isoCirc to 12 human tissues, we determined full-length structures and examined tissue specificities of circRNA isoforms in human transcriptomes.

overall_design: Short-read (Illumina) and long-read (Oxford Nanopore, ONT) sequencing were used to examine circRNA isoforms in total RNA extracted from human embryonic kidney (HEK293) cells (6 replicates). Long-read sequencing was used to examine circRNA isoforms in total RNA extracted from 12 human tissues.

first: Ruijiao

last: Xin

first: Yan

last: Gao

first: Robert

last: Wang

first: Kathryn

last: Kadash-Edmondson


title: Epigenetic subtypes of neuroblastoma [neuroblastoma]

first: Carl

last: Herrmann

summary: In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 60 primary neuroblastoma samples.

overall_design:
H3K27ac histone modifications in 60 primary neuroblastoma samples
Raw data files will be submitted to EGA

first: Frank

last: Westermann


title: Comparative gene expression profiling in livers of A1cf-transgenic, A1cf-knockout, and wild-type mice

first: Jesse

last: Riordan

overall_design: Samples from A1cf-transgenic mice or A1cf-knockout mice were compared to samples from age-matched wild-type C57BL/6J or C57BL/6NJ mice, respectively, as a reference. For each genotype and condition, pools were prepared containing RNAs from 3-4 separate mice. For hepatocyte studies, livers from 12-week-old mice were perfused and digested with 0.05% collagenase (Type IV, C5138, Sigma) and hepatocytes plated on collagen-coated dishes overnight, for a total of 3 replicate pools per genotype. For whole-liver studies, 4 replicates each of A1cf-transgenic and wild-type C57BL/6J RNA pools were sequenced in one study, while 3 replicates each of A1cf-knockout and wild-type C57BL/6NJ RNA pools were sequenced in another.

first: Valerie

last: Blanc

first: Saeed

last: Soleymanjahi

first: Joseph

last: Nadeau

first: ILKe

last: Nalbantoglu

last: Xie

first: Elizabeth

last: Molitor

first: Blair

last: Madison

last: Brunt

middle: C

last: Mills

first: Deborah

last: Rubin

first: Irene

last: Ng

first: Yeonjung

last: Ha

first: Lewis

last: Roberts

first: Nicholas

last: Davidson


title: Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes

status: Public on Aug 20 2020

city: Dunedin

first: Christopher

last: Brown

address: 710 Cumberland Street

department: Biochemistry

institute: University of Otago

summary: RNA-seq of Huh7 cells transfected with replication competent clones of HBV genotypes A2, B2, C2, and D3.

overall_design: Total RNA samples were purified using RNeasy kit (Qiagen, Hilden, Germany). The libraries were prepared using TruSeq stranded Total RNA sample preparation kit with Ribo-Zero according to the manufacturer’s protocol and sequenced using HiSeq 2500 (Illumina, CA, USA), generating 125-bp paired-end reads.

first: Chun

middle: S

last: Lim

first: Vitina

last: Sozzi

first: Peter

last: Revill

first: Chris


title: Rab7D small GTPase is involved in phago-, trogocytosis and cytoskeletal reorganization in the enteric protozoan Entamoeba histolytica

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

institute: National Institute of Infectious Diseases

summary: To know the role of Rab7 isotypes in enteric protozoan parasite Entamoeba histolytica, one out of nine Rab7 isotypes, Rab7D, was specifically silenced and examined the effect on virulence-related phenotypes. To clarify transcriptomic difference caused by rab7d gene silencing, RNA-seq analysis was conducted.

overall_design: Examine RNA-seq analysis of mock transfected and rab7d gene silenceing strain. (n=3)

first: Ratna

last: Wahyuni

first: Tomoyoshi

last: Nozaki


title: Comprehensive transcriptome analysis of the brain in CNS-specific PRMT1 knockout mice.

status: Public on Aug 14 2020

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: Arginine methylation is a common post-translation modification that is catalyzed by protein arginine methyltransferases (PRMTs). We generated the central nervous system-specific PRMT1 deficient (PRMT1-CKO) mice by Cre-loxP recombination system. Recently, we have discovered that PRMT1 is essential for development of CNS, and it is especially crucial for oligodendrocyte lineage progression and the subsequent myelination. In this study, we performed a comprehensive analysis of gene expression changes in whole brains, cortices or cerebella of wild type (WT) and PRMT1-CKO mice using RNA sequencing (RNA-seq). Filtering characteristics were used to identify the differentially expressed genes using the CLC Genomics Workbench software

overall_design: mRNA profiles of mouse brain were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Misuzu

last: Hashimoto

first: Akiyoshi

last: Fukamizu


title: Global assessment of integrated stress response in CF patients lung explants and organoids

status: Public on Aug 30 2020

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: Freshly acquired lung tissue from CF patients with advanced disease and prolonged exposure to pathogenic microorganisms display a clear molecular signature of activated unfolded protein response (UPR) and chronic inflammation.

overall_design: RNA sequencing and gene expression analysis of CF lung explants and organoids (ileum and colon)

first: Giovana

last: Bampi

first: Sebstian

last: Kirchner

first: Robert

last: Rauscher

first: Marcel

last: Bijvelds

first: Ray

last: Frizell

first: Hugo

last: de Jonge


title: Epigenetic age-predictions in mice using pyrosequencing, droplet digital PCR or barcoded bisulfite amplicon sequencing

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

type: Methylation profiling by high throughput sequencing

summary: Age-associated DNA methylation reflects aspect of biological aging - therefore epigenetic clocks for mice can help to elucidate the impact of treatments or genetic background on the aging process in this model organism. Initially, age-predictors for mice were trained for genome-wide DNA methylation profiles and we have recently described a targeted assay based on pyrosequencing of DNA methylation at only three CG dinucleotides (CpGs). Here, we have re-evaluated pyrosequencing approaches in comparison to droplet digital PCR (ddPCR) and barcoded bisulfite amplicon sequencing (BBA-seq). At individual CpGs the correlation of DNA methylation with chronological age was slightly higher for pyrosequencing and ddPCR as compared to BBA-seq. On the other hand, BBA-seq revealed that neighboring CpGs tend to be stochastically modified at murine age-associated regions. Furthermore, the binary sequel of methylated and non-methylated CpGs in individual reads can be used for single-read predictions, which may reflect heterogeneity in epigenetic aging. In comparison to C57BL/6 mice the epigenetic age-predictions using BBA-seq were also accelerated in the shorter-lived DBA/2 mice, and in C57BL/6 mice with a lifespan quantitative trait locus of DBA/2 mice. Taken together, we describe further optimized and alternative targeted methods to determine epigenetic clocks in mice.

overall_design: DNA methylation profiles of bisulfite converted blood specimens from 63 C57BL/6 mice, 33 DBA/2 mice and 15 Line A mice

first: Miloš

last: Nikolić

first: Michael

last: Gobs

first: Julia

last: Franzen

first: Gerald

last: de Haan

first: Hartmut

last: Geiger

first: Wolfgang

last: Wagner


title: Distinct metabolic programmes established in the thymus control the effector functions of γδ T cell subsets in tumour microenvironments

status: Public on Aug 25 2020

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

summary: RNA sequencing of PLZF+ and PLZF- γδ T cell subsets from the spleen, inguinal lymph nodes, lungs and adipose tissue for gene expression analysis

overall_design: PLZF+ and PLZF- γδ T cells were sorted from the spleen, inguinal lymph nodes, lungs and adipose tissue of PLZF-GFP mice for subsequent RNA sequencing and gene-expression analysis. Two replicates for each subset pooled from 10 mice each were used for the study.

first: AC

last: Kohlgruber

first: L

first: MB

last: Brenner

first: S

last: Gal-Oz

first: T

last: Shay


title: Neurog3 gene dosage effect on the differentiaiton of intestinal enteroendocrine progenitors

status: Public on Aug 13 2020

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary: Analysis of FACS-sorted intestinal Neurog3+/+ and Neurog3+/- cells from Neurog3 fluorencent reporter mice carrying two-(+/+) or one- (+/-) Neurog3 alleles. In the intestine, Neurog3 is an enteroendocrine (EE) lineage determinating transcription factor that transiently expressed in early EEC progenitors. By comparison the molecular profiles of Neurog3+/+ and Neurog3+/- cells, we hypothesized that Neurog3 gene dosage regulates the allocation of EE progenitor fates towards EEC vs. goblet cells.

overall_design: Two mutant Neurog3 fluorescent reporter mice carring two- or one- Neurog3 alleles were used. Intestinal Neuog3 expressing cells were isolated by FACS and transcriptomes were profiled by RNA seq.

first: Hui

last: Li

first: Subir

middle: K

last: Ray

first: Gerard

last: Gradwohl

first: Andrew

last: Leiter


title: Harmine treatment of PMA-treated J-Lat 5A8 cells

status: Public on Aug 21 2020

city: Gainesville

first: Mark

last: Wallet

address: 1275 Center Drive

department: Pathology

institute: University of Florida

summary: Transcriptome analysis was performed to determine what gene expression changes occur in response to treatment of the plant-derived compound harmine and to determine its effect on protein kinase C agonist reactivation of latent HIV.

overall_design: J-Lat 5A8 cells were treated with the inhibitor harmine with or without PMA to assess differential gene expression

first: Jared

middle: P

last: Taylor

first: Lucas

last: Armitage

first: Daniel

last: Aldridge

first: Melanie

middle: N

last: Cash


title: Inactivation of AdeABC and AdeIJK efflux pumps elicits specific non-overlapping transcriptional and phenotypic responses in Acinetobacter baumannii

status: Public on Aug 10 2020

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

summary:
Purpose: In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075.
Methods: To further characterize the functional interactions between AdeABC and AdeIJK, we carried out RNAseq analysis of the exponential AB5075 and its single and double efflux knockout cells. High quality total RNA was further processed by removing 23S and 16S rRNAs using the MicrobExpress bacterial mRNA enrichment kit. Samples were analyzed in duplicate using Illumina MiSeq. Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark).
Results: Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK. We identified additional efflux pumps and transcriptional regulators that contribute to MDR phenotype of clinical A. baumannii isolates.
Conclusion:  Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK.

overall_design: RNAseq analysis of the exponential AB5075 and its single and double efflux knockout cells (parent, adeB::T26, ΔadeIJK, adeB::T26 ΔadeIJK); 4 samples in duplicate

first: Helen

middle: I

last: Zgurskaya

first: Inga

last: Leus

first: Anhthu

last: Trinh


title: DNA damage-induced transcriptome changes in budding yeasts Saccharomyces cerevisiae and Candida glabrata

status: Public on Aug 05 2020

city: Nutley

first: Erika

last: Shor

state: New Jersey

address: 111 Ideation Way, , CDI

institute: Center for Discovery and Innovation

summary: This study compared the transcriptional response to DNA damage in two closely related yeasts, S. cerevisiae and C. glabrata.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: We cultured S. cerevisiae and C. glabrata in YPD containing 0.1% methyl methanesulfonate (MMS) for 1 hour, harvested the cells, isolated total RNA using the Qiagen Rneasy kit, and sent the RNA to Genewiz for RNAseq. Untreated cells were used as controls. 3 biological replicates for every condition were collected, except the S. cerevisiae no MMS condition, which had 2 biological replicates.

first: David

last: Perlin


title: Targeting of glioma stem-like cells with a parthenolide derivative ACT001 through inhibition of AEBP1/PI3K/AKT signaling

status: Public on Sep 11 2020

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: Glioblastoma (GBM) is the most lethal primary brain tumor in adults with a median survival of around 15 months. A potential treatment strategy involves targeting glioma stem-like cells (GSCs) that are able to initiate, maintain, and repopulate the tumor mass. Here, we identify ACT001, a parthenolide derivative, targeting GSCs through regulation of adipocyte enhancer binding protein 1 (AEBP1) signaling.GSCs exhibit high response to ACT001 in compared with normal human astrocytes. AEBP1 is a putative target of ACT001 by RNA-Seq analysis, which expression associates with prognosis of GBM patients. Knockdown of AEBP1 inhibits GSC proliferation whereas ectopic expression of AEBP1 increases GSC proliferation and xenograft tumor growth. AEBP1 overexpression also attenuates ATC001-inhibited GSC orthotopic xenograft tumor growth. Treatment with ACT001 or PI3K inhibitor or AEBP1 depletion decreases AKT phosphorylation and GSC proliferation. However, constitutive AKT activation rescues ACT001 treatment or AEBP1 knockdown-inhibited cell proliferation. Additionally, ACT001 blocks TGF-β-activated AEBP1/AKT signaling in GSCs. ACT001 exhibits antitumor activity either as a single agent or in combination with SHP099, which provides significant survival benefits for GSC xenograft tumor -bearing animals.

overall_design: Examination of differential gene expression in GSC 83 cells treated with or without ACT001 .


title: circNDUFB2 inhibits non-small cell lung cancer progression via destabilizing IGF2BPs and activating anti-tumor immunity

status: Public on Aug 22 2020

city: shanghai

first: Botai

address: Line 2200Xie-tu Road

institute: Botai Li

summary: Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNAs that have been demonstrated to involve in cancer progression. Here, we identify circNDUFB2 is downregulated in non-small cell lung cancer (NSCLC) tissues, and it negatively correlates with the malignant features. Elevated circNDUFB2 inhibits growth and metastasis of NSCLC cells. circNDUFB2 functions as a scaffold to enhance interaction of TRIM25 with IGF2BPs by forming a TRIM25/circNDUFB2/IGF2BPs ternary complex. The resultant ternary complex facilitates ubiquitination degradation of IGF2BPs, and N6-methyladenosine (m6A) modification of circNDUFB2 increases ubiquitination efficiency of TRIM25 for IGF2BPs. Moreover, circNDUFB2 can be recognized by RIG-I, then activates RIG-I-MAVS signaling cascades and recruits immune cells into tumor microenvironment (TME). Our data provide evidences that circNDUFB2 participates in degradation of IGF2BPs and activation of anti-tumor immunity in NSCLC progression. These findings reveal a dual-role pattern of circNDUFB2 action involved in protein ubiquitination degradation and cellular immune response.

overall_design: mRNA profiles in A549 cells with circNDUFB2 overexpression (circNDUFB2) versus control (Vector)

first: Lili

last: Zhu

first: Liyan

last: Jiang

first: Wenxin

last: Qin


title: SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]

status: Public on Aug 04 2020

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: Three distinct enzymes are known to be capable of methylating lysine 9 residue of the histone H3 in Drosophila melanogaster: Su(var)3-9, SetDB1, and G9a. Here, we explored functional specialization of the two of them: SetDB1 and Su(var)3-9. Using DamID approach, we generated the binding profile for SetDB1 in salivary gland chromosomes, and matched it to the previously published profile of Su(var)3-9. Unlike Su(var)3-9, SetDB1 is an euchromatic protein that is absent from repeated DNA compartment, and is largely restricted to TSSes and 5'UTRs of moderately active ubiquitously expressed genes. Significant SetDB1 association is also observed at or near insulator protein CP190 binding sites. Extensive, yet not exact colocalization SetDB1 with Su(var)3-9 occurs only along the chromosome 4. Importantly, SetDB1 and H3K9me2/3-enriched sites tend to display poor overlap. At the same time, SetDB1 has clear connection with the distribution of H3K27me3 mark. SetDB1 binds outside the domains possessing this modification, and about half of the borders of H3K27me3 domains are decorated by SetDB1 binding sites together with actively transcribed genes. Given that SetDB1 displays low correlation with H3K9 methylation and binds to the TSSes of active genes, that are usually nucleosome-poor, we speculate that in somatic cells, SetDB1 may contribute to the methylation of a broader set of chromosomal proteins than just H3K9. In addition, via association with insulator proteins and transcription machinery, SetDB1 can be expected to play a role in the establishment of chromatin functional domains.

overall_design: Examination of expression of genes in salivary glands of oregon flies

first: Darya

last: Kalashnikova

first: Stanislav

middle: E

last: Romanov

first: Petr

last: Laktionov

first: Dmitry

last: Koryakov


title: SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [DamID-seq]

overall_design: Examination of SetDB1 and CP190 proteins binding on chromosomes of salivary glands using DamID technique.


title: Novel insights into retinal microvascular endothelial cells revealed through single cell RNA-seq analysis.

city: Belfast

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

institute: Queen's University Belfast

summary:
Purpose: To better characterise the population structure of primary bovine retinal microvascular endothelial cells (RMECs) based upon their individual transcriptomes.
Methods: Individual RMECs were captured on the Fluidigm C1 system (Fluidigm), cDNA libraries were prepared using a Nextera XT kit and sequencing performed on a NextSeq (Illumina).
Results: Application of a single cell RNA-seq analysis workflow showed that RMECs form a relatively homogeneous population in culture, with the main subgroup being proliferating cells. Expression of markers from along the arteriovenous tree suggests that most cells originate from capillaries. An in silico model of the blood retinal barrier was created, including junctional proteins not previously reported within the retinal vasculature. Numerous alternative splicing events involving exons within microvascular barrier genes were observed and in many cases individual cells expressed exclusively one isoform.
Conclusions: We have optimised a workflow for single-cell transcriptomics in primary RMECs. Our results have provided fundamental insights into the genes involved in retinal microvascular barrier formation.

overall_design: Single cell RNA-seq analysis of retinal microvascular endothelial cells from two separate Fluidigm C1 runs, 49 cells from run 1 and 51 cells from run 2.

first: Mark

last: Watson


title: Verteporfin treatment controls morphology, phenotype, and global gene expression for cells of the human nucleus pulposus

status: Public on Aug 03 2020

city: St Louis

first: Lori

last: Setton

state: MO

address: 1 Brookings Drive, Campus box 1097

department: Department of Biomedical Engineering

institute: Washington University in St. Louis

summary:
Purpose: It has been observed that the drug verteporfin (VP), a known disruptor of YAP-TEAD signaling, causes cell rounding and changes  in phenotype and biosynthesis in human nucleus pulposus cells. In this study the time-dependent effects of VP treatment on the transcriptome of human NP cells was explored.
Methods: mRNA profiles of NP cells treated for 24 hours, 48 hours, or 4 days with VP or vehicle (DMSO) control  were generated for cells from 3 adult human tissue samples, using Illumina NovaSeq. Unaligned reads were trimmed based on quality score (minimum quality level (Phred) = 20, minimum read length = 25) and aligned to the whole human genome (STAR 2.6.1d; hg19) using Partek Flow software. This software suite was also used to calculate the counts/normalized counts of genes and to perform gene specific analysis (GSA), principle component analysis (PCA), hierarchical clustering, and gene set enrichment. Differentially regulated genes were considered to be those with a fold change value (VP/DMSO) for a given time point that was greater than or equal to 2 or less than or equal to negative 2 and a FDR-adjusted p-value of less than or equal to 0.05.
Results: Using a data analysis workflow buit in Partek Flow, we identified 1810 differentially regulated genes at 24 hours, 4287 differentially regulated genes at 48 hours, and 9272 differentially regulated genes at 4 days. Hierarchical clustering and PCA analysis demonstrated clustering of the data by patient and time point, but separation by treatment group. We further observed that while generally the expression of  fibroblastic markers decreased with VP treatment,  a number of markers of NP phenotype were increased. We also identified enriched gene sets (ex. 2026 at the 4 day time point) which represented a variety of cellular components, processes, and functions potentially implicated by VP treatment.
Conclusions: The data from this RNA-sequencing demonstrate that VP treatment which induces cell rounding in NP cells was also accompanied by pronounced and time-dependent changes in the transcriptome of adult NP cells in culture. The enriched gene sets and differentially regulated genes suggest a major role for cell adhesion, cytoskeletal remodeling, vacuolar lumen, and M APK activity in the NP phenotypic and functional response to changes in cell shape.

overall_design: Nucleus pulposus (NP) cells from 3 human patients (20M, 38M, 41M; all at passage 0) were used for this study. Cells of each patient were seeded in triplicate  on well plates coated with PEGylated-Laminin-111 and treated with daily exchanges of media containing verteporfin (VP) or vehicle-containing (DMSO) media. Cells were harvested and lysed at 24 hours, 48 hours, or 4 days and triplicates of the respective timepoint and patient were pooled. Thus for each patient there are samples for 3 time points and 2 treatment conditions, resulting in 18 total samples.

first: Bailey

middle: F

last: Fearing

first: Julie

last: Speer

first: Liufang

last: Jing

first: Aravind

last: Kalathil

first: Michael

last: Kelly

first: Jacob

middle: M

last: Buchowski

first: Lukas

last: Zebala

first: Scott

last: Luhmann

first: Munish

last: Gupta


title: SCF -licensed induction of a mucosal mast cell-like transcriptional program by TGF-b

city: Boston

first: Daniel

last: Dwyer

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: This study evaluates the effects of 72h stimulus with stem cell factor (SCF) (100 ng/mL) and TGF-b (1 ng/mL or 10 ng/mL), both alone and in combination, on the transcriptome of bone marrow-derived cultured mast cells (BMMCs) grown in IL-3 for 6-8 weeks. Through this approach, we find that SCF dramatically enhances TGF-b mediated upregulation of signature genes associated with mucosal mast cells, including transcripts encoding the proteases mMCP-1 (Mcpt1) and mMCP-2 (Mcpt2). Replicates indicate biologic duplicates. Samples were sequenced on an Illumina NextSeq 500.

overall_design: RNA-seq analysis of bone marrow-derived cultured mast cells grown in IL3 (5 ng/mL) and stimulated with TGF-b, SCF, or the two factors in combination for 72 hours at the listed concentrations

first: Tahereh

last: Derakhshan


title: Expression data from human skeletal muscle in endurance-trained athletes

status: Public on Jul 31 2020

city: bunkyo-ku

first: saori

last: kakehi

state: Tokyo

address: 2-1-1 hongo

department: Graduated shool of medicine

institute: Juntendo University

summary:
Endurance-trained athletes have high oxidative capacity, enhanced insulin sensitivity, and high intracellular lipid accumulation in muscle. These characteristics are likely due to altered gene expression levels in muscle.
We used microarrays to detect gene expression profile in endurance-trained athlete skeletal muscle.

overall_design: Human skeletal muscle sample selected from Vastus lateralis for RNA extraction and hybridization on Affymetrix microarrays.

first: Saori

last: Kakehi


title: Progression of spermatogonial differentiation in the mouse:  the pathway to meiosis

status: Public on Jul 29 2020

city: Pullman

last: Griswold

state: WA

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

summary: We report bulk RNA-sequencing data for undifferentiated and defined subpopulations of differentiating murine spermatogonia.  We have sequenced two replicates each of wild-type and STRA8 knock-out sets of spermatogonia to assess transcriptional changes that occur throughout spermatogonial development prior to meiotic entry.

overall_design: Transcriptional profiling of STRA8 wild-type and knock-out spermatogonial subpopulations

first: Rachel

last: Gewiss

first: Eric

last: Shelden


title: Lineage-specific transcriptomes define differential expansion and development of inducible and constitutive mast cells

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

overall_design: Refer to individual Series


title: Transcriptional profiling of mouse cavenous endothelial cells in normal and high glucose condition

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Purpose: To investigate the potential target genes associated with diabetic condition in mouse cavernous endothelial cells (MCECs) for diabetic induced erectile dysfunction (ED) treatment.    Materials and Methods: Mouse cavernous tissue was embedded into Matrigel and sprouted cells were subcultivated for other studies. To mimic diabetic condition, the MCECs were exposed to normal-glucose (NG, 5 mmoL) and high-glucose (HG, 30 mmoL) condition for 72 hours. RNA-sequencing assay was performed to evaluate gene expression profiling and RT-PCR was used for sequencing data validation.

overall_design: normal glucose ( n=2) and high glucose ( n=2)

first: Guo

last: Yin

first: Jiyeon

last: Ock

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: EBV LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells [RNA-seq]

status: Public on Jul 28 2020

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

summary: Here, we report EBV oncogene LMP1 modified EV have the ability to enhance metastatic potential of non-cancer cell lines. After 24h treatment of HK1-LMP1 EV, about 179 transcripts were upregulated and 235 transcripts were downregulated comparing with HK1 EV. Those differentially expressed genes showed an enrichment and potential function in cell cycle, cellular growth and proliferation, cell death and survival and cancer.

overall_design: MCF10A cell were treated with EV isolated either from HK1 or HK1-LMP1 cell.

first: Li

last: Sun

first: Dingani

last: Nkosi


title: EBV LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells [miRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

summary: EBV oncogene LMP1 modified EV contents. We identified about 32 upregulated and 25 downregulated miRNAs which were statistically significant (P<0.05) and most of them were changed dramatically with Log2-fold change more than 5.

overall_design: Extracellular vesicles were isolated either from HK1 or LMP1 transfected HK1 cell line.


title: EBV LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [RNA-seq]

status: Public on Jul 27 2020

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

summary: Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1 deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.

overall_design: ChIP-seq, ATAC-seq, genome-wide bisulftie sequencing, 4C-seq, RNA-seq and single cell RNA-seq from different stages of the PGCLC differentiation.

first: Tore

last: Bleckwehl


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [WGBS]


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [ChIP-seq 1]


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [ATAC-seq]


title: The Tumor Microenvironment and Inflammation Influence toxicity in patients with Large B Cell Lymphoma Treated with Axicabtagene Ciloleucel [Nanostring]

city: Tampa

first: Marco

last: Davila

address: 12902 Usf Magnolia Dr

department: BMT-CI

institute: Moffitt Cancer Center and Research Institute

summary: Tumor biopsies were taken within one month prior to CAR T infusion for evaluation of gene expression. Baseline tumor gene expression was compared between patients who went on to have severe (grade 3 or higher) neurotoxicity vs. those with non-severe neurotoxicity (grade 0 - 2).

overall_design:
Tumor biopsies were taken within one month of CAR T infusion in a cohort of 36 patients. RNA expression was measured by the Nanostring IO360 panel consisting of 770 genes found in the tumor microenviroment in cancer.  We compared gene expression of the pre-treatment biopsy samples  of patients who developed severe immune mediated toxicities ( Grade > 3 neurotoxicity) vs. those with grade 0-2 toxcities after CAR T infusion.

We compared patients who went on to have a durable response (DR) to those with a non-durable response (NDR) in patients that had sufficient follow up (minimum 6 months post-CAR T infusion).

first: Michael

middle: D

last: Jain

first: Rawan

last: Faramand


title: Androgen deprivation in PTEN/LXR -/- mice

city: AUBIERE

first: silvere

last: BARON

address: 10 avenue Blaise Pascal

department: Endocrine, Signaling and Cancer

institute: Université Clermont Auvergne

summary: The project is based on the transcriptomic analysis from 8 groups of animal samples : Wild Type Sham Wild Type Castrated LXR-/- Sham LXR-/- Castrated PTEN-/- Sham PTEN-/- Castrated PTEN-/-LXR-/- Sham PTEN-/-LXR-/- Castrated.

overall_design: The goal is to define a transcriptomic signature associated with the tumor escape phenotype in response to castration in the PTEN-/-LXR-/- model.

first: Silvere

last: Baron


title: The Tumor Microenvironment and Inflammation Influence toxicity in patients with Large B Cell Lymphoma Treated with Axicabtagene Ciloleucel


title: Non-steroidal mineralocorticoid receptor antagonism by finerenone is sufficient to improve function in preclinical muscular dystrophy

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

summary:
The objective of this study was to test the novel non-steroidal mineralocorticoid receptor antagonist (MRA) finerenone as a monotherapy in a preclinical Duchenne muscular dystrophy (DMD) model.
Microarray was used to detail gene expression differences in ventricular heart tissue from finerenone-treated dystrophin-deficient, utrophin-haploinsufficient Het (utrn+/−; mdx) mice versus untreated Het mice.

overall_design: Heart ventricular tissues from three biological replicates from each group (finerenone-treated and untreated Het male mice) were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Jeovanna

last: Lowe

first: Peter

last: Kolkhof

middle: J

last: Haupt

first: Kyra

last: Peczkowski

first: Neha

last: Rastogi

first: J

last: Hauck

first: Feni

last: Kadakia

first: Jonathan

middle: G

last: Zins

first: Pierce

last: Ciccone

first: Suzanne

last: Smart

last: Sandner

first: Subha

middle: V

last: Raman

first: Paul

last: Janssen

middle: A


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [ChIP-seq 2]

first: Alvaro

last: Rada-Iglesias

first: Tore

last: Bleckwehl


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence


title: Ovarian senescence, transcriptomic, and epigenomic changes with aging

status: Public on Jul 23 2020

city: Oklahoma City

first: VICTOR

middle: AFRIYIE

last: ANSERE`

state: Oklahoma

address: Genes and Human Disease Research Program MS57, Oklahoma Medical Research Foundation 825 NE 13th Street

department: PHYSIOLOGY

institute: UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER

summary: Ovarian aging is characterized by the progressive depletion of primordial follicle reserve, leading to irregular patterns of ovulation and menopause. The basic mechanisms that underlie the ovarian aging and follicle decline is unknown. We sought to explore the role of cellular senescence and epigenomic mechanisms in ovarian aging. Here, we present the transcriptomic changes observed in the ovaries with age using the age groups 3mo, 6mo, 9mo and 12mo (n=5 per group except for 12mo which has an n=4). The age groups capture timepoints from sexual maturation to reproductive health decline.

overall_design: RNA sequencing analysis on isolated ovarian RNA from 3mo, 6mo, 9mo, and 12mo female C57BL/6 mice.

first: Victor

last: Ansere

first: Willard

last: Freeman

first: Augusto

last: Schneider

first: Michael

middle: B

last: Stout

first: Sarah

middle: R

last: Ocañas


title: Effects of aeroallergen challenge on inducible and constitutive lower airway mast cells

first: Daniel

last: Dwyer

summary: This study are compares the transcriptomes of lower airway constitutive connective tissue mast cells (MCs), characterized by low expression of b7 integrin (B7low), and induced mucosal MCs, characterized by high b7 integrin (B7hi) at rest and in response to repeated inhalation of house dust mite extract (HDM). Lower airway b7hi and b7low MCs were flow cytometrically isolated from female 5-7 week old C57BL/6 mice following 6 challenges (2x/week for three weeks) with saline (PBS) or 3 ug house dust mite extract (HDM). Each sample is derived from pooled lung digests from three mice to reduce experimental variance. Samples were sequenced on an Illumina NextSeq 500

overall_design: RNA-seq analysis of flow sorted MCs from the lower airways of mice challenged with 3 ug HDM extract (administered 2x/week for 3 weeks in 20 ul PBS) or vehicle control

first: Nora

last: Barrett


title: RNA-Seq analysis of HCV-related HCC and NBNC-HCC tumor and non-tumor part gene analysis

status: Public on Jul 22 2020

city: Kaohsiung

first: Shu-Chi

last: Wang

address: No.100, Shin-Chuan 1st Road, Sanmin Dist.,

department: Department of Medical Laboratory Science and Biotechnology.

country: Taiwan

institute: Kaohsiung Medical University.

summary: We performed RNA-seq analysisfor 2 HCV-HCC and 3 NBNC-HCC tumor and non-tumor regions, total for 10 samples to find the lncRNAs candidates in HCV-related HCC.

overall_design: To identify lncRNAs relevant to HCV-HCC in a screening set, we first determined significantly differentially expressed (SDE) lncRNAs with a >2-fold change (p < 0.05) between (A) T vs. ANT in HCV-HCC considered to be relevant to HCV-related carcinogenesis; (B) T vs. ANT in NBNC-HCC considered to be relevant to non-HCV-related carcinogenesis; (C) HCV-ANT vs. NBNC-ANT tissues considered to be relevant to HCV-related non-oncogenic effects; and (D) HCV T vs. NBNC T tissues considered to be relevant to HCV-related carcinogenesis.

first: S

middle: C


title: Gene expression in the pancreas of 12 week old Non-Obese Diabetic (NOD) mice vs. healthy age-matched NOD.B10 control mice

status: Public on Jul 21 2020

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

summary: Gene expression in the pancreas of NOD vs. NOD.B10 mice at  12 weeks of age

overall_design: The pancreas of 12 week old NOD and NOD.B10 mice were isolated and homogenized in Trizol reagent (Invitrogen; 1 ml/100 mg tissue). 0.2 ml of chloroform was added per ml Trizol.  Samples were shaken vigorously and centrifuged at 12,000xg at 4°C. The clear aqueous phase was combined with an equal volume of 70% ethanol, and bound to a RNeasy mini column (Qiagen). RNA was extracted according to manufacturer’s instructions and RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Reagent Kit (Agilent). Total RNA (1ug) extracted from the pancreas of NOD mice were labelled with Cy5 and run individually against a pool of Cy3-labeled total RNA (1 ug) isolated from the pancreas of age-matched NOD.B10 mice (pool of 8 animals). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays (Agilent Technologies).


title: Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified Antigen-Reactive T cell Enrichment (ARTE) assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patients segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was ‘exhausted’ or not. SARS-CoV-2-reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in COVID-19 patients with mild compared to severe illness. In contrast, SARS-CoV-2-reactive cells in the dominant non-exhausted subset from patients with severe disease showed enrichment of transcripts linked to co-stimulation, pro-survival NF-κB signaling, and anti-apoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy subjects displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2-reactive cells from both COVID-19 patients and healthy controls non-exposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2.

overall_design: Single-cell RNA-seq were performed from pure populations of virus-reactive memory CD8+ T cells isolated ex vivo from SARS-CoV-2 infected individuals (n=39) and healthy controls (n=10).

first: Anthony

last: Kusnadi

first: Ciro

last: Ramírez-Suástegui

first: Vicente

last: Fajardo

first: Serena

last: Chee

first: Benjamin

last: Meckiff

first: Hayley

last: Simon

first: Emanuela

last: Pelosi

first: Ferhat

last: Ay

first: Grégory

last: Seumois

first: Christian

middle: H

last: Ottensmeier


title: The Tumor Microenvironment and Inflammation Influence toxicity in patients with Large B Cell Lymphoma Treated with Axicabtagene Ciloleucel [RNA-Seq]

first: Marco

last: Davila

summary: We aimed to identify factors that place patients with Large B Cell Lymphoma at higher risk of developing severe immune mediated toxicities after CAR T infusion. Tumor biopsies were taken within one month prior to CAR T infusion for evaluation of gene expression. In pre-treatment patient tumor biopsies, we found that gene expression of  myeloid markers was associated with higher toxicity.

overall_design:
Tumor biopsies were taken within one month of CAR T infusion in a cohort of 25 patients and prospectively snap-frozen. We compared gene expression of the pre-treatment biopsy samples  of patients who developed severe immune mediated toxicities ( Grade > 3 neurotoxicity) vs. those with grade 0-2 toxcities after CAR T infusion.

We compared patients who went on to have a durable response (DR) to those with a non-durable response (NDR) in patients that had sufficient follow up (minimum 6 months post-CAR T infusion).

first: Michael

last: Jain

first: Rawan

last: Faramand


title: Whole blood transcriptional variations between responders and non-responders in asthma patients receiving omalizumab

status: Public on Jul 19 2020

city: Scottsdale

first: Sangkon

last: Oh

state: AZ

address: 13400 east Shea street

department: immunology

institute: Mayo Clinic

summary: To investigate blood transcriptional changes induced by omalizumab treatment and to determine variations between omalizumab responders and non-responders.

overall_design: Total RNA isolated from whole blood of asthma patients (X) before and during weeks of omalizumab treatment (W); asthma patients seperated based on response to omalizumab treatment; healthy controls (BD) recruited as well

first: Katherine

last: Upchurch


title: The effect of circadian rhythm on gene expression in human skin III

status: Public on Jul 20 2020

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary:
Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of skin
The purpose of this study was to gain insight into the evolutionarily-conserved rhythmic patterns of the circadian transcriptome in human skin and how it relates to published transcriptomes from other human tissues.

overall_design: Twenty healthy male subjects aged 21-49 years (median age = 24.5 years) were enrolled in an overnight, time-ordered study. Four 2mm punch biopsies from the forearm were collected from each subject over the course of 24 hours (12pm, 6pm, 12am, and 6am the following day). In a separate unordered study, punch biopsies were taken from the face (cheek), forearm, and buttocks from approximately 150 females between 20-80 years old to 1) determine circadian phase, and 2) compare circadian phase across body sites. All samples were processed for RNA extraction and hybridized on the Affymetrix U219 GeneTitan array. Laser capure microdissection was performed to isolate the epidermal compartments for subsequent gene expression profiling.

first: Kevin

last: Mills

first: John

last: Oblong


title: Investigating the Mechanism of Adherent-Invasive E. coli Induced Mitochondrial Fission in the Intestinal Epithelium (Exp. 2)

status: Public on Jul 10 2020

city: Calgary

first: Hena

middle: Rehman

last: Ramay

state: AB

address: 6 Erlton Terrace SW

department: International microbiome centre

institute: University of Calgary

summary: RNA-seq was performed to interogate the transcriptional changes in response to infection with Adherent Invasive E. coli and a control, non-invasive E. coli

overall_design: 12 samples were analyzed, 4 experimental groups (control/untreated, 16h E. coli HB101, 16h E. coli F18, and 16h E. coli LF82), 3 replicates within each experimental group

first: Nicole

middle: L

last: Mancini

first: Timothy

middle: S

last: Jayme

first: Matthew

last: Workentine

first: Derek

last: McKay


title: Sex-Specific Programming of Cardiac DNA Methylation by Developmental Phthalate and Lead Exposures

status: Public on Jul 15 2020

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

summary:
DEHP study
Phthalate plasticizers are ubiquitous chemicals linked to several cardiovascular diseases in animal models and in humans. In spite of this, the mechanisms by which phthalate exposures cause adverse cardiac health outcomes are unclear. In particular, whether phthalate exposures during pregnancy interfere with normal developmental programming of the cardiovascular system, and the resulting implications this may have for long-term disease risk, are unknown. Recent studies suggest that the effects of phthalates on metabolic and neurobehavioral outcomes are sex-specific. However, the influence of sex on cardiac susceptibility to phthalate exposures has not been investigated. One mechanism by which developmental exposures may influence long-term health is through altered programming of DNA methylation. In this work, we utilized an established mouse model of human-relevant perinatal exposure and enhanced reduced representation bisulfite sequencing to investigate the long-term effects of diethylhexyl phthalate (DEHP) exposure on DNA methylation in the hearts of adult male and female offspring at 5 months of age (n=5-7 mice per sex and exposure). Perinatal DEHP exposure led to hundreds of sex-specific, differentially methylated cytosines (DMCs) and differentially methylated regions (DMRs) in the heart. Pathway analysis of DMCs revealed enrichment for several pathways in females, including insulin signaling, regulation of histone methylation, and tyrosine phosphatase activity. In males, DMCs were enriched for glucose transport, energy generation, and developmental programs. Notably many sex-specific genes differentially methylated with DEHP exposure in our mouse model were also differentially methylated in published data of heart tissues collected from human heart failure patients. Together these data highlight the potential role for DNA methylation in DEHP-induced cardiac effects, and emphasize the importance of sex as a biological variable in environmental health studies.

Lead study
Environmental factors play an important role in the etiology of cardiovascular diseases. Cardiovascular diseases exhibit marked sexual dimorphism; however, the sex-specific effects of environmental exposures on cardiac health are incompletely understood. Perinatal and adult exposures to the metal lead (Pb) are linked to several adverse cardiovascular outcomes, but the sex-specific effects of this toxicant on the heart have received little attention. Perinatal environmental exposures can lead to disease through disruption of the normal epigenetic programming that occurs during early development. Using a mouse model of human-relevant perinatal environmental exposure, we investigated the effects of exposure to Pb during gestation and lactation on DNA methylation in the hearts of adult offspring mice (n=6 per sex). Two weeks prior to mating, dams were assigned to control or Pb acetate (32 ppm) water, and exposure continued until offspring were weaned at 3 weeks of age. Enhanced reduced-representation bisulfite sequencing was used to measure DNA methylation in the hearts of offspring at 5 months of age. Although Pb exposure stopped at 3 weeks of age, we discovered hundreds of differentially methylated cytosines (DMCs) and regions (DMRs) in males and females at 5 months of age. DMCs/DMRs and their associated genes were sex-specific, with a small, but statistically significant subset overlapping between sexes. Pathway analysis revealed altered methylation of genes important for cardiac and other tissue development in males, and histone demethylation in females. Together, these data demonstrate that perinatal exposure to Pb induces sex-specific changes in cardiac DNA methylation that are present long after cessation of exposure, and highlight the importance of considering sex in environmental epigenetics and mechanistic toxicology studies.

overall_design: A total of 36 DNA methylation profiles of 5-month mouse heart exposed to DEHP or control, measured by Enhanced Reduced Representation Bisulfite Sequencing (ERRBS)

first: Dana

last: Dolinoy

first: Maureen

last: Sartor

first: Justin

last: Colacino

first: Laurie

last: Svoboda

first: Jaclyn

last: Goodrich

first: Kai

last: Wang

first: Kari

last: Neier

first: Christine

last: Rygiel

first: Tamara

last: Jones

first: Raymond

last: Cavalcante

first: Claudia

last: Lalancette


title: Investigating the Mechanism of Adherent-Invasive E. coli Induced Mitochondrial Fission in the Intestinal Epithelium (Exp. 1)

first: Hena

last: Ramay

overall_design: 12 samples were analyzed, 4 experimental groups (control/untreated, 16h E. coli LF82, 4h E. coli F18, and 4h E. coli LF82), 3 replicates within each experimental group


title: Microarray analysis of long noncoding RNA expression profile in pORF5-transfected HeLa cells

status: Public on Jul 14 2020

city: Hengyang

first: Yating

last: Wen

state: Hunan

address: No. 28, Changsheng West Road

institute: University of South China

summary: Numerous studies have provided evidence for the involvement of lncRNAs in bacterial infections, including Mycobacterium tuberculosis, Helicobacter pylori, Listeria monocytogenes, and so forth. However, few studies have evaluated the alternation of lncRNAs in obligate intracellular bacterium C. trachomatis.The molecular mechanisms underlying pathogenesis of C. trachomatis are still elusive, and lncRNAs may provide new insights into the potential mechanisms. pORF5 (Accession number: NP_040384) is the only secreted protein in eight plasmid-encoded proteins in C. trachomatis. Our previous studies also verified that pORF5 influenced the expression of host proteins.Here, we performed a microarray analysis to detect the global lncRNAs and mRNAs expression in pORF5-transfected HeLa cells, and tried to identify pORF5-related lncRNAs. Our study may help to understand the interplay between lncRNAs and coding genes anticipated in the pathogenesis of C. trachomatis.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from pORF5-transfected HeLa cells and GFP-transfected HeLa cells.

first: Zhongyu

last: Li

first: Qiulin

last: Huang

first: Hongliang

last: Chen

first: Fangzhen

last: Luo

first: Lanhua

last: Zhao

first: Mingyi

last: Shu

first: Shengmei

last: Su

first: Yuqi


title: A splicing regulatory axis of SRSF2-NUMB-NOTCH governs the generation of hemogenic endothelial progenitors derived from human pluripotent stem cells

status: Public on Jul 09 2020

city: Tianjin

first: Yapu

state: China

address: 288 Nanjing Road

institute: PUMC

summary:
Purpose: The goals of this study are to verify the dynamic changes of hematopoietic endothilium treated by PLB in H1 derived different population of cells during human early hematopoietic differentian.
Methods: mRNA profiles of hESC samples collected from FACS sorted APLNR+ cells treated with PLB during day 2.5 to 5 after hematopoiesis differentiation were generated by deep sequencing using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the gene and transcript isoform level STAR followed by Cufflinks. The differentially expressed splicing events were analyzed by rMASTs
Conclusions: Our study represents the first detailed analysis the change of hemogenic endothelial progenitors generation treated by PLB , with biologic replicates, generated by RNA-seq technology. By detaied analysis of this data,we found splicing inhibition gave rise to the aberrant splicing of NUMB, which consequently led to the reduced expression of NUMB-S isoform in HEPs

overall_design: hESC samples collected from FACS sorted APLNR+ cells and  FACS sorted APLNR+ cells treated with PLB during day 2.5 to 5 a were generated by deep sequencing, in duplicates, using Illumina HISeq

first: Lihong

last: Shi


title: Characterization of erythroid cells generated through ex vivo differentiation

status: Public on Jul 08 2020

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

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

overall_design: Refer to individual Series


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [4C-seq]

first: Alvaro

last: Rada-Iglesias

summary: Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1 deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.

overall_design: ChIP-seq, ATAC-seq, genome-wide bisulftie sequencing, 4C-seq, RNA-seq and single cell RNA-seq from different stages of the PGCLC differentiation.

first: Tore

last: Bleckwehl


title: ChIP-seq from erythroid cells generated through ex vivo differentiation

summary: CD34+ Haematopoietic stem cells were differentiated ex vivo to generate ChIP-seq data for machine learning of rules underlying open chromatin dynamics.

overall_design: CD34+ cells were isolated from peripheral blood from three healthy donors (Two males, one female) and differentiatied ex vivo. ChIP-seq for key histopne marks (H3K27ac, H3K4me3) and transcription factors (CTCF, Gata-1) were performed at day 13 of differentiation.

first: Matthew

last: Gosden

first: Lea

last: Nussbaum

first: Jim

last: Hughes