title: Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules

city: Tallahassee

first: Michelle

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

summary: Drosophila reproductive behaviors are directed by fruitless neurons. A reanalysis of genomic studies shows that genes encoding dpr and DIP Immunoglobulin superfamily (IgSF) members are expressed in fru P1 neurons. We find that each fru P1 and dpr/DIP (fru P1 ∩ dpr/DIP) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number. Behavioral studies of fru P1 ∩ dpr/DIP perturbation genotypes indicates that the mushroom body functions together with the lateral protocerebral complex to direct courtship behavior. A single-cell RNA-seq analysis of fru P1 neurons shows that many DIPs have high expression in a small set of neurons, whereas the dprs are often expressed in a larger set of neurons at intermediate levels, with a myriad of dpr/DIP expression combinations. Functionally, we find that perturbations of sex hierarchy genes and of DIP-ε change the sex-specific morphologies of fru P1 ∩ DIP-α neurons.

overall_design: scRNA-seq using 10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry of 48hr after puparium formation (APF) male Drosophila Central Nervous System (CNS) cells where fru P1-expressing cells were genetically labeled with GFP.

first: Colleen

last: Palmateer


title: Tumor-specific mechanism of Treg enrichment mediated by the integrin avb8

status: Public on Feb 23 2021

city: San Francisco

first: Stephen

last: Nishimura

state: CA

address: 1001 Potrero Ave, Bldg 3, Rm211

department: Pathology

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: Subcutaneous tumors from mock transfected LLC or b8 transfected LLC were established on flanks of C57B/6 FoxP3-Ires GFP mice. Mice were treated with isotype control antibodies or anti-b8 and Tregs (CD4+ GFP+) were sorted, pooled and total RNA isolated for RNAseq.

overall_design: Three CD4+ GFP+ pools, each from 3-4 mice, for 3 conditions (Tregs from tumors from mock transfected LLC, b8 expressing LLC treated with isotype control or b8 expressing LLC treated with anti-b8 )

first: Robert

last: Seed


title: Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation

city: New York

first: Chao

last: Lu

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: In this study, our results support a functional divergence between H3K36me2 and H3K36me3 and their non-redundant roles in H3K36M-driven oncogenesis

overall_design:
17 ChIP-seq samples, 3 RNA-seq samples with 3 bioreplicates for each, 4 ATAC-seq samples and 2 WGBS samples.
The RNA-seq samples for Parental-1/-2/-3 were re-used from GSE118785 and are included here in this series as well.

first: Xiao

last: Chen

first: Haifen


title: The Fusobacterium Nucleatum (Fn) in colorectal carcinogenesis

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

summary: To elucidate whether  Fusobacterium Nucleatum(Fn) plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  Fn treated HCT116 colorectal cancer cell lines.

overall_design: RNA-seq was performed in HCT116 colorectal cancer cells after  Fusobacterium Nucleatum treatment.

first: Shiyuan


title: WDR5 facilitates cholangiocarcinoma metastasis and EMT by promoting HIF-1α accumulation via directly interaction with c-Myc and HDAC2-PHD2 axis

city: Jinan

first: Tianli

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

summary: WDR5 was an important co-factor for c-Myc-induced transcriptional activation and malignant progression.  We analyzed the differentially expressed genes in scramble and shWDR5 QBC-939 cells.

overall_design: QBC-939 cells were stably transfected with scramble shRNA(scr) and WDR5-knockdown shRNA(sh) and subjected to differential gene expression studies by RNA-seq

first: Yunfei

last: Xu


title: Long non-coding RNAs are  involved in the  activation  of glycolysis in colorectal cancer

type: Non-coding RNA profiling by high throughput sequencing

summary: Previous studies have documented that long non-coding RNAs participate in a wide-spectrum of biological processes. We hypothesized that long non-coding RNAs may promote glycolysis and tumorigenesis in colorectal cancer by manipulating of target genes. To test this hypothesis, we performed a global non-coding RNA expression profiling in 10 CRC tissues.

overall_design: RNA-seq was performed on 10 human colorectal cancer tissues derived from 10 different patients

first: Fangfang

last: Guo


title: Sequencing profiling data of tRNA-derived small RNAs (tsRNAs) in human colorectal cancer.

first: En-Wei

last: Tao

address: 145 Middle Shandong Road, Shanghai, 200001, China.

institute: Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine

summary: To explore which tsRNAs are dysregulated in the tissues of CRC.

overall_design: 4 pairs CRC and corresponding normal tissues were selected for next-generation sequencing analysis.

first: Qin-Yan

last: Gao


title: RNA-seq of adherent MDA-MB-231 cells, and their 16hour and 5day mammospheres and siRNA treatment

city: London

first: Sladana

last: Zagorac

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: To examine the transcriptional landscape of breast cancer stem cells enriched population in triple negative breast cancer, we compared transcript change between adherent MDA-MB-231 cells and the same cells cultured in mammosphere  conditions for 16 hours or 5 days.  Mammosphere assay is a recognised in vitro model of the breast cancer stem cells , and we wished to identify transcriptional dynamics and novel noncoding RNAs implicated in the regulation of this cell type. To define the role of identified player in mammospheres we next performed RNAi in these cells followed by RNA-seq

overall_design: MDA-MB-231, in adherent, 16h sphere, and 5d sphere conditions, in duplicate. RNAi of crucial player in mammosphere formation.

first: Sladjana

first: Leandro

last: Castellano


title: Genome wide map of EZH2 and SOX2 binding in mammospheres reveals common set of bound regions.

summary: We generated genome wide map of EZH2 and SOX2 protein binding in MDA-MB-231 mammospheres and we discovered enrichment of both protein on the genes regulated by SCIRT

overall_design: The genome-wide EZH2 and SOX2 binidng profile in MDA-MB-231 mammospheres


title: Genome wide map of H3K27me3 histone mark remeains unaltered after silecing of lncRNA SCIRT

summary: We generated genome wide map of H3K27me3 histone mark in mammospheres where we silenced lncRNA SCIRT, PRC2 member EZH2. We discovered that upon silencing of lncRNA SCIRT and EZH2, the distribution of this histone mark does not change. This  indicates that lncRNA SCIRT is important for EZH2 function that is independant of its activity as a histone methyltranspherase.

overall_design: The genome-wide H3K27me3 profile in MDA-MB-231 mammospheres after siRNA downregulation of lncRNA SCIRT and EZH2.


title: Long non coding RNA (lncRNA) SCIRT regulates mitotic and stemness genes in breast cancer stem cells

summary: CHART sequencing has been carried out in order to evaluate SCIRT target genes in MDA-MB-231 sphere derived cells. We discovered that lncRNA SCIRT binds promoter region of genes whose expression changes after SCIRT siRNA downregulation, suggesting that those are target SCIRT target genes.

overall_design: The genome-wide binding profile of lncRNA SCIRT was determined using Capture Hybridization Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in MDA-MB-231 sphere-derived cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous SCIRT transcripts and genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence). We identified SCIRT binding sites in comparison both to DNA recovered using the control LacZ oligonucleotide and to an input DNA sample from MDA-MB-231 sphere derived cells.


title: Endoderm differentiation of human embryonic stem cells (hESCs) [RNA-Seq]

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Purpose: The goal of this study is to identify the whole-genome transcriptome profiling of differentially expressed genes during human embryonic stem cell differentiation.  Methods: Triplicate RNA profiles were generated from hESCs and induced endoderm cells, by deep sequencing with Illumina NextSeq 500.   Results: We identified 6320 genes differentially expressed between hESCs and induced endoderm cells, with foldchange  1.5 and P < 0.05.  Conclusion: Our study confirms that endodermal gene were dramatically induced during endoderm differentiation.

overall_design: RNA profiles of human embryonic stem cells and endoderm cells induced from ES cells for 3 days were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Yi

last: Fang

first: Xiaoling


title: Genome-wide maps of histone crotonylation in pluripotent and endoderm cells. [ChIP-Seq]

summary: We examined the genome-wide distribution of histone crotonylation and H3K27ac in human embryonic stem cells and induced endoderm cells, by obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA. When compared to H3K27ac, histone crotonylation was more enriched in metabolic genes and in promoters at pluripotent state, while H3k27ac was enriched in the enhancers of endoderm genes. After endoderm differentiation, histone crotonylation and H3K27ac were both enriched in endoderm genes. Moreover, the enrichment of histone crotonylation was more remarkable than that of H3K27ac. Our data indicate that histone crotonylation correlates with endoderm differentiation.

overall_design: Examination of 2 different histone modifications in 2 cell types.


title: RNA sequencing for cancer tissues and adjacent tissues of third-stage rectal cancer patients with and without blood vascular thrombus

city: Changsha

first: Kangtao

last: Wang

state: Hunan

address: No. 87 Xiangya Road, Kaifu District

department: Gastrointestinal Surgery

institute: Central South University

summary:
The Agilent Human Gene Expression(8*60K，Design ID：039494) was used in this experiment of sequencing of the 12 samples.
A total of 12 tissues were sequenced from adjacent and cancerous tissues of 6 patients with TNM stage 3 colon cancer. Three patients had cancer thrombus and three patients had no cancer thrombus.

overall_design: 12 samples

first: Haiping

last: Pei

first: Qian

first: Fengbo

last: Tan


title: Histone crotonylation promotes endoderm differentiation. [scRNA-Seq]

summary: In this study we report that histone crotonylation promotes human embryonic stem cell differentiation to endoderm cells. Addition of crotonate, a precursor for crotonyl-CoA and therefore histone crotonylation, dramatically enhanced endoderm cell differentiation from human embryonic stem cells, while incubation of acetate, a precursor of acetyl-CoA and therefore histone acetylation, did not change the efficiency of endoderm differentiation.

overall_design: Human embryonic stem cells, endoderm cells induced for 3 days, endoderm cells induced with crotonate for 3 days, endoderm cells induced with acetate for 3 days, were processed for single-cell sequencing.


title: LncRNA SCIRT acts in a negative feedback loop to regulate the transcriptional program for cancer self-renewal

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

overall_design: Refer to individual Series


title: Histone crotonylation


title: Elucidation of the metabolic and transcriptional responses of an oriental herbal medicine, Bangpungtongseong-san, to non-alcoholic fatty liver disease in diet-induced obese mice

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

summary: We investigated the effect of Bangpungtongseong-san on phenotype characteristics and elucidated anti-obesity mechanism based on RNA-seq transcriptomic profiles in an obesity animal model.

overall_design: Total RNA of liver was obtained from high-fat diet and Bangpungtongseong-san (BT) extract added high-fat diet-fed mice and mRNA expression-associated with lipid, and glucose metabolism was measured.

first: Myung-Sook


title: The altered DNA methylation landscape in chronic lymphocytic leukemia emerges early and persists after treatment

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Here we measured genome-wide DNA methylation in patients with chronic lymphocytic leukemia as it provides an opportunity to capture the emergence of altered methylation landscapes as well as track their dynamics over disease progression including after treatment. Specifically, our cohort includes 21 CLL cases with up to six different time points, 20 precursor states of monoclonal B cell lymphocytes (MBL) and 5 matched samples from MBL and CLL states of the same patients. We find that across all CLL cases, a highly aberrant methylation state was present consistently already at the first time point and maintained with remarkable stability over disease progression. To improve our resolution and address heterogeneity we sequenced the methylome of single cells from CD5 positive and negative naïve and memory B cells as well as unsorted B cells and CLL cells. Methylation levels were highly similar within groups pointing to a rather homogeneous population and contrasted by pronounced differences between naïve and memory B cells that do not distinguish CD5 positive and negative subgroups. Our 20 patients with MBL further confirmed the early emergence of this landscape and surprisingly, the chemotherapy did not have a notable impact on the altered methylome despite a strong depletion of white blood cells.

overall_design:
RRBS and scRRBS data was collected on CLL and MBL diagnosed individuals. Each CLL patient was sequenced at two to six time points and white blood counts were tracked. Single cell RRBS was performed in 96-well plates for 48 cells of CLL cells from two individuals.  Samples include unsorted B cells as well as CD5 positive and negative naive and memory B cells from two healthy individuals.

>>>Submitter states that raw data will be submitted to dbGaP<<<

first: Kendell

last: Clement

first: Michaela

last: Gruber

first: Hongcang

last: Gu

first: Brian

last: Anat

first: Laura

last: Rassenti

first: Noelia

last: Purroy

first: Connie

last: Lesnick

first: Neil

middle: E

last: Kay

first: Mohammad

last: Arman

first: Lili

first: Donna

last: Neuberg

first: Bernd

last: Timmermann

first: Elias

last: Campo

first: Thomas

last: Kipps

first: Andreas

last: Gnirke

first: Catherine

last: Wu

first: Alexander

last: Meissner


title: Identification of novel human Wnt target genes using adult endodermal tissue-derived organoids

status: Public on Feb 22 2021

city: Utrecht

first: Joep

last: de Ligt

address: Universiteitsweg 100

department: Genetics

country: Netherlands

institute: University Medical Center Utrecht

summary: WNT and/or Rspondin was withdrawn from the medium and Wnt pathway inhibitors IWP2 and DKK1 were added to the growth medium of human stomach, liver, pancreas, small intestinal and colon organoids and RNA was harvested at time points 0h, 6h and 24h to identify Wnt regulated genes.

overall_design: RNA transcriptomics analysis upon WNT pathway inhibition in five different human tissue derived organoid lines of time point 0h, 6h, 24h. N=3

first: Kim

last: Boonekamp

first: Inha

last: Heo


title: Cell-intrinsic tumorigenic functions of PPARg in bladder urothelial carcinoma

city: Philadelphia

first: M

middle: Celeste

last: Simon

state: Pennsylvania

address: 421 Curie Boulevard, Rm 456 BRB II/III

department: Abramson Family Cancer Research Institute

institute: University of Pennsylvania


title: Cell-intrinsic tumorigenic functions of PPARg in bladder urothelial carcinoma [RNA-seq]

summary: PPARg promotes UC progression through cell-autonomous mechanisms linked to sonic hedgehog (SHH) signaling.

overall_design: Treatment of UC cells with PPARg inverse agonist or PPARG deletion reduces proliferation, migration, and invasion of multiple UC cell lines. Genome-wide approaches define a novel set of PPARg-regulated genes in UC, including SHH.

first: D

middle: J

last: Sanchez

first: R

last: Missiaen

first: N

last: Skuli

last: Steger

middle: C


title: Cell-intrinsic tumorigenic functions of PPARg in bladder urothelial carcinoma [ChIP-seq]

overall_design: ChIP-seq of 5637 urothelial carcinoma cells using PPARg, RXR, and control IgG antibodies.


title: Renal transcriptome profiles from mice infected with Leptospira spp.

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

summary:
Leptospirosis caused by pathogenic Leptospira spp. leads to kidney damage that may progress to chronic kidney disease. However, how leptospiral infections lead to renal damage is unclear. Here, we apply microarray platforms to determine the murine renal transcriptome-wide investigation of gene expression changes and biological pathways associated with leptospiral infection-related kidney damage. The aims of this study are to investigate a global analysis of renal gene expression associated with renal damage that was induced by leptospiral infection using experimental murine models.
The result of microarray analysis showed that 467 and 927 genes to be differentially expressed in mice kidney with pathogenic leptospiral infection after day 7 and 28, respectively. Moreover, the result also showed that the 508 significantly differentially expressed genes in the kidneys of mice after infection with non-pathogenic leptospires at 7 days post-infection, and the 1,067 transcripts significantly differentially expressed in these kidneys at 28 days post-infection. Biological pathways performed using KEGG pathway enrichment analysis (P-value < 1E-5) showed that a total of 6 and 7 pathways were significantly enriched at 7 and 28 days post-infection with pathogenic leptospires, respectively. A total of 25 pathways were significantly enriched at day 28 following the non-pathogenic leptospiral infection. However, none of pathways were found in microarray data at day 7 post-infection with non-pathogenic leptospires. In addition, the antigen processing and presentation pathways was significantly enriched at 7 and 28 days post-infection with pathogenic leptospires, and at day 28 following the non-pathogenic leptospiral infection.

overall_design: C57BL/6 female mice were inoculated using intraperitoneal challenge with a high infective dose of L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) and L. biflexa serovar Patoc (ATCC number 23582) , respectively. The control groups were inoculated with sterile EMJH medium . The mice were sacrificed at 7 and 28 days post-infection, and the kidneys were harvested. Total RNA was extracted from kidneys and subjected to Affymetrix whole genome transcriptomic analysis.

first: Chih-Wei

last: Yang


title: SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells

city: Melbourne

first: Conor

last: Kearney

address: Grattan Street

country: Australia

institute: Peter MacCallum cancer Centre

first: Stephin

last: Vervoort

first: Ricky

middle: W

last: Johnstone

first: Jane

last: Oliaro


title: SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [TIL scRNA-seq]

summary: Multi-modal single cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states, but does not allow for simultaneous integration of critical post-translational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq); a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes and the transcriptome at the single cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

overall_design: Single cell sequencing analysis (Including detection of L-Pha lectin) of pooled TILs from B16-Ova and MC38-Ova tumor infiltrating lymphocytes (TILs). The experiment comprises of a single 10x Genomics capture reaction with hashtag 1 marking B16_Ova TILs and hashtag 2 marking MC38-Ova TILs


title: SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [3'RNA-seq]

overall_design: Bulk 3' RNA sequencing of TILs from pooled day 14 B16-OVA tumors (CD8+, TCR+) which were FACS sorted on L-Pha low and L-Pha high.


title: SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [ATAC-seq]

overall_design: TILS (TCR+ CD8+) from day 14 B16-OVA tumors (pooled tumors) were FACS sorted  for L-Pha low and L-Pha high binding. Cells were then subject to ATAC-seq (duplicates).


title: SUGAR-Seq enables simultaneous detection of glycans, epitopes and the transcriptome in single cells [LN scRNA-seq]


title: Nutritional regulation of pathogenesis gene expression in Pseudomonas syringae

first: Joshua

middle: Aaron

last: Granek

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

summary:
Pseudomonas syringae was grown on minimal media and King's B medium.

The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. The summer course was funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".

overall_design: Three biological replicates were assayed for each condition

middle: A

first: Paul

last: Zwack

first: Musoki

last: Mwimba

first: Jonathan

last: Motley


title: The fibrous cap of atherosclerotic lesions arise from multiple cellular origins by PDGFRB- and bioenergetic mechanisms

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

summary: Stable atherosclerotic plaques are characterized by a thick extracellular matrix (ECM)-rich fibrous cap populated by protective ACTA2+ myofibroblast (MF)-like cells, assumed to be almost exclusively derived from smooth muscle cells (SMC). Herein, we show that in murine and human lesions, ~20-40% of ACTA2+ fibrous caps cells, respectively, are derived from non-SMC sources, including endothelial cells (EC) or macrophages that have undergone Endothelial-to-Mesenchymal (EndoMT) or Macrophage-to-Mesenchymal (MMT) transitions. In addition, weshow that SMC-specific knockout of the platelet-derived growth factor receptor beta (PDGFRB) in Apoe-/- mice fed a Western diet (WD) for 18 weeks results in brachiocephalic artery (BCA) lesions nearly devoid of SMC. While absence of SMCs does not affect lesion size, remodeling, or ACTA2+ fibrous cap cell content, prolonged WD feeding results in reduced indices of stability, indicating that EndoMT and MMT-derived MFs cannot compensate indefinitely for loss of SMC-derived MFs. Using RNA-seq analysis of the BCA region and in vitro models, we demonstrate that SMC to MF transitions (SMC-MFT) is induced by PDGF and TFGβ and is dependent on aerobic glycolysis, while EndoMT is induced by IL1β and TGFβ. Together, we provide the first quantitative evidence that the ACTA2+ fibrous cap originates from a tapestry of cell types, which transition to an MF state through distinct signaling pathways that are either dependent on or associated with extensive metabolic reprogramming.

overall_design: scRNA-seq of atherosclerotic plaques of Apoe-/- mouse (with or without specific SMC KO of PDGFRB)

first: Alexandra

last: Newman

first: Vlad

last: Serbulea

first: Richard

last: Bailys

first: Laura

middle: S

last: Shankman

first: Xenia

last: Bradley

first: Gabriel

middle: F

last: Alencar

first: Katherine

last: Owsiany

first: Rebecca

last: Deaton

first: Santosh

last: Karnewar

first: Sohel

last: Shomsuzzaman

first: Anita

last: Salamon

first: Mahima

last: Reddy

first: Liang

last: Guo

first: Aloke

last: Finn

first: Renu

last: Virmani

first: Olga

last: Cherepanova


title: Synaptic small and total RNAome from hippocampal Synaptosomes and the synaptic compartments of microfluidic chambers

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Here we isolate high quality synaptosomes from the hippocampus of young wild type mice and provide, at an unprecedented level, the coding and small non-coding synaptic RNAome. These data are complimented by a novel approach to analyze the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers.  Our data show that synaptic microRNAs control almost the entire synaptic mRNAome and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluid chamber system, we also provide evidence to support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable to study the dynamics of the synaptic RNAome in response to stimulation as shown with KCL treatment.

overall_design: Synaptosomes from hippocampi of 3 month old mice. The other samples are isolated neurites from microfluidic chambers

first: Robert

last: Epple

first: Dennis

last: Krüger

first: Tea

last: Berulava

first: Gerrit

last: Brehm

first: Rezaul

last: Islam

first: Sarah

last: Köster


title: DNA methylome of Canis lupus basenji

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

summary: Using WGBS we investigated blood DNA methylation profiles of Canis lupus basenji and determined putative regulatory elements (unmethlated regions, UMRs, and lowly methylated regions, LMRs).

overall_design: Whole genome bisulphite sequencing of basenji's blood DNA

first: Ozren

last: Bogdanovic


title: Local calcium accumulations promote phagocyte-mediated synapse removal in cortical neuroinflammation

city: Framingham

first: Joseph

last: Gans

state: Ma

address: 49 New York Ave

department: Genomics

institute: Sanofi Genzyme

summary: Cortical pathology contributes to chronic cognitive impairment of patients suffering from the neuroinflammatory disease multiple sclerosis (MS). How such gray matter inflammation affects neuronal structure and function is not well understood. Here we use functional and structural in vivo imaging in a mouse model of cortical MS to demonstrate that bouts of cortical inflammation disrupt cortical circuit activity coincident with a widespread, but transient loss of dendritic spines. Spines destined for removal show local calcium accumulations and are subsequently removed by invading macrophages or activated microglia. Targeting phagocyte activation with a new antagonist of the colony-stimulating factor 1 receptor prevents cortical synapse loss. Overall, our study identifies synapse loss as a key pathological feature of inflammatory gray matter lesions that is amenable to immunomodulatory therapy.

overall_design: RNA-seq of sorted cells from brain of Cortical MS mouse treated with vehicle or CSF1R inhibitor

first: Nellwyn

last: Hagan

first: Dimitry

last: Ofengeim

first: Martin

last: Kerschensteiner


title: C57Bl6J retina lysates in oxygen-induced retinopathy

city: Montreal

first: Mike

last: Sapieha

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

summary: Schemic retinopathies such as diabetic retinopathy (DR) and retinopathy of prematurity (ROP), are the main causes of blindness in working age and pediatric populations in industrialized countries. It is estimated that close to 100 million individuals worldwide suffer from DR and 15 million preterm infants born each year are predisposed to ROP. Regrettably, relatively little is known of the cellular processes at play during late stages of pathological angiogenesis in these diseases and consequently current standards of care target all neovascularization. Oxygen-induced retinopathy (OIR) allows to reproduce experimentally in the mouse retina the pathological features observed in human pathological retina such as ischemic avascular regions as well as epi-retinal neovascularization. Using agnostic and orthogonal approaches, in our work we demonstrate that in contrast to healthy blood vessels, pathological vessels engage pathways of cell cycle arrest, resulting in cellular senescence. These findings combined with further genetic and pharmacological approaches provide mechanistic evidence supporting that targeting selectively senescent vessels in DR represents a potential treatment for neovascular retinal disease.

overall_design: 6 samples were analyzed: control postnatal 14 (2 replicates), OIR postnatal 14 (2 replicates), control postnatal 17 (3 replicates), OIR postnatal 17 (3 replicates), control postnatal 30 (3 replicates), OIR postnatal 30 (3 replicates)

first: Przemyslaw

first: Sergio

last: Crespo-Garcia

first: Agnieszka

last: Dejda

first: Manuel

last: Buscarlet


title: Short term effects of a Methionine Restricted Diet

city: Baton Rouge

first: Thomas

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

summary: Thirty-two, seven-week old male C57BL/6J mice were obtained from Jackson Labs.  Mice were adapted to a 12h/12h reverse light cycle and put on Control diet at 8 weeks of age for 10 days. Food was removed during lights on and restored at lights off. On the day of the experiment, mice were fed Control or MR diet for either 3 or 6 hours. There were 8 mice in each group.  Animals were sacrificed  using CO2 inhalation and decapitation. The hepatic transcriptome was analyzed for the initial effect of low dietary methionine.

overall_design: Comparison of the effect of feeding a methionine restricted (MR) diet for either 3 or 6 hours (each 6 samples from Control and MR fed mice)  on the hepatic transcriptome. The Control diets contain 0.86% methionine, the MR diets 0.17% methionine.

first: Laura

last: Bobart

first: Kirsten

last: Stone

first: Richard

last: Carmouche

first: Jasleen

last: Kaur

first: Susan

last: Newman

middle: P

first: Sara

middle: M

last: Webb

first: Sujoy

last: Ghosh


title: RNA sequencing data from parthenogenetic and biparental cells

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk University

summary: Parthegenetic induced pluripotent stem cells (PgHiPSCs) were generated from parthenogenetic fibroblasts derived mature cystic ovarian teratoma. PgHiPSCs can be used in regenerative medicine, for analysis of genomic imprinting, to study imprinting-related development, and for disease modeling in humans.

overall_design: To investigate the pluripotency state of PgHiPSCs, we analyzed their cellular and molecular characteristics (morphology, RT-PCR, qPCR, immunochemistry, and differentiation capacity in vitro and in vivo). We tested the DNA methylation status of imprinted genes using bisulfite sequencing and demonstrated the androgenetic identity of PgHiPSCs.

last: Choi


title: Transcriptome landscape in fruit flies with mitochondrial methylation deficiency

city: Solna

first: Florian

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

country: Sweden

institute: Karolinska Institutet

summary: Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.

overall_design: RNA-sequencing on four-day old larvae with genetic manipulation of mitochondrial SAM import

first: David

last: Moore

first: Ilian

last: Atanassov

first: Marco

last: Moedas

first: Paula

last: Clemente

first: Ákos

last: Végvári

first: Najla

last: El Fissi

first: Roberta

last: Filograna

first: Anna-Lena

last: Bucher

first: Yvonne

last: Hinze

first: Matthew

last: The

first: Erik

last: Hedman

first: Ekaterina

last: Chernogubova

first: Arjana

last: Begzati

first: Rolf

last: Wibom

first: Mohit

last: Jain

first: Roland

last: Nilsson

first: Lukas

last: Käll

first: Anna

last: Wedell

first: Christoph

last: Freyer

last: Wredenberg


title: The transcriptome analysis of WUS targets

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

summary: WUS is a key transcription factor and plays important role in plant stem cell maintenance. WUS expresses in organizing center and its protein moves upward to stem cells to activate CLV3 expressions. Only a few target genes of WUS were reported which involved in stem cell maintenance. To indentify new targets of WUS, we performed RNA high throughput sequencing after inducing WUS activity with DEX (dexamethasone) and CHX (Cycloheximide).

overall_design: The 4-week-old PUBI10:Mcherry-GR-Linker-WUS plants were inoculated with Cucumber mosaic virus (CMV) in leaves, the shoot apexes were collected at 8dpi. The PUBI10:mCherry-GR-Linker-WUS  plants without CMV inoculation were defined as the mock treated. The shoot apexes with or without CMV infection were treated with CHX (10 μM) alone or CHX+ DEX (15μM) for 2 hours, and then total RNA were isolated from the shoot apexes. Strand-specific RNA-seq libraries were prepared and sequenced on the Illumina Hi-Seq2500 platform. Reads were aligned to the Arabidopsis TAIR10 reference genome, and differentially expressed genes were identified using DEG seq. Two biological replicates were performed for RNA-seq.

first: Haijum

last: Wu


title: Setdb1 in required for intestinal epithelial differentiation and the prevention of intestinal inflammation

city: Dresden

first: Sebastian

last: Zeissig

state: Saxony

address: Fetscherstraße 105

department: Center for Regenerative Therapies (CRTD)

institute: TU Dresden

summary: The intestinal epithelium is a complex, constitutively renewing tissue composed of functionally distinct intestinal epithelial cells (IECs), whose specific cell fates are established and maintained through cell-specific activity of transcription factors, as well as precise gene silencing by chromatin compaction. By facilitating chromatin condensation through histone modification, SETDB1, a histone-lysine N-methyltransferase, is one of the central factors involved in regulation of epigenetic transcriptional repression. Therefore, we set out to study the potential roles of SETDB1 in intestinal epithelial homeostasis and inflammatory bowel disease (IBD). We used RNA-sequencing to profile gene expression changes in intestinal epithelial cells of mice with tamoxifen (TAM)-inducible (Villin-CreERT2) IEC-specific deletion of Setdb1 on day 2 post TAM-injection start, compared to TAM-treated wild-type littermates. We find an expression profile which indicates intestinal epithelial cell death and induction of type I interferon signaling, as a result of de-repression of endogenous retroviruses.

overall_design: RNA seq analysis of mouse intestinal epithelial crypt cells in mice with intestinal epithelial-specific loss of Setdb1, and wildtype littermates on day 2 post-tamoxifen injection start.

first: Lea

last: Juznic

first: Kenneth

last: Peuker

first: Anne

last: Strigli

first: Mario

last: Brosch

first: Alexander

last: Herrmann

first: Robert

last: Haesler

first: Michael

last: Koch

first: Liz

last: Matthiesen

first: Britt-Sabina

last: Löscher

last: Nuber

first: Gunnar

last: Schotta

first: Volker

last: Neumeister

first: Traintaffylos

last: Chavakis

first: Thomas

last: Kurth

first: Mathias

last: Lesche

first: Andreas

last: Dahl

last: von Mässenhausen

last: Linkermann

first: Stefan

last: Schreiber

first: Konrad

last: Aden

first: Philip

last: Rosenstiel

first: Andre

last: Franke

first: Jochen

last: Hampe


title: Culturing human fusion-positive rhabdomyosarcoma cell lines as rhabdospheres enriches for stemness and Notch signaling

city: Durham

first: Corinne

middle: Mary

last: Linardic

address: Box 102382, DUMC

department: Pediatrics

institute: DUKE UNIVERSITY

summary:
The development of three-dimensional cell culture techniques has allowed cancer researchers to study the stemness properties of cancer cells in in vitro culture. However, a method to grow PAX3-FOXO1-positive fusion-positive rhabdomyosarcoma (FP-RMS) - an aggressive soft tissue sarcoma of childhood - has thus far not been achieved, hampering efforts to identify the dysregulated signaling pathways that underlie FP-RMS stemness. Here, we first examine the expression of canonical stem cell markers in human RMS tumors and cell lines. We then describe a method to grow FP-RMS cell lines as rhabdospheres and demonstrate that these spheres are enriched in expression of canonical stemness factors as well as Notch signaling components. Specifically, FP-RMS rhabdospheres have increased expression of SOX2, POU5F1 (OCT4), and NANOG, and several receptors and transcriptional regulators in the Notch signaling pathway. FP-RMS rhabdospheres also exhibit functional stemness characteristics including multipotency, increased tumorigenicity in vivo, and chemoresistance. This method provides a novel practical tool to support research into FP-RMS stemness and chemoresistance signaling mechanisms.
We used microarray to understand the transcriptome profile of rhabdomyosarcoma in different culture condition (adherent, sphere, and xenograft).

overall_design: RNA was isolated from adherent, sphere, xenograft cells using an RNeasy kit (Qiagen) according to the manufacturer’s protocol. Affymetrix U133 Plus 2.0 arrays were used and performed by the Duke University Microarray Facility according to manufacturer’s instruction.

first: Katherine

last: Slemmons

first: Po-Han

last: Chen

first: Jen-Tsan

last: Chi


title: Causal network inference from gene transcriptional time-series response to glucocorticoids [A549_dedex]

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: Gene regulatory network inference is essential to uncover complex relationships among gene pathways and inform downstream experiments, ultimately enabling regulatory network re-engineering. Network inference from transcriptional time-series data requires accurate, interpretable, and efficient determination of causal relationships among thousands of genes. Here, we develop Bootstrap Elastic net regression from Time Series (BETS), a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets. We show competitive accuracy on a community benchmark, the DREAM4 100-gene network inference challenge, where BETS is one of the fastest among methods of similar performance and additionally infers whether the causal effects are activating or inhibitory. We apply BETS to transcriptional time-series data of 2,768 differentially-expressed genes from A549 cells exposed to glucocorticoids over a period of 12 hours. We identify a network of 2,768 genes and 31,945 directed edges (FDR <= 0.2). We validate inferred causal network edges using two external data sources: overexpression experiments on the same glucocorticoid system, and genetic variants associated with inferred edges in primary lung tissue in the Genotype-Tissue Expression (GTEx) v6 project. BETS is available as an open source software package at https://github.com/lujonathanh/BETS

overall_design: unperturbed: A549 cells were stimulated with dexamethasone for 12 hours, after which the conditioned media was repaced and dex removed. mRNA profiles were measured in the 12 hours following dex removal

first: Jonathan

last: Lu

first: Bianca

last: Dumitrascu

first: Ian

last: McDowell

first: Brian

last: Jo

first: Alejandro

last: Barrera

first: Linda

last: Hong

first: Sarah

last: Leichter

first: Timothy

last: Reddy

first: Barbara

last: Engelhardt


title: Causal network inference from gene transcriptional time-series response to glucocorticoids [A549_OE]

overall_design: overexpression samples: mRNA profiles from A549 cells stimulated with dexamethasone and overexpressing one transcription factor, over 12 hours


title: ATAC-seq on parental and acquired resistant cells (AqR)

city: Cincinnati

first: Biplab

last: Dasgupta

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Parental and AqR cells were obtained. DNA was purified and submited for sequencing. Differential chromatin accessiblity was observed. AqR cells were derived from parental cells by adding inhibitor (CAY10566) every 3 days until cells became resistant (at about 3 weeks).

overall_design: 1 parental cell in duplicate and 1 AqR cell in duplicate was submitted and analyzed.

first: Matthew

last: Weirauch

first: Sreeja

last: Parameswaran


title: Small-RNA sequencing of WUS-induced GFP RNA degradation in Nicotiana benthamiana leaves

first: Zhong

last: Zhao

summary: The 35S::GFP fluorescence was silenced 6-day after infiltration to Nicotiana benthamiana leaves due to the post-transcriptional gene silencing, but became stable by adding the viral suppressor 2b which repressed RNA silencing in plants. We performed the small RNA high throughput sequencing to test whether WUS can inhibit 2b functions in repressing plant RNA silencing.

overall_design: The abaxial surface of leaves in 3-week-old N. benthamiana were infiltrated with the mixture of Agrobacterium tumefaciens harbored different constructs, including 35S::GFP + 35S::GUS, 35S::GFP + 35S::2b + 35S::GUS, 35S::GFP + 35S::2b + 35S::WUS. Six days after infiltration, the leaves were used to isolate the small RNA with two biological replicates. Small RNA high-throughput sequencing data was cleaned by removing adaptor and low quality reads. The 18-30 nt reads were mapped with GFP sequence to analysis the total reads with different length in each samples.

first: Haijun

last: Wu

first: Zhicheng

last: Dong


title: RNA-seq on parental and acquired resistant cells (AqR)

summary: Parental and AqR cells were obtained at diferent time-points (Day1 and Day 18). Total RNA was extracted and submitted for RNA-seq. Differential expression was observed between parental and AqR cells. AqR cells were derived from parental cells by adding inhibitor (CAY10566) every 3 days until cells became resistant (at about 3 weeks).

overall_design: 2 parental cell lines in duplicate (G68 D1 A,B and G82 D1 A,B) and 2 AqR cell lines in duplicate (G68 D18 A,B and G82 D18 A,B) were submitted and analyzed.

first: Nupur


title: Lymph node gene expression profiling in hyperlipidemic mice

status: Public on Feb 21 2021

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

department: Biochemistry

country: Japan

institute: Showa University School of Medicine

summary:
Total RNA in mesenteric LNs from chow- or high fat diet-fed Ldlr–/– mice were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion.
The DNA array was conducted using a Mouse Oligo chip 24k (TORAY Industries Inc.) and a 3D-Gene® Scanner (TORAY Industries Inc.) by Kamakura Techno-Science, Inc. (TORAY Industries Inc.).

overall_design: Total RNA in mesenteric LNs from chow- and high fat diet-fed Ldlr–/– mice.


title: Single-nucleotide-polymorphism-adjacent super enhancer network mediates enhanced osteogenic differentiation of mesenchymal stem cells in ankylosing spondylitis [ChIP-seq]

city: Shenzhen

first: Wenhui

last: Yu

state: Guangdong

address: 3025# Shen Nan Road

department: Department of Orthopedics

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

summary: In order to recapitulated the primary mechanism of the pathologically enhanced osteogenesis of mesenchymal stem cells from ankylosing spondylitis patients (ASMSCs) over MSCs from healthy donor, we performed multiomic high-throughput sequencing. We analysed the H3K27ac ChIP-seq data according to ROSE algorithm, and identified super enhancers (SEs) in ASMSCs and HDMSCs. The ASMSC-unique SEs (ASUSEs) are associated with osteogenic differentiation and AS pathogenesis. By integrated analysis of H3K27ac ChIP-seq, ankylosing spondylitis (AS) SNPs and RNA-seq data, we discovered the transcription network regulated by AS SNP-adjacent super enhancers (SASEs) during the enhanced osteogenic differentiation of MSCs from AS patients (ASMSCs), which helped us gain insight into the crutial mechanism of AS pathological osteogenesis. And based on the inhibition effect of SE inhibitor JQ1 on the enhanced osteogenic differentiation of ASMSCs, we proposed that SEs may be attractive targets to treat AS pathological osteogenesis.

overall_design: Examination of the H3K27ac modification in ASMSCs and HDMSCs during osteogenic differentiation

first: Huiyong

last: Shen

first: Zhongyu

last: Xie


title: Radiosensitizing pancreatic cancer with PARP inhibitor and gemcitabine: an in vivo and a whole-transcriptome analysis after proton or photon irradiation

city: Strasbourg

first: Helene

last: Burckel

address: 3 rue de la porte de l'hopital

country: France

institute: ICANS

summary: RNA sequencing profiling showed differentially expressed genes implicated in categories such as DNA repair, type I interferon signaling and cell cycle. Moreover, a large amount of lncRNA were dysregulated after proton therapy, gemcitabine and olaparib. RNA sequencing profiling analysis presented dynamic alteration of transcriptome after chemoradiation and identified a classifier of gemcitabine response.

overall_design: We performed an in vivo study and a whole-transcriptome analysis to determine whether PARP inhibition enhanced gemcitabine-based chemoradiosensitization of pancreatic cancer xenografts, combined with either proton or photon irradiation. NMRI mice bearing MIA PaCa-2 xenografts were treated with olaparib and/or gemcitabine and irradiated with 10 Gy photon or proton.

first: Waisse

last: Waissi

first: Anais

last: Nicol

first: Matthieu

last: Jung


title: Single-nucleotide-polymorphism-adjacent super enhancer network mediates enhanced osteogenic differentiation of mesenchymal stem cells in ankylosing spondylitis.

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

overall_design: Refer to individual Series


title: Single-nucleotide-polymorphism-adjacent super enhancer network mediates enhanced osteogenic differentiation of mesenchymal stem cells in ankylosing spondylitis [RNA-seq]

overall_design: Examination of the mRNA profiles in ASMSCs and HDMSCs during osteogenic differentiation


title: SRPK3 regulates alternative pre-mRNA splicing required for B lymphocyte development and humoral responsiveness

city: Aurora

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

summary: Alternative splicing (AS) of pre-mRNA is a critical component of transcriptional regulation that diversifies the cellular proteome. The Serine-Arginine Protein Kinases (SRPK) initiate early events in AS. Using conditional knockout mice (cKO), we demonstrated the importance of the X-linked Srpk3 gene in B lymphocyte development and in response to immunization in vivo. Significantly decreased numbers of immature and mature B cells were observed in Srpk3-cKO mouse bone marrow relative to wild-type (WT). Immunization of Srpk3-cKO mice with the T lymphocyte-independent type 2 antigen 4-hydroxy-3-nitrophenylacetyl-Ficoll (NP-Ficoll) elicited greatly reduced amounts of NP-specific IgG3. Srpk3 deletion resulted in hundreds of differentially spliced mRNAs in B cells, including mRNAs encoding proteins associated with signaling pathways and mitochondrial function. We conclude that Srpk3 is an immunomodulatory kinase that controls humoral immunity via its regulation of pre-mRNA splicing, antibody production, and metabolism in B cells.

overall_design: Profiling of RNA metabolism in immune cells from wildtype and SRPK3 knockout mice

first: James

last: Hagman

first: Tessa

last: Arends


title: Causal network inference from gene transcriptional time-series response to glucocorticoids

first: Charles

last: Gersbach


title: Impact of antibiotics, cell-free supernatant, LPS, and live cells on Nematostella vectensis gene expression

status: Public on Feb 20 2021

city: Charlotte

first: Adam

last: Reitzel

address: 9201 University City Blvd

department: Biological Sciences

institute: University of North Carolina Charlotte

summary: We used bacteria isolated from field samples of Nematostella vectensis to quantify gene expression through comparisons of transcriptomes.

overall_design: ntotal = 76. 19 conditions (4 replicates each) (19*4 = 76).

first: Quinton

last: Krueger


title: Modulating the unfolded protein response: Impacts of radiation on the response of prostate cancer cells to ONC201.

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

institute: Queen's University Belfast

summary: RNA-Seq analysis of prostate cancer cells primed to irradiation for 24hours with ONC201 shows a sustained suppression of transcripts encoding cell cycle regulators as well as components of the DNA damage response pathways.

overall_design: Evaluation of ONC201 as radio-sensitizer in prostate cancer samples.

first: Ian

middle: G

last: Mills


title: Perturbation panel profiling of human iPSC-derived cardiac myocytes and primary dermal fibroblasts

city: New York

last: Mellis

state: NY

institute: Columbia University

summary: We report gene expression by RNAtag-seq after treatment with 75 different small molecule perturbations in culture of human iPSC-derived cardiac myocytes and genetically matched primary dermal fibroblasts. Perturbations were chosen from the SelleckChem Bioactive Library, among all molecules targeting any kinases or G-protein coupled receptors, and chosen to have as little overlap in annotated targets as possible. Based on these experiments (and others) we show that transcription factors important for cardiac development and cardiac myocyte identity maintenance were frequently up-regulated (i.e., "responsive") after small molecule perturbations of cultured iPSC-derived cardiac myocytes (i.e., responsive). We also show that the set of highly responsive transcription factors in fibroblasts are enriched for barriers to fibroblast reprogramming to iPSC.

overall_design: RNAtag-seq-based RNA sequencing of 2 human cells types (iPSC-derived cardiac myocytes and primary dermal fibroblasts), each in 75 different small molecule perturbation conditions (each in triplicate) and 1 DMSO vehicle control condition (59 replicates for fibroblasts, 63 replicates for cardiac myocytes), and 4 DMSO vehicle control-treated HeLa samples. 576 total samples, multiplexed by RNAtag-seq in batches of 32 to make a total of 18 paired-end libraries. The 75 perturbation conditions, the same for both cell types, consist of 50 single-drug conditions and 25 two-drug conditions. See Mellis et al. citation for dosing and analysis strategy.

first: Rajan

last: Jain

first: Arjun

last: Raj


title: Genomic Profiling of Native R-Loops with a DNA-RNA Hybrid Recognition Sensor Protein

city: Wuhan

first: Kaiwei

last: Liang

state: Hubei

address: # 185 Dong Hu Road

institute: Wuhan University

summary: R-Loops are unique RNA-containing chromatin structures, which participate in various key biological processes and associate with multiple human diseases. Accurately and comprehensively profiling R-Loops in the genome is crucial to study their functions under the physiological and pathological conditions. However, the existing methodologies have produced broad discrepancies in R-Loop profiling and an independent strategy is urgently needed. Here, we constructed an artificial DNA-RNA hybrid recognition sensor protein GST-His6-2XHBD with the hybrid-binding domain of RNase H1, and found GST-His6-2XHBD could specifically interact with DNA-RNA hybrids and behaves similarly to the anti-DNA-RNA hybrid S9.6 antibody in DRIPc-seq. Furthermore, we established a convenient method, R-loop CUT&Tag, by combination of GST-His6-2XHBD with a Tn5-based cleavage under targets and tagmentation approach. R-Loop CUT&Tag generates highly specific signals for native R-Loops, and can sensitively detect the R-Loop signals at the promoter, genebody and enhancer. R-Loop CUT&Tag also provides possibilities to genome-widely map the native R-Loops with limited materials, and may benefit the resolving of the broad discrepancies between multiple R-Loop mapping methods.

overall_design:
Determination of R-Loops in the human genome with DRIPc-seq, DRIP-seq, and CUT&Tag; Determination of PRO-seq, TT-seq and chromatin-associated RNA-seq in HEK293T cells; Determination of H3K27ac in HEK293T cells.
Third-party reanalysis of samples from GSE97072, GSE102474, GSE120637.  Related files are linked below.

first: Pingping

last: Fang


title: Renal Cyclosporin-A (CsA) toxicity

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

institute: Charité - Universitätsmedizin Berlin

summary:
The calcineurin inhibitor immunosuppressant cyclosporin A (CsA) soon gained clinical application, and became a standard of care in organ transplantation, as well as an important treatment option in a variety of autoimmune diseases. The immunosuppressive effect of CsA is mainly attributed to inhibiting calcineurin phosphatase activity, consequently favouring the inactive phosphorylated form of nuclear factor of activated T cells (NFAT). Renal toxicity is a serious adverse effect of CsA, but the underlying mechanisms are insufficiently understood.
CsA has also been shown to induce episodic hypoxia (Fähling et al, 2017; doi: 10.1111/apha.12811). Here, we sought to identify molecular mechanisms of CsA nephrotoxicity.

overall_design: Renal injury is observed following 6 weeks of daily CsA treatment. To identify pathways leading to CsA nephrotoxicity, mice were subjected to one week of daily CsA treatment. Kidneys were harvested and global gene expression profiles were analyzed.

first: Christian

last: Rosenberger

first: Susanne

last: Mathia


title: Transcriptional profiling of endocardial and (arterial or venous-enriched) coronary vascular endothelial cells, purified from murine embryonic hearts at E17.5.

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: A specific tracing system, selectively labeling tomato+ intramyocardial vessels with the Nes-CreER driver, was used together with the Nes-Gfp reporter and endomucin marker to separate, from the same hearts, the three subsets of Ecs (ventricular endocardium, intramyocardial arterial-enriched, and subepicardial venous-enriched endothelial cells), which were subject to transcriptome profiling by RNASeq.

overall_design: Hearts from E17.5 Nes-Gfp(Tg/0); Nes-CreER(Tg/0); R26 (tom/+) embryos (0.1 ug tamoxifen given at E15,5) were dissected and collected, based on GFP+ and Tomato+ fluorescence. Ventricles were minced (after removing atria and aortic region) and subjected to enzymatic digestion with liberase (Roche). Single-cell suspensions were stained, and the following primary immunophenotypic populations were simultaneously FACS sorted:  (1) Endocardial EC-enriched population: viable (dapi-)/Ter119- CD45-/CD31+/GFP+ ;   (2A) Coronary EC-enriched in (intramyocardial) arterial  vessels and capillaries: viable (dapi-)/Ter119- CD45-/CD31+/GFP+/Emcn-low/Tomato+ ;   (2B) coronary EC-enriched in (subepicardial) venous vessels: viable (dapi-)/Ter119- CD45-/CD31+/GFP+/Emcn-low/Tomato-/GFP-low .

first: Sara

last: Gonzalez

first: Joan

last: Isern


title: Differentially expressed mRNAs after silencing lncRNA DDGC

city: jinan

first: Duan

last: Li

address: Wenhua Xi Road

institute: Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University

summary: We have completed the mRNA expression profiling of human granulosa-like tumor cell line KGN to reveal the differentially expressed mRNAs upon lncRNA DDGC knockdown.

overall_design: In this study, we applied mRNA sequencing in human granulosa-like tumor cell line KGN.

first: Xiaoyan

last: WANG

first: Yingying

last: Qin

first: Shidou

last: Zhao


title: Single Nucleus Methylation Sequencing of Mouse Pituitary

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: The pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries, and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable pathway analysis detected corresponding transcriptome and chromatin accessibility programs showing both inter-sexual and inter-individual variation. Multi-omics analysis of gene regulatory networks identified regulons whose composition and function within specific cell types were shaped by the promoter accessibility state of target genes. Co-accessibility analysis comprehensively identified putative cis-regulatory regions, including a domain upstream of Fshb that overlapped the fertility-linked rs11031006 human polymorphism; In vitro CRISPR-deletion at this locus increased Fshb levels, supporting this domain’s inferred regulatory role. The sn pituitary multi-omics atlas [link] is a public resource for elucidating cell-type specific gene regulatory mechanisms and principles of transcription circuit control. This GEO series contain raw (FASTQ) and processed data (ALLC) files for the sn methylation dataset generated by the snmC-seq2 method.

overall_design: Apply snmC-seq2 to individual nuclei isolated from pituitary pooled from 30 adult male C57BL/6 mice

first: Frederique

last: Ruf-Zamojski

first: Michel

last: Zamojski

first: Zidong

last: Zhang

first: Gregory

last: Smith

first: Natalia

last: Mendelev

first: Hanqing

last: Liu

first: German

last: Nudelman

first: Mika

last: Moriwaki

first: Hanna

last: Pincas

first: Rosa

last: Castanon

first: Yongchao

last: Ge

first: Venugopalan

middle: D

last: Nair

first: Nitish

last: Seenarine

first: Mary

last: Amper

first: Xiang

last: Zhou

first: Luisina

last: Ongaro

first: Chirine

last: Toufaily

first: Gauthier

last: Schang

last: Nery

first: Anna

last: Bartlett

first: Andrew

last: Aldridge

first: Nimisha

first: Gwen

last: Childs

first: Olga

last: Trojanskaya

first: Judith

middle: L

last: Turgeon

first: Corrine

last: Welt

first: Daniel

last: Bernard

first: Stuart

last: Sealfon


title: Developmental transcriptome profiling of cardiac vascular endothelial subsets

first: Manuel

last: Gomez


title: Transcriptional profiling of purified endocardial and coronary vascular endothelial cells, isolated from murine embryonic hearts, at two developmental stages

summary: Given that the Nes-gfp allele specifically labels coronary ECs, endogenous GFP and the endomucin marker (which was highly expressed in endocardial cells) were used together to separate endocardial and coronary vascular endothelial cell subpopulations in different developmental stages

overall_design: For the E13.5 developmental stage, GFP+ hearts from E13.5 Nes-gfp (Tg/0) embryos were dissected and collected. Ventricles were minced (after removing atria and aortic region) and subjected to enzymatic digestion with liberase. Single-cell suspensions were stained, and the following primary immunophenotypic populations were simultaneously FACS sorted:    (1)endocardial EC-enriched population: viable (dapi-)/Ter119- CD45-/CD31+/GFP-low/Emcn-high ;  (2) coronary EC-enriched population: viable (dapi-)/Ter119- CD45-/CD31+/GFP+ .    For the E17.5 developmental stage, hearts from E17.5 Nes-Gfp(Tg/0); Nes-CreER(Tg/0); R26 (tom/+) embryos (0.1 ug tamoxifen given at E15,5) were dissected and collected, based on GFP+ and Tomato+ fluorescence. Ventricles were minced (after removing atria and aortic region) and subjected to enzymatic digestion with liberase (Roche). Single-cell suspensions were stained, and the following primary immunophenotypic populations were simultaneously FACS sorted:    (1) endocardial EC-enriched population: viable (dapi-)/Ter119- CD45-/CD31+/GFP+ ;  (2A) coronary EC-enriched in (intramyocardial) arterial  vessels and capillaries: viable (dapi-)/Ter119- CD45-/CD31+/GFP+/Emcn-low/Tomato+ ;  (2B) coronary EC-enriched in (subepicardial) venous vessels: viable (dapi-)/Ter119- CD45-/CD31+/GFP+/Emcn-low/Tomato-/GFP-low .

first: Sara

last: Gonzalez

first: Joan

last: Isern


title: Unraveling the mechanism behind Porphyromonas gingivalis-mediated intestinal inflammation

city: Buffalo

first: Jiho

last: Sohn

state: New York

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

summary: To investigate the mechanism behind P. gingivalis-mediated intestinal inflammation, RNAseq was performed on ileal tissue of mice treated with P. gingivalis or PBS control.

overall_design: 6 PBS controls vs. 6 P. gingivalis treated group.


title: Roles of PINK1 in regulation of systemic growth inhibition induced by mutations of PTEN in Drosophila

city: Beijing

first: Yongchao

last: Han

address: No. 7, Park Road, Zhongguancun Life Science Park, Changping District

institute: National Institute of Biological Sciences, Beijing

summary: The maintenance of mitochondrial homeostasis requires PTEN-induced kinase 1 (PINK1)-dependent mitophagy, and mutations in PINK1 are associated with Parkinson's disease (PD). PINK1 is also downregulated in tumor cells with PTEN mutations. However, there is limited information concerning the role of PINK1 in tissue growth and tumorigenesis. Here, we show that loss of pink1 caused multiple growth defects independent of its pathological target, Parkin. Moreover, knocking-down pink1 in muscle cells induced hyperglycemia and limited systemic organismal growth by induction of Imaginal morphogenesis protein-Late 2 (ImpL2). Similarly, disrupting PTEN activity in multiple tissues impaired systemic growth by reducing pink1 expression, resembling wasting-like syndrome in cancer patients. Furthermore, re-expression of PINK1 fully rescued defects in carbohydrate metabolism and systemic growth induced by the tissue-specific pten mutations. Our data suggest a new function for PINK1 in regulating systemic growth in Drosophila, and shed light on its role in wasting in context of PTEN mutations.

overall_design: Muscle mRNA profiles of 3-day old control (dMef2>GFPRNAi) and muscle-specific knockdown pink1 flies (dMef2>pink1RNAi).

last: Zhuang

first: Tao

last: Wang


title: Distinct amyloid-b and tau associated microglia profiles in Alzheimer's disease

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

institute: UMCG

summary: Alzheimer’s disease (AD) is the most prevalent form of dementia and is characterized by abnormal extracellular aggregates of amyloid-b and intraneuronal hyperphosphorylated, tau tangles and neuropil threads. Microglia, the tissue-resident macrophages of the central nervous system (CNS), are important for CNS homeostasis and implicated in AD pathology. In amyloid mouse models, a phagocytic/activated microglia phenotype has been identified. How increasing levels of amyloid-b and tau pathology affect human microglia transcriptional profiles is unknown. Here, we performed snRNAseq on 482,472 nuclei from non-demented control brains and AD brains containing only amyloid-b plaques or both amyloid-b plaques and tau pathology. Within the microglia population, distinct expression profiles were identified of which two were AD pathology-associated. The phagocytic/activated AD1-microglia population abundance strongly correlated with tissue amyloid-b load and localized to amyloid-b plaques. The AD2-microglia abundance strongly correlated with tissue phospho-tau load and these microglia were more abundant in samples with over tau pathology. This full characterization of human disease associated microglia phenotypes provides new insights in the pathophysiological role of microglia in AD and offers new targets for microglia-state-specific therapeutic strategies.

overall_design: 36 single-nucleus- and 59 bulk- RNAseq samples of nuclei from human brain tissue of 18 donors (2 brain regions per donor). 10 donors were diagnosed with AD, 8 were controls.

first: E

first: N

last: Brouwer

first: S

last: Kooistra

first: M

middle: E

last: Woodbury

first: Y

last: Vermeiren

last: Lambourne

first: J

last: Mulder

last: Kummer

first: T

last: Moller

first: K

last: Biber

first: W

last: den Dunnen

first: P

last: De Deyn

first: B

last: Eggen

first: H

last: Boddeke


title: Setdb1 is required for formation of pancreatic ductal adenocarcinoma by inhibiting p53-mediated apoptosis in mice

city: Kyoto

first: Satoshi

last: Ogawa

state: Kyoto

address: 54 Syogoinkawahara-cho, Sakyo-ku, Kyoto

institute: Kyoto University Graduate School of Medicine

summary: Setdb1, a histone methyltransferase that trimethylates histone H3 on lysine 9, promotes tumorigenesis in various cancers. However, the functional role of Setdb1 in pancreatic ductal adenocarcinoma formation is still unknown. To reveal the role of Setdb1 in murine pancreata, we have employed whole genome microarray expression profiling of Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox pancreata. We found that apoptotic signaling pathway is upregulated in Setdb1-deficient pancreata.

overall_design: We used the isolated acinar cells of Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox pancreata as samples and compared to those of Ptf1aCre; KrasLSL-G12D pancreata.

first: Akihisa

last: Fukuda


title: RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: To identify proteins involved in activity dependent synaptic remodeling that are not caused by changes in mRNA levels we performed RNA-seq and TMT-based quantitative MS.

overall_design: Examination of cLTP induced gene temporal transcription

first: Yi-Zhi

last: Wang

first: Jeffrey

last: Savas

middle: T


title: Expression Data from CD4-CD25+regulatory T cells of VAVcreKeapfl/fl mice

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: The transcription factor Nrf2 regulates oxidative stress responses. The specific role played by Nrf2 in regulatory T cells (Treg), the central regulators of immune homeostasis, is unclear. We used microarrays to detail the global programme of gene expression in CD4+CD25+ T cells of VAVcreKeapfl/fl mice

overall_design: Genome-wide transcriptome analyses for VAVcreKeapfl/fl and WT CD4+CD25+ T cells were performed in independent triplicates using Gene Chip® Mouse Gene 2.0 arrays

first: Kim

last: Ohl

first: Klaus

last: Tenbrock

first: Patricia

last: Klemm


title: Jejunal long noncoding RNAs are associated with glycemic control via gut-brain axis after bariatric surgery in diabetic mice

city: Shanghai

first: Yongjun

last: Liang

address: 2800 Gongwei Road

institute: Shanghai Pudong Hospital

summary: To investigate the alterations in the jejunal Roux limb lncRNA expression signatures after DJB and analyze the functional pathways associated with metabolic improvement on a genome-wide scale in high-fat diet (HFD)-induced diabetic mice.

overall_design: Diabetic mice induced by HFD were randomly assigned into two groups undergoing either DJB or sham surgery. The lncRNA and mRNA expression profiles of the Roux limb segment of the jejunum in both groups were investigated using microarray.

first: Peng

last: Zhang


title: Nanostring Cancer Immune Panel Pre and Post ETC-159

status: Public on Feb 19 2021

city: Durham

first: Nicholas

last: DeVito

state: NC

address: 2301 Erwin Road

institute: Duke University

summary: Tumor specimen samples from the multi-site, international, phase I advanced solid tumor ETC-159 clinical trial (NCT02521844, A*STAR Research Entities, Singapore), were analyzed using the PanCancer IO panel

overall_design:
PanCancer IO panel (NS_CANCERIMMUNE_) contains immune genes including cytokines, chemokines, myeloid cells, T-, B-, and NK-cells, and genes associated with antigen processing.
Pre and post ETC-159 (PORCN inhibitor) samples were taken from Patient 1 (colorectal cancer with RSPO fusion) and Patient 2 (presumed cholangiocarcinoma)

middle: C

first: Brent

last: Hanks


title: Tregs coculture with control or Capns1-knockdown SVEC4-10 cells

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

institute: Showa University School of Medicine

summary:
Purpose: The goals of this study are to compare NGS-derived Treg transcriptome profiling (RNA-seq) to microarray methods and to evaluate phenotypic difference between Tregs cocultured with control and Capns1-knockdown SVEC4-10 cells.
Methods: Isolated splenic CD4+CD25+ Tregs were cocultured with SVEC4-10 cells for 5 days. Then total RNA in cocultured Tregs were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion. Three replicates per each groups were pooled, and were subjected to the RNA-seq analysis using a NovaSeq6000 (Illumina, San Diego, CA) to obtain ~40 million 150 bp paired-end reads by Eurofins genomics (Tokyo, Japan).
Contlusions: There is no remarkable difference in gene profiels between Tregs cocultured with the control and Capns1-knockdown SVEC4-10 cells.

overall_design: Treg mRNA profiles of coculturing with control and Capns1-knockdown SVEC4-10 cells


title: Chip-seq, ATAC-seq, and RNA-seq of murine P14 T cells WT or FOXO1 KO, responding in vivo to LCMV-ARM

first: Stephen

middle: M.

last: Hedrick

address: 9500 Gilman Drive

institute: UC San Diego

summary: P14 CD8+ murine T cells were adoptively transferred to C57BL/6 hosts and infected with LCMV-ARM.  At indicated times post-infection (see sample name), P14 T cells of the indicated cell-surface phenotype were isolated and sujectected to ChIP-seq, RNA-seq or ATAC-seq.

overall_design: Stephen,M,Hedrick

first: Andrew

last: Doedens

first: Arnaud

last: Delpoux

first: Karmel

last: Allison

first: Carol

last: Katayama

first: Rodrigo

middle: H

last: Michelini


title: Single-cell RNA-seq of long bone epiphyses from control and Sox9 mutant mice

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

summary: Using a conditional inactivation approach in the mouse, we examined the importance of SOX9 in adult growth plate and articular cartilage. We specifically investigated the roles of SOX9 in the expression of the pancartilaginous, growth-plate and articular programs and in maintaining the chondrocyte lineage fate.

overall_design: Examination of articular and growth plate chondrocytes mRNA profiles of 3-month-old control,  Sox9 mutant and Sox8 and Sox9 mutant mice.

first: Abdul

last: Haseeb

first: Ranjan

last: Kc

first: Marco

last: Angelozzi


title: RNA seq of larval Cyprinidon variegatus exposed to oil, hypoxia or both for 48 hr, followed by 48 hrs depuration

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

institute: Francis Marion University

summary: The objective of this project was to expose larval Cyprinodon variegatus to oil/hypoxia stressors for 48 hrs, then allow 48 hours of recovery and depuration.

overall_design: Transcriptional profiles were defined at each timepoint to identify recovery processeranscriptional profiles were also compared with genomic methylation patterns to ascertain to correlation between methylation and transcription..

first: Eliabeth

first: Robert

middle: J

last: Griffitt


title: Exposure of CF and WT primary human monocyte derived macrophages to extracellular vesicles secreted by CF or WT primary human airway epithelial cells.

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

summary: Mutations in CFTR have been shown to alter the immune response of macrophages, for example, by reducing the ability of macrophages to phagocytose and kill bacteria. This contributes to chronic bacterial infection and inflammation in the lungs, which leads to significant morbidity and mortality in cystic fibrosis (CF). Extracellular vesicles (EVs) are secreted by a variety of cell types in the lungs and participate in the host immune response to bacterial infection. However, nothing is known about the effect of EVs secreted by CF airway epithelial cells (AEC) on CF macrophages. Therefore, we examined the effect of EVs secreted by primary CF AEC on CF monocyte derived macrophages (MDM) and compared it with the effect of EVs secreted by wild type (WT) AEC on WT MDM. EVs increased pro-inflammatory cytokine secretion and enhanced the expression of numerous innate immune genes in WT MDM. However, the response of CF MDM to EVs was significantly attenuated compared to WT MDM, a difference that was also observed when EVs were isolated from WT and CF AEC exposed to Pseudomonas aeruginosa. Attenuated responses by CF MDM can be attributed to defects in the CF macrophages themselves rather than differences between CF and WT EVs, because EVs secreted by CF AEC or WT AEC elicited similar cytokine secretion by CF MDM. EVs secreted by P. aeruginosa exposed AEC resulted in the upregulation of immune response genes and increased secretion of pro-inflammatory cytokines, chemoattractants and chemokines involved in tissue repair by WT MDM, whereas the response of CF MDM was attenuated by comparison. To our knowledge, this is the first study examining the effect of EVs secreted by CF AEC on CF MDM, and it demonstrates that the Phe508del mutation in CFTR attenuates the innate immune response of MDM to EVs.

overall_design: M-CSF differentiated human monocyte derived macrophages from three CFTR Phe508del homozygous cystic fibrosis donors and three CFTR wild type (WT) donors were exposed to either extracellular vesicles (EV) secreted by Phe508del homozygous CF or WT airway epithelial cells from multiple donors, extracelluar vesicles secreted by CF or WT airway epithelial cells after Pseudomonas aeruginosa exposure (EV-PA), or PBS (Ctrl).

first: Fred

middle: W

last: Kolling

first: Amanda

last: Nymon

first: Roxanna

last: Barnaby

first: Zhongyou

last: Li

first: Thomas

last: Hampton

first: Alix

last: Ashare

first: Bruce

middle: A

last: Stanton


title: Bulk RNA-seq of articular and growth plate chondrocytes from control and Sox9 mutant mice


title: Oil and hypoxia induced alterations to DNA methylation profiles in larval Cyprinodon variegatus

summary: To explore the methylation altering effects of oil  on developing fish, we exposed larval Cyprinodon variegatus to oil for 48 h and used immunoprecipitation coupled with high-throughput sequencing (MeDIP seq) to evaluate genome-wide methylation changes.

overall_design: In this study, we sought to determine the genome-wide effects of oil exposure on the methylome of larval C. variegatus. To examine the persistence of altered methylation, organisms were exposed to oil for 48h, followed by 48h of depuration to allow stabilization of methylation patterns.  We then used immunoprecipitation coupled with high-throughput sequencing (MeDIP seq) to evaluate genome-wide methylation changes.


title: Genome-wide circular RNA expression patterns reflect resistance to immunomodulatory drugs in multiple myeloma cells

city: Aarhus C

first: Theresa

last: Jakobsen

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: Immunomodulatory drugs (IMiDs), such as lenalidomide and pomalidomide, may induce significant remissions in multiple myeloma (MM) patients, but relapses are frequently observed and the underlying molecular mechanisms for this are not completely understood. Circular RNAs (circRNAs) constitute an emerging class of non-coding RNAs with important roles in cancer. Here, we profiled genome-wide expression patterns of circRNAs in IMiD sensitive MM cells and their resistant counterparts as well as in IMiD resistant cells treated with specific epigenetic drugs alone or in combination. We found that genome-wide circRNA expression patterns reflect IMiD-sensitivity and ciRS-7 (also known as CDR1as) was the most downregulated circRNA upon acquired resistance. The depletion of ciRS-7 correlated with increased methylation levels of the promoter CpG island of its host gene, LINC00632. Expression of LINC00632 and ciRS-7 was partly restored by treatment with a combination of an EZH2 inhibitor (EPZ-6438) and a DNA methyl transferase inhibitor (5-azacytidine), which also restores the IMiD sensitivity of the cells. However, knockdown of ciRS-7 did not affect IMiD sensitivity and we found that ciRS-7 also becomes epigenetically silenced after prolonged cell culture without drug-exposure. In conclusion, we found that genome-wide circRNA expression patterns reflect IMiD sensitivity in an in vitro model of acquired resistance.

overall_design: circRNA profiles of multiple myeloma cell line H929 and its IMiD resistant counterparts were generated by deep sequencing using Illumina Hiseq 4000

first: Mette

last: Dahl

first: Konstantinos

last: Dimopoulos

first: Kirsten

last: Grønbæk

first: Jørgen

last: Kjems

first: Lasse

middle: S

last: Kristensen


title: Combined pitavastatin and capmatinib inhibits tumor growth though completed shutdown of MET signal

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

institute: Tokyo Medical and Dental University

summary:
To reveal the function of pitavastatin in cancer, we performed several experiments.  In the present study, we show that pitavastatin inhibits the tumor growth through the inactivation of ERK and AKT signals by MET immaturation, and combination of pitavastatin and capmatinib, a MET inhibitor, might be useful cancer therapy in OSCC and ESCC.  It could be reduced the dose of pitavastatin by using this combination therapy, resulting in decreasing the risk of adverse events such as myopathy.  Taken together, the mevalonate pathway regulates the processes of MET maturation and promotes the cell growth in cancer.  Moreover, the expression of GGPS1, an enzyme that synthesizes geranylgeranyl pyrophosphate (GGPP) from farnesyl pyrophosphate (FPP), associates with the sensitivity of pitavastatin, suggesting that GGPS1 could be a biomarker in cancer therapy with pitavastatin.
Identification of the function of pitavastatin in oral and esophageal squamous cell carcinoma.

overall_design: Extraction of difference of gene expression level between control and treatment of pitavastatin in HOC313-LM, KYSE150 and KYSE200.  Also, extraction of difference of gene expression level between transfection of si-NC and si-GGPS1 in HOC313-LM.

first: Xu

last: Bo

first: Johji

last: Inazawa


title: Lgr5+tuft marker+ intestinal tumor cells

city: Cambridge

first: Norihiro

last: Goto

state: MA

address: 500 Main Street, Building 76

department: Department of Biology

institute: Massachusetts Institute of Technology

summary: We previously identified Dclk1, a tuft cell marker, marks tumor stem cells (TSCs) in mouse intestinal tumors. In this study, we have identified IL17RB as a cell surface marker distinctively expressed by Dclk1+ tuft-like tumor cells in mouse intestinal tumors. Using this tuft cell marker, we compared and analyzed the transcriptome of Lgr5-tuft marker-, Lgr5+tuft marker-, Lgr5-tuft marker+, and Lgr5+tuft marker+ tumor cells. These analyses revealed that tuft-like tumor cells in the intestinal tumors comprise two distinct subsets: highly differentiated tuft-like tumor cells (Lgr5-tuft marker+ cells) and tuft-like tumor cells with TCS potential (Lgr5+tuft marker+ cells).

overall_design: Lgr5-tuft marker(IL17RB)-, Lgr5+tuft marker(IL17RB)-, Lgr5-tuft marker(IL17RB)+, and Lgr5+tuft marker(IL17RB)+ tumor cells were sorted from the EpCAM+ intestinal tumor epithelial cells of Lgr5CreERT2/+; Ctnnb1lox(ex3)/ox(ex3) mice 14 days after tamoxifen administration. Total RNA was extracted from the sorted cells and gene expression profiles were compared.

first: Hiroshi

last: Seno


title: T cell transcriptomes in the course of allogeneic hematopoietic stem cell transplantation II

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: RNA seq data of pooled T cells isolated from skin and blood at multiple time points before and after hematopoietic stem cell transplantation

overall_design: Examination of 1 cell type at 5 time points before and after treatment

first: R

middle: V

last: Pandey

first: J

last: Strobl


title: Transcriptional responses by human skin cells to high-voltage electric field: Sham vs. SE-14000 stimulation

city: bunkyo

first: Masayo

last: Aoki

state: tokyo

address: 1-1-5 Sendagi

department: Plastic Surgery

institute: Nippon Medical School

summary:
Transcriptional profiling of SE-14000 stimulated wound healing associated cells (HaCat, NHDF, HMEC-1) comparing sham-treated cells.
Goal was to determine the effects of SE-14000 in the human skin cells (HaCat, NHDF, HMEC-1).

overall_design: Two-condition experiment, Sham vs. SE-14000 stimulated cells. Biological replicates 3 sham cells, 3 stimulatred cells.

first: Noriko

middle: M

last: Matsumoto


title: GEP signatures of primary breast cells radiation treated.

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Breast cancer (BC) recovery has considerably increased thanks to the advances achieved from research in this field. However, despite the important results obtained, BC remains a complex multifactorial disease with distinct subtypes associated with different outcomes.So, many efforts from radiobiological research are needed to help clinicians in understanding molecular features of a specific tumor subtype, in order to better define the most successful treatment plan, including the choice of the best Radiation Teraphy (RT) modality and schedule in clinical practice. The aim of the present study was to analyze the GEPs in primary breast cancer cells following irradiation with doses of 9 Gy and 23 Gy electron beam delivered by IOERT treatment, in order to define gene signatures of response to high doses of IR.

overall_design: Radiation-induced gene expression changes in healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures obtained from surgical biopsies, were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. Samples were named as follow: ; HMEC_9Gy; HMEC_23Gy; BCpc7_9Gy; BCpc7_23Gy, BCpcEMT_9Gy,  BCpcEMT_23Gy.


title: The impact of exposure to excess zinc on the transcriptome of Streptococcus mutans

status: Public on Feb 18 2021

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

institute: University of Florida

summary: Zinc is a micronutrientient that serves as an important co-factor necessary for enzymatic function.  In the host environment, access to metals can be highy restricted.  As excess metals can be toxic to the bacterial cell, the host immune system can utilize zinc intoxication as a defense mechanism against bacterial infection.  Here, we wanted to identify the transcriptomic response when S. mutans UA159 is exposed to an excess of zinc.

overall_design: Streptococcus mutans UA159 was grown in the chemically defined medium FMC.  Cultures were grown to mid-exponential phase (OD600 = 0.4).  At this point, control samples were  harvested for transcriptional profiling.  To the remaining samples, 4mM ZnSO4 was added.  The incubation of cells was continued to allow for exposure to the excess zinc for 15 or for 90 minutes, at which point these samples were harvested.

first: Tridib

last: Ganguly

first: Jose

last: Lemos


title: Hsa_circRNA_405159 Is A Novel Biomarker to Evaluate the Efficacy of Neoadjuvant chemoradiotherapy in Rectal Cancer

city: Jinan

first: Ying

middle: ying

last: Zhang

state: Shandong

address: Jingshi 16766

institute: The first Affiliated Hospital of Shandong first Medical University

summary: Our study was the first to investigate the role of hsa_circ_004119 in RC of NACRT, providing a biomarker about the efficacy of NACRT. Hsa_circRNA_405159 could be the therapeutic target of rectal cancer to improve the efficiency of neoadjuvant chemoradiation.

overall_design: A total of 6 RC patients were enrolled. Based on the response to NACRT, the subjects were divided into two groups. The differently expressed circRNAs were analysis by microarray.

first: Feng

last: Li

first: Ying-Ying

first: Wei-Zhong

last: Jiang

first: Qing-Liang

last: Lin


title: Floral transition trajectories dissected by single meristem transcriptomes at high temporal resolution.

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

summary: We developed a method we denote as single meristem transcriptome profiling (SMT) and utilize it in this work to analyze hundreds of single tomato shoot-apical-meristems of several genotypes, which were collected during or when approaching floral transition. This provide us with dense temporal sampling of the wild-type process which we used in order to generate a pseudo-time reference, anchored by morphology-based scores. This allows for examination of molecular changes in the genetically-perturbed processes by temporal alignment.

overall_design: Prior to RNA extraction from each homogenized meristem, we recorded the number of leaves it produced, and assigned one of five morphological scores to it (describing subtle nuances in meristem doming). UMI-based cDNA libraries were generated from 12-24 technical replicates of each meristem. UMIs from different wells were then summed together to generate one transcriptional profile for each meristem (see quality-control panels for SMT estimates in Meir, Aviezer et al., 2021).

first: Yuval

last: Eshed

first: Amos

last: Tanay


title: Detection of microRNAs in the plasma of cardiac surgery patients of high and low risk of developing non occlusive mesenteric ischemia

city: Auckland

first: Jiwon

last: Hong

state: Auckland

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

summary: Aim to identify circulating plasma miRNA markers of heart surgery and NOMI

first: Cherie

last: Blenkiron

first: Anthony

last: Phillips


title: Formative pluripotent stem cells show features of epiblast cells poised for gastrulation

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

summary: The pluripotency of mammalian early and late epiblast could be recapitulated by naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), respectively. However, these two states of pluripotency may not be sufficient to reflect the full complexity and developmental potency of the epiblast during mammalian early development. Here we report the establishment of self-renewing formative pluripotent stem cells (fPSCs) which manifest features of epiblast cells poised for gastrulation. fPSCs can be established from different mouse ESCs, pre-/early-gastrula epiblasts and induced PSCs. Similar to pre-/early-gastrula epiblasts, fPSCs show the transcriptomic features of formative pluripotency, which are distinct from naïve ESCs and primed EpiSCs. fPSCs show the unique epigenetic states of E6.5 epiblast, including the super-bivalency of a large set of developmental genes. Just like epiblast cells immediately before gastrulation, fPSCs can efficiently differentiate into three germ layers and primordial germ cells (PGCs) in vitro. Thus, fPSCs highlight the feasibility of using PSCs to explore the development of mammalian epiblast.

overall_design: We established formative pluripotent stem cells (fPSCs) with long-term self-renewal capacities from mESCs, and mouse pre-gastrula epiblast cells, through mimicking the in vivo environment of postimplantation developing embryos combined with suppression of the Wnt/β-catenin pathway. Then we performed transcriptome and epigenome analyses to investigate whether fPSCs represent a stable intermediate state between naïve ESCs and primed EpiSCs.

first: Xiaoxiao

last: Wang

first: Yunlong

last: Xiang

first: Yang

last: Yu

first: Lei


title: Establishing the copper response of Burkholderia cenocepacia K56-2

city: Exeter

first: Jack

last: Plume

address: Geoffrey Pope, University of Exeter, Stocker Road

country: United Kingdom

institute: University of Exeter

summary: Purpose - To establish the response of B. cenocepacia K56-2 to growth in copper, and to characterise the BCAM0442/3 copper-sensing TCS. Methods - RNA-seq of the response WT and Δbcam0442/3 B. cenocepacia K56-2 to mid-log phase growth in LB with or without 1 mM CuCl2 was performed. Results - Characterisation of the overall response of B. cenocepacia K56-2 to copper, as well as establishing that BCAM0442/3 regulates the CopABCDE system in B. cenocepacia

overall_design: WT and Δbcam0442/3 B. cenocepacia K56-2 were grown for 8 hours in LB with or without 1 mM CuCl2. Total RNA was then extracted and processed. Three replicates per conditions.

first: Alan

middle: R

last: Brown


title: Next Generation Sequencing Quantitative Analysis of Wild Type and Mki67-/- 4T1 mouse mammary carcinoma cell histone modification

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

institute: CNRS

summary: Ki-67 chromatin associated proteins that has been shown to broadly affect the transcription profiles of cells when knocked-out. To understand if those transcriptome changes are regulated by histone modifications we performed ChIP-seq analysis for three of the most recognized histone marks (H3K27me3, H3K4me3 and H3K27ac) as the regulators of gene expression, in wild-type (WT) and  Ki-67 knockout (Mki67−/−) mouse 4T1 cells.

overall_design: ChIP-seq profiles for H3K27me3, H3K4me3 and H3K27ac histone marks of wild-type (WT) and two clones of Ki-67 knockout (Mki67−/−) mouse 4T1 cells, all in duplicate, were generated by deep sequencing using Illumina Hiseq2500.

first: Dhanvantri

last: Chahar

first: Karim

last: Mrouj

first: Geronimo

last: Dubra

first: Liliana

last: Krasinska


title: Next Generation Sequencing Quantitative Analysis of the transcriptomes of Wild Type and Mki67-/- MDA-mb231 (human breast adenocarcinoma) cell line

summary:
Purpose: The goals of this study were to compare gene expression profiles of MDA-mb231 cell lines with intact or disrupted Mki67 gene.
Methods: mRNA profiles of wild-type (WT) and three Ki-67 knockout (Mki67−/−) clones in the MDA-mb231 cell line, were generated by deep sequencing using DNBSEQ-G50 in paired-end read mode, 100bp. The sequence reads that passed quality filters were aligned to the mouse genome, quantified, and differential gene expression (DGE) analysis was performed using DEseq2.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (GRCh38) and identified differentially expressed genes.  This revealed widespread changes in gene expression
Conclusions: Ki-67 knockout causes genome-scale transcriptome alterations

first: Adres

last: Sanchez Nuria


title: Human HeLa cells: Control shRNA vs Ki-67 shRNA, in vitro and xenografts

summary: Transcriptional profiling of isogenic human cervical cancer cell line HCT-116, comparing cells treated with control shRNA  or with Ki-67 shRNA, grown either in vitro or as tumours in nude mice. The aim was to assess effects of loss of Ki-67 on gene expression during exponential cell growth and in tumours

overall_design: Four condition experiment. 3 biological replicates of each condition

first: Michal

last: Sobecki


title: Adipocyte-derived extracellular vesicles regulate survival and function of pancreatic β-cells

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

institute: University of Turin

summary: We explored the effects of extracellular vesicles (EVs), released from both rodent and human isolated adipocytes, on survival and function of pancreatic β-cells and human pancreatic islets.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Analysis of differential expression of microRNAs in EVs from healthy and inflamed 3T3-L1 and human primary adipocytes

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