title: Impact of ZFAND3 knockdown on whole-genome gene expression in GBM cells

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

summary: ZFAND3 was beforehand identified to be invasion essentiel in GBM cells using genome-wide shRNA library screen to identify invasion-defective and invasion-essentiel genes. The knockdown of ZFAND3 decreases invasion behaviour of GBM cells. To determine the differences in gene expression upon knockdown, whole-genome RNA sequencing was performed.

overall_design: Control GBM cell line vs two different ZFAND3 knockdown cell lines

first: Simone

last: Niclou

last: Schuster


title: Transcriptional responses of autophagy proficient and deficient pancreatic tumors and cells treated with TNFα

status: Public on Sep 30 2020

city: New York

first: Xiphias

middle: Ge

last: Zhu

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

type: Expression profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma (PDAC) cells require substantial metabolic rewiring to overcome nutrient limitations and immune surveillance. However, the metabolic pathways necessary for pancreatic tumor growth in vivo are poorly understood. To address this, we performed metabolism-focused CRISPR screens in PDAC cells grown in culture or engrafted in immunocompetent mice. While most metabolic gene essentialities are unexpectedly similar under these conditions, a small fraction of metabolic genes are differentially required for tumor progression. Our screens identify autophagy as a metabolic requirement for pancreatic tumor immune evasion. Mechanistically, autophagy protects cancer cells from CD8+ T cell killing through TNFα-induced cell death in vitro. This data set contains RNA-seq data of KP pancreas Atg7_KO cells expressing empty vector or Atg7 cDNA. These cells were grown as subcutaenous tumors and also cultured in vitro with and without TNFα.

overall_design: RNA sequencing: KP panc Atg7_KO cells expressing empty vector or Atg7 cDNA. Cells were grown as subcutaneous tumors in C57BL/6J mice or in vitro with or without TNFα. Three replicates were done for each condition.

middle: G

first: Kivanc

last: Birsoy


title: TRIB3 Promotes C-Myc-Associated Lymphomagenesis through Inhibition of UBE3B-Mediated c-Myc Degradation

status: Public on Oct 01 2020

city: bei jing

first: wang

last: feng

address: nan wei road

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: EZH2-GATA6 axis in Pancreatic ductal adenocarcinoma

city: GOETTINGEN

first: SHILPA

last: PATIL

state: No further selection needed

address: ROBERT KOCH STRASSE 40

country: Germany

institute: UNIVERSITY MEDICAL CENTER GOETTINGEN


title: Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray

city: Oklahoma City

first: Susan

middle: Kasko

last: Munster

state: OK

address: 6500 S. MacArthur Blvd.

department: Office of Aerospace Medicine

institute: Federal Aviation Admininistration

summary:
Comparison of total RNA-seq and Affymetrix GeneChip(R) Human Transcriptome Array 2.0 analysis methods and Affymetrix GeneChip® WT PLUS Reagent and NuGEN Ovation® PICO WTA System V2 amplification methods for the detection of significant differentially expressed genes isolated from whole blood and brain RNA samples

Affymetrix and NuGEN amplification methods are compared to determine which is most efficient, cost effective, and accurate in the detection of differentialy expressed transcript clusters on the HTA 2.0 microarray
The optimum amplification microarray data is compared to total RNA-seq analysis of the same samples to determine which is the most efficient, cost effective, and accurate method of detecting differentially expressed genes

overall_design:
Samples containing 100% blood, 67% blood/33% brain, 33% blood/67% brain, and 100% brain -derived RNA were amplified and hybridized onto HTA 2.0 microarrays. In R, limma was used to test for differential expression.  These same samples were analyzed using total RNA-seq and results were also analyzed for differential expression.  A subset of overlapping microarray and RNA-seq genes were compared for differential expression and log fold change ranges.  Counts of differentially expressed genes were also compared from complete microarray and RNA-seq datasets as well as log fold change ranges for both methodologies

Please note that Affymetrix and NuGEN datasets were normalized separately.

middle: K

first: Vicky

middle: L

last: White

first: David

middle: C

last: Hutchings

first: Dennis

middle: M

last: Burian

first: Scott

middle: J

last: Nicholson


title: Transcriptome and Proteome Mapping in the Sheep Atria Reveal Molecular Features of Atrial Fibrillation Progression

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

summary: Atrial fibrillation (AF) is often a progressive cardiac arrhythmia that increases the risk of hospitalization and adverse cardiovascular events. There is a clear demand for more inclusive and large-scale approaches to understand the molecular drivers responsible for AF, as well as the fundamental mechanisms governing the transition from paroxysmal to persistent and permanent forms. We aimed to create a molecular map of AF and find the distinct genetic programs underlying cell type-specific atrial remodeling and AF progression. We used a sheep model of long-standing, tachypacing-induced AF, sampled right and left atrial tissue and isolated cardiomyocytes from control, intermediate (transition) and late time points during AF progression, and performed transcriptomic and proteome profiling. We have merged all these layers of information into a meaningful 3-component space in which we explored the genes and proteins detected and their common patterns of expression. Our data-driven analysis points at extracellular matrix remodeling, inflammation, ion channel, myofibril structure, mitochondrial complexes and chromatin remodeling as hallmarks of AF progression. Most important, we prove that these changes occur at early transitional stages of the disease, but not at later stages, and that the left atrium undergoes significantly more profound changes than the right atrium in its expression program. The pattern of dynamic changes in gene and protein expression correspond closely with the electrical and structural remodeling demonstrated previously in the sheep and in humans. The results provide novel insight into the dynamics of gene and protein expression changes that underlie AF-induced atrial remodeling and that make the arrhythmia become more stable and long lasting.

overall_design: Left and right atrial appendages and posterior left appendage, whole-tissue and isolated cardiomyocytes, mRNA profiles of sham, transition and chronic sheeps were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Alba

last: Alvarez-Franco

first: Raquel

last: Rouco


title: Properties of PD1+ B cells in Rheumatoid Arthritis (RA) Patients

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

summary: We study a new pathogenic, glycolytic PD1+ B cell population in sites of inflammation of patients with Rheumatoid Arthritis (RA).

overall_design: RNASeq of PD1+ and PD1- B cells to understand mechanisms of pathogenicity.

first: Sunil

last: Nagpal


title: Comparision of the transcriptomes of two muskmelon (Cucumis melo L.) cultivars in response to salt stress

city: shanghai

first: yidong

last: zhang

address: Dongchuan road 800

institute: shanghai jiao tong university

summary: The object of this study was to integrate physiological characteristics and genome-wide transcriptome analysis to understand the molecular basis of genetic variation in response to salt stress in melon. The comparison of transcriptome showed a number of variety-specific responsive genes were related to salt tolerance.

overall_design: RNA sequencing two melon cultivars under salt stress

first: Yidong

last: Zhang


title: Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis

status: Public on Sep 29 2020

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular RNAs (exRNAs) have attracted great attention due to their essential role in cell-to-cell communication as well as their potential as non-invasive disease biomarkers. Recent studies have shown that exRNAs are associated with a variety of biological processes. Thus, the study of deregulated exRNAs would provide insight into disease progression. At present, there is no consensus on the best method to profile exRNA expression, which leads to significant variability across studies. To address this issue, we established a robust pipeline for comprehensive profiling of small exRNAs isolated from cell culture. With this method, we performed small RNA sequencing of exosomes (EXOs), microvesicles (MVs) and source cells from 14 cancer cell lines.

overall_design: small RNA-seq to identify miRNA expression in extracellular RNAs.

first: Fangjia

last: Tong

first: Arlise

last: Andress

first: Gongyu

last: Tang

first: Ping

last: Liu


title: Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions

city: London

first: Dervis

middle: A

last: Salih

address: Gower St

department: Dementia Research Institute

country: United Kingdom

institute: University College London

summary: The purpose of this project was to investigate whole genome expression in primary microglia cultured from homozygous Trem2 R47H knock-in mice versus wild type littermates under basal conditions and in response to IL-4 treatment. The primary phenotype of microglia from Trem2 R47H knock-in mice was decreased expression levels of Trem2. IL-4 induced the expression of an anti-inflammatory programme of genes in microglia, which was attenuated when Trem2 expression was decreased.

overall_design: Two genotypes: homozygous Trem2 R47H knock-in and wild type mice. Two treatment groups: untreated or IL-4 treated.

first: Wenfei

first: Orjona

last: Taso

first: Rui

first: Sevinc

last: Bayram

first: Andrew

last: Graham

first: Pablo

last: Garcia-Reitboeck

first: Anna

last: Mallach

first: William

middle: D

last: Andrews

first: Thomas

last: Piers

first: Juan

last: Botia

first: Jennifer

last: Pocock

first: Damian

last: Cummings

first: John

last: Hardy

first: Frances

last: Edwards


title: Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

city: Solna

first: Federico

last: Agostini

state: Stockholm

address: Tomtebodavägen 23a

country: Sweden

institute: Science for Life Laboratories

summary: sBLISS (in-suspension Break Labeling In Situ and Sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs), in any cell type that can be brought into suspension. After in situ labeling, DSB ends are linearly amplified followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, followed by a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which circumvents the need to work with delicate coverslips as in the original BLISS, (ii) the possibility for adaptation to a high-throughput robotics or single-cell workflow, and (iii) its flexibility and applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks, and it is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.

overall_design: Step-by-step protocol for genome-wide DSB labeling using our newly developed sBLISS method. Deposited data (one mouse tissue-sorted jejunum enterocytes, and one human cancer cell experiment set-TK6 cells treated with etoposide or not) aims to provide examples and can be used to work through the included mapping pipeline and analysis tutorial.

first: Britta

last: Bouwman

first: Silvano

last: Garnerone

first: Giuseppe

last: Petrosino

first: Henrike

last: Gothe

first: Sergi

last: Sayols

first: Andreas

middle: E

last: Moor

first: Shalev

last: Itzkovitz

first: Magda

last: Bienko

first: Vassilis

last: Roukos

first: Nicola

last: Crosetto


title: Temporal- and Orbital Shear Stress-Dependent Changes in Opossum Kidney (OK) Cell Transcription

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

summary: We previously demonstrated that OK cells cultured under orbital shear stress have morphological and functional features that more closely resemble the proximal tubule in vivo. This study was designed to identify progressive transcriptional changes with increasing exposure time to shear stress and to compare the transcriptome of cells cultured under shear stress vs static conditions.

overall_design: OK cells plated on permeable supports were transferred to an orbital shaker the following day (t=0) and cultured up to 96h. Filters were harvested at 12, 48, and 96h for RNASeq analysis. Parallel filters maintained under static conditions were harvested at 0, 48, and 96h.

first: Hyun

last: Park

first: Ora

last: Weisz


title: Rosmarinic acid methyl ester regulates ovarian cancer cell migration and reverses cisplatin resistance by inhibiting the expression of Forkhead box M1

status: Public on Sep 28 2020

city: SUWON

first: Ki Hong

last: Nam

state: GYEONGGI-DO

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

summary: Rosmarinic acid methyl ester (RAME), a derivative of rosmarinic acid (RA), has been reported to have several therapeutic effects, including anti-tumor effects, against cervical cancer. However, its anti-tumor effects in ovarian cancer is unclear. In this study, we studied the molecular pathways associated with the anti-tumor effects of RAME in ovarian cancer. To identify the effects of RAME in ovarian cancer, RNA sequencing was performed in RAME-treated ovarian cancer cells; we found that RAME treatment downregulated genes closely involved with the target genes of the transcription factor Forkhead box M1 (FOXM1). It has been reported that FOXM1 is overexpressed in a variety of cancer cells and is associated with cell proliferation and tumorigenesis. Therefore, we hypothesized that FOXM1 is a key target of RAME; this can result in its anti-tumor effects. Treatment of ovarian cancer cells with RAME inhibited cell migration and invasion, as shown by wound healing and transwell migration assays. To examine whether RAME represses the action of FOXM1, we performed quantitative RT-PCR and ChIP-qPCR. Treatment of ovarian cancer cells with RAME decreased the mRNA expression of FOXM1 target genes and the binding of FOXM1 to its target genes. Moreover, FOXM1 expression was increased in cisplatin-resistant ovarian cancer cells, and combination treatment with RAME and cisplatin sensitized the cisplatin-resistant ovarian cancer cells, which was likely due to FOXM1 inhibition. Our research suggests that RAME is a promising option in treating ovarian cancer patients by revealing a novel molecular pathway underlying its anti-tumor effects.

overall_design: The mRNA expression profiles of RAME treated SKOV3 ovarian cancer cell line

first: Soo

last: Lim

first: Ki

first: Kyungtae

last: Kim

first: Sang

last: Yi

first: Jaecheol

last: Lee

first: Jeung-Whan

last: Han


title: Gene expression profile in cisplatin-resistant lung cancer cells

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

institute: National Cancer Center

summary: Gene expression profile in parental and cisplatin-resistant A549 cells

overall_design: mRNA expression profiles of the A549 cells before and after drug treatment were examined by Illumina Hi-seq 2000.

first: Hee-Yeon


title: Gene expression in drug-resistant and circulating tumor cell cultured H460 or A549 cells

summary: Gene expression in drug resistant and circulating tumor cell cultured H460 or A549 cells

overall_design: mRNA expression profiles of 2-dimensionally cultured and circulating tumor cell cultured H460 and A549 cells, parental and drug-resistant H460 cells were examined by Illumina Hi-seq 2500.


title: Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ATAC-Seq]

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

summary: Breast cancer is one of the most prevalent cancers in women worldwide. Through the regulation of many coding and non-coding target genes, estrogen (E2 or 17b-estradiol) and its nuclear receptor ERα play important roles in breast cancer development and progression. Despite intensive studies on estrogen-regulated coding genes over the past decades, molecular mechanisms underlying estrogen-regulated non-coding RNAs in breast cancer remain to be elucidated. Here, we performed extensive epigenomic studies including GRO-seq and ATAC-seq, and identified genome-wide estrogen-regulated long non-coding RNAs (lncRNAs). Similar to the coding targets of ERα, the transcription of estrogen-regulated lncRNAs correlates with the activation status of ERα-bound enhancers, measured by eRNA production, chromatin accessibility, and the occupancy of the enhancer regulatory components including P300, MED1, and ARID1B. Our 3D chromatin architecture analyses suggest that lncRNAs and their neighboring E2-resonsive coding genes, exemplified by LINC00160 and RUNX1, might be regulated as a 3D structural unit resulted from enhancer-promoter interactions. Finally, we evaluated the expression levels of LINC00160 and RUNX1 in various types of breast cancer and found that their expression positively correlated with the survival rate in ER+ breast cancer patients, implying that the estrogen-regulated LINC00160 and its neighboring RUNX1 might represent potential biomarkers for ER+ breast cancers.

overall_design: Assay for Transposase-Accessible Chromatin followed by high throughput sequencing (ATAC-seq)

first: Zhang

last: Zhao

first: Liu

last: Zhijie


title: BAHCC1 couples H3K27me3 to gene silencing and tumorigenesis via a conserved BAH module [Gw760_E2aPbx1_mouse_Rnaseq]

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: BCBP

institute: UNC Lineberger Comprehensive Cancer Center

summary: Tri-methylation of histone H3 lysine 27 (H3K27me3) regulates transcriptional repression, cell-fate determination and differentiation. We report that a conserved Bromo-Adjacent Homology (BAH) module harbored within BAHCC1, a previously uncharacterized chromatin regulator, ‘recognizes’ H3K27me3 specifically and enforces silencing of H3K27me3-demarcated genes in mammalian cells. Biochemical, structural and ChIP-seq-based analyses demonstrate that direct ‘readout’ of H3K27me3 by BAHCC1 is achieved through a hydrophobic trimethyl-lysine-binding ‘cage’ formed by the BAH domain, mediating co-localization of BAHCC1 and H3K27me3-marked genes. BAHCC1 is significantly overexpressed in human acute leukemia and biochemically, BAHCC1 interacts with repressors SAP30BP and HDAC. In acute leukemia, depletion of BAHCC1, or disruption of the BAHCC1 BAH-mediated ‘readout’ of H3K27me3, causes de-repression of H3K27me3-targeted genes that are involved in tumor suppression and cell differentiation, leading to the suppressed tumor growth. In mice, introduction of a germ-line mutation at Bahcc1 to disrupt its H3K27me3 engagement causes postnatal lethality, supporting a role of this pathway in development. Collectively, this study unveils a novel H3K27me3-directed transduction pathway in mammal cells that relies on a conserved BAH ‘reader’, deregulation of which contributes to oncogenesis.

overall_design: Transcriptome profilings of the E2a-Pbx1-transformed murine acute leukemia lines, which were established by using primary hematopoietic stem/progenitor cells (HSPCs) derived from bone marrow of either WT mice or those carrying the engineered homozygous mutations of the Bahcc1 BAH domain (i.e., Y2537A).

first: Huitao

last: Fan

first: Yiran

last: Guo

first: Greg


title: Determination of transcriptional start sites in the presence of GABA for Corynebacterium glutamicum

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: In this study, we analyzed the regulation of ƴ-aminobutyrate (GABA) utilization in Corynebacterium glutamicum by the PucR-type transcriptional regulator GabR and by alternative nitrogen and carbon sources.

overall_design:
RNAseq analysis was performed to determine transcriptional start sites of genes that are related to GABA utilization.

Cappable-seq RNA treatment was done by vertis Biotechnologie AG (Freising-Weihenstephan, Germany):
Capping of the 5' triphosphorylated RNA with 3'- desthiobiotin-TEG-guanosine 5' triphosphate (DTBGTP) (NEB) using the vaccinia capping enzyme (VCE) (NEB) for reversible binding of biotinylated RNA species to streptavidin

Capturing of biotinylated RNA species on streptavidin beads and elution to obtain the 5' fragment of the primary transcripts

The Cappable enriched RNA samples were poly(A)-tailed using poly(A) polymerase. In order to remove residual 5'P-ends, the RNAs were treated with Antarctic Phosphatase (NEB). Then, the 5'PPPcap structures were converted to 5’P using the RppH enzyme (NEB; analog to CAP-Clip Acid Pyrophosphatase). Afterwards, an RNA adapter was ligated to the newly formed 5'-monophosphate structures. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase.

For Illumina sequencing, 100 – 300 bp long 5' fragments were isolated from the full-length cDNAs. Forthis purpose the cDNA preparations were fragmented and the 5'-cDNA fragments were then bound to streptavidin magnetic beads. The bound cDNAs were blunted and the 3' Illumina sequencing adapter was ligated to the 3' ends of the cDNA fragments. The bead bound cDNAs were finally PCR-amplified.

The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

first: Michael

last: Bott

first: Meike

last: Baumgart

first: Christina

last: Mack


title: miRNA and gene expression profiling in human thyroid carcinomas and non-neoplastic thyroids [RNA]

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We performed miRNA and gene expression profiling in a series of 30 thyroid carcinomas and 6 non-neoplastic thyroids.

overall_design: MiRNA and gene expression profiles were established by microarray analysis in a series of 36 snap-frozen tissues using SurePrint G3 Human miRNA 8x60K microarrays (Agilent Technologies) and HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina), respectively. Tissue samples were obtained from Fondazione IRCCS Istituto Nazionale dei Tumori (Milan) and include various thyroid carcinoma histotypes: 20 papillary carcinomas (PTCs) consisting of different histological variants, 7 poorly differentiated thyroid carcinomas (PDTCs) and 3 lymph node metastases derived from PTC.

first: M

last: Borrello

first: P

last: Romeo

first: E

last: Minna

first: L

last: De Cecco

first: S

last: Pilotti


title: BAHCC1 couples H3K27me3 to gene silencing and tumorigenesis via a conserved BAH module [BAHCC1_KD_k27me3_293_ChIPseq]

overall_design: Examination of the genome-wide distribution of H3K27me3 in Jurkat T-ALL cells with either WT BAHCC1 or the homozygous mutations of the BAHCC1 BAH domain (i.e., W2554G). Examination of the genome-wide distribution of H3K27me3 in HEK293 cells.


title: Gene expression signatures identify pediatric patients with multiple organ dysfunction who require advanced life support in the intensive care unit

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

summary: Multiple organ dysfunction syndrome (MODS) can result  from a variety of initiating events such as infection or trauma. The clinical condition of some MODS patients may deteriorate and require intense resource and  high-risk cardiopulmonary support via extracorporeal membrane oxygenation (ECMO). Until now, no diagnostic criteria/molecular biomarker has been developed to identify MODS patients who require subsequent ECMO support. We used multi-time point (0h, 72h and 8d) whole transcriptomics from total blood of 27 patients (contro-4, MODS-17 and ECMO-6) to derived the molecular signatures to diagnose the MODS patients required ECMO support. We observed that immune response (neutrophil level) was compromised in MODS patients, who required ECMO support. Differential gene expression analysis and gene ontology enrichment has revealed that epigenetic modifications has got activated during the MODS deterioration to ECMO. In addition, signature of 6 genes were identified using logistic regression, which can be used as putative diagnostic markers for patients needed ECMO support.

overall_design:
RNA was isolated from each samples using KAPA RNA HyperPrep Kit as per manufucturar description. Further, ribodepleted RNA was obtained from total RNA using ribominus kit. RNA-Seq library was generated for individual samples from the ribo-depleted RNA. Sequencing of library was done on illumine Nextera 500 sequencing platform.
Raw data files were not provided due to patient privacy concerns.

first: R

last: Shankar

first: ML

last: Leimanis

last: Newbury

first: K

first: J

last: Xing

first: D

last: Nedveck

last: Kort

middle: W

last: Prokop

first: G

last: Zhou

first: A

middle: S

last: Bachmann

first: B

last: Rajasekaran


title: Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ChIP-Seq]

first: Zhijie

last: Liu

overall_design: Chromatin Immunoprecipitation (ChIP) assay followed by high throughput sequencing (ChIP-seq)

first: Zhang

last: Zhao

first: Liu

last: Zhijie


title: PD-1 restraint of regulatory T cell suppressive activity is critical for immune tolerance

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

summary: We report that PD-1 restraint of regulatory T cell suppressive activity via the PI3K-AKT pathway and metabolism is critical for immune tolerance. We generated mice that selectively lack PD-1 in Treg cells. Mice lacking PD-1 selectively in Treg cells had ameliorated experimental autoimmune encephalomyelitis (EAE) and protection from diabetes in non-obese diabetic (NOD) mice . We identified reduced signaling through the PI3K-AKT pathway as a mechanism underlying the enhanced suppressive capacity of PD-1 deficient Treg cells by undertaking bulk RNA-seq of CNS-infiltrating Treg cells.  Our findings demonstrate that cell-intrinsic PD-1 restraint of Treg cells is a significant mechanism by which PD-1 inhibitory signals regulate T cell tolerance and autoimmunity.

overall_design: Analysis of Treg cells from mice that selctively deleted PD-1 on Treg cells compared to WT Treg cells using bulk RNA seq

first: Catherine

last: Tan

first: Juhi

middle: R

last: Kuchroo

first: Arlene

middle: H

last: Sharpe

middle: T


title: Histone H3 Lys27 trimethylation readout by a BAH domain of BAHCC1 directs gene silencing [RNAseq_jurkat_O3SH2_RS4SH2]

first: Gang

last: Wang

summary: The Polycomb Repressive Complex 2 (PRC2) and its trimethylation of histone H3 at lysine 27 (H3K27me3) control gene silencing, genome organization, cell-fate determination, as well as normal and pathological development. To date, functional transduction of H3K27me3 is believed to be achieved through the H3K27me3-‘recognizing’ chromodomain harbored within the chromobox (CBX) subunit of Polycomb Repressive Complex 1 (PRC1), which mediates gene silencing partly through H2A monoubiquitination. Here, we report a novel H3K27me3-readout mechanism in mammal, which utilizes an evolutionarily conserved Bromo-adjacent homology (BAH) domain of BAHCC1 (BAH domain and Coiled-Coil Containing 1) for silencing polycomb gene targets. Biochemical, structural and chromatin-immunoprecipitation followed by sequencing (ChIP-seq) analyses revealed that the BAH domain of BAHCC1 specifically engage H3K27me3 through a hydrophobic trimethyl-lysine-binding cage and multiple intermolecular interactions to its flanking residues, mediating co-localization of BAHCC1 with H3K27me3-marked genomic regions in cells. Additionally, we find that BAHCC1 is overexpressed in several human leukemia subtypes including T-cell acute lymphoblastic leukemia (T-ALL), and interacts with transcriptional repressors SAP30-binding protein (SAP30BP) and histone deacetylase 1 (HDAC1). BAHCC1 loss, or disrupting the BAH-mediated interaction of BAHCC1 with H3K27me3 via structure-based mutagenesis, causes chromatin remodeling at the H3K27me3-targeted loci and reactivates polycomb-related gene-silencing programs intimately associated with tumor suppression and cell differentiation, which leads to significantly suppressed T-ALL tumor growth in vitro and in vivo.

overall_design: Transcriptome profilings of the Jurkat T-cell acute lymphoblastic leukemia (T-ALL) cells with stable expression of a BAHCC1-targeting shRNA (either sh988 or sh993) versus empty vector (shEV), Jurkat cells post-treatment with UNC1999 (an EZH2/EZH1 small-molecule inhibitor) versus DMSO, as well as the Jurkat cells with either wildtype BAHCC1 allele (WT) or the homozygous mutations of the BAHCC1 BAH domain (W2554G introduced into a non-luciferase-labeled Jurkat line, or Y2533A introduced into a luciferase-GFP-labeled Jurkat line). Transcriptome profiling of the RS4;11 B-cell ALL cells with stable expression of the BAHCC1-targeting shRNA (sh988) versus shEV.  Transcriptome profiling of the OCI-AML3 acute myeloid leukemia (AML) cells with stable expression of the BAHCC1-targeting shRNA (sh988) versus shEV..

first: Huitao

last: Fan

first: Yiran

last: Guo

first: Greg


title: EWS-FLI1-regulated Core Transcriptional Regulatory Circuit promotes Ewing sarcoma progression

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

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

summary: We identify and validate an Ewing sarcoma-specific CRC, which is under control of EWS-FLI1. Formed by KLF15, TCF4 and NKX2-2, this CRC apparatus coordinates the gene expression programs in Ewing sarcoma cells. These data advance the understanding of the mechanistic basis of transactional dysregulation in Ewing sarcoma, and provide potential novel therapeutic strategies against this malignancy.

overall_design: To elucidate the co-regulatory mechanism between CRC TFs and how they are controlled by EWS-FLI1 in Ewing sarcoma, ChIP-Seq was performed using specific antibodies against KLF15, TCF4 or NKX2-2 in A673 cells. Importantly, KLF15, TCF4 and NKX2-2 co-occupied both the super-enhancers and promoters of all TFs including themselves, forming an interconnected circuitry as predicted by our method. To further establish the regulatory effect of CRC TFs on the transcriptome, we performed RNA sequencing (RNA-seq).

first: Xianping

last: Shi

first: Liling

last: Jiang

first: Wei

last: Yang

first: Bo

first: Moli

last: Huang

first: Sigal

last: Gery

first: De

last: Lin

first: H.

middle: P

last: Koeffler


title: Transcription profiling of the wild-type strain, mhy1Δ mutant and MHY1-overexpressing mutant strain.

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

summary: To explore the cellular functions of Mhy1, how Mhy1 promotes filamentation, we wanted to identify genes that are transcriptionally controlled by Mhy1. To this end, RNA-Seq analysis was conducted in cells of wild-type strain, mhy1Δ mutant and wild-type strain overexpressing MHY1 grown in filament-inducing YNDC7 medium.

overall_design: Transcriptome profiling conducted in wild-type strain, mhy1Δ mutant and MHY1-overexpressing mutant.

first: Heng

last: Wu

first: Tao

last: Shu

first: Yi-Sheng

last: Mao


title: T cell receptor signal strength and antigen affinity differentially regulate memory CD8+ T cell development

city: Ithaca

first: sabrina

last: solouki

address: 530 Campus Rd.

department: Immunology and Infectious Disease

institute: Cornell university

summary: IL-2 inducible tyrosine kinase (Itk) is a Tec family non-receptor tyrosine kinase that is known to regulate T cell receptor signal strength (TcR) and T cell development and differentiation. TcR signal strength and antigen affinity are parameters known to regulate the development of CD8+ T cell memory. However, the intersection between TcR signal strength and antigen affinity on CD8+ memory T cell development remains unclear. Therefore, we compared the transcriptomes of WT and Itk-/- OT-1/Rag-/- CD8+ T cells at day 0 and day 7 following infection with Listeria monocytogenes expressing the SIINFEKL (N4) or SIITFEKL (T4) OVA peptide variant (different affinities for TcR) by RNA sequencing.

overall_design: CD44lowCD122low naïve CD8+ T cells were isolated from the spleens of 4-6 week old male and female WT and Itk-/- mice (on a OT-1/Rag-/- background) using flow sorting (day 0 timepoint). To generate an effector population, naïve CD45.2 WT and Itk-/- CD8+ T cells (0.5 million/mouse) were adoptively transferred through retro-orbital injection into CD45.1 recipients (male and female, 4-6 week old) and Listeria monocytogenes (LM) expressing the SIINFEKL (N4) or SIITFEKL (T4) OVA epitope was administered intraperiotneally 24 hours post transfer. Following infection, on day 7, donor CD8+ T cells (CD45.1-CD45.2+) were isolated through flow sorting (day 7 LMN4 and day 7 LMT4 timepoints). Donor CD8+ T cells were pooled for isolating total RNA. RNA sequencing was conducted with triplicate RNAseq libraries.

first: Sabrina

last: Solouki

first: Avery

last: August

first: Weishan


title: Context-dependent requirement of H3K9 dimethyltransferase activity during reprogramming to pluripotency

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: The methylation of histone 3 at lysine 9 (H3K9) is widely regarded as a major roadblock for cellular reprogramming and interference with associated methyltransferases such as EHMT1 and EHMT2 (also known as GLP and G9A) facilitates the derivation of induced pluripotent stem cells (iPSCs). In addition, activation of demethylases by ascorbic acid (AA) has become a common approach to facilitate the extensive epigenetic remodeling required for iPSC formation. The functional interaction between the H3K9 methylation machinery and AA-stimulated enzymes, and consequences of interfering with these pathways, remain insufficiently explored. Here, we show that reduction of EHMT1/2 activity paradoxically counteracts iPSC formation in an optimized reprogramming system in the presence of AA. At the cellular and molecular level, EHMT1/2 activity is required for efficient downregulation of somatic genes and transition into an epithelial state. Genetic interference with the demethylase KDM3B partially rescues the adverse effect of EHMT1/2 inhibition on iPSC formation. Transient inhibition of EHMT1/2 during reprogramming yields iPSCs that fail to efficiently give rise to viable mice, suggesting persistent molecular defects in these cells. Together, our observations document a more nuanced function of H3K9 methyltransferases during iPSC formation and suggest that the balancing of AA-stimulated enzymes by EHMT1/2 is required for efficient and error-free reprogramming to pluripotency.

overall_design: RNA-seq in MEF samples (in duplicates) and MEF undergoing reprogramming (in triplicates) after Dox induction of OSKM with or without the presence of C3 and or UNC

first: Matthias

last: Stadtfeld

first: Effie

last: Apostolou


title: Unraveling the Genome-Wide Impact of Recombinant Baculovirus Infection in Mammalian Cells for Gene Delivery

city: Gwangjin-gu, Seoul

first: Nayoung

last: Park

address: 120 Neungdong-ro

institute: Konkuk University

summary: Baculovirus expression systems have been widely used to produce recombinant mammalian proteins owing to the lack of viral replication in vertebrates. Although several lines of evidence have demonstrated impacts of baculovirus infection in mammalian hosts, genome-wide effects have not been fully elucidated. Here, we provide comparative transcriptome profiles of baculovirus and host-immune response genes in recombinant baculovirus-infected mammalian and insect cells. Specifically, to decipher the impacts of baculovirus infection in mammalian cells, we conducted total RNA-seq on human 293 cells and insect Sf9 cells infected with recombinant baculovirus. We found that baculovirus genes were rarely expressed under the control of baculoviral promoters in 293 cells. Although some baculovirus early genes, such as PE38 and IE-01, showed limited expression in 293 cells, baculoviral late genes were mostly silent. We also found modest induction of a small number of mammalian immune response genes associated with Toll-like receptors, cytokine signaling, and complement in baculovirus-infected 293 cells. These comprehensive transcriptome data will contribute to improving recombinant baculovirus as tools for gene delivery, gene therapy, and vaccine development.

sample_organism:
Spodoptera frugiperda
Homo sapiens

platform_organism:
Spodoptera frugiperda
Homo sapiens

overall_design: Total RNA-seq for uninfected 293TT cells, AcHERVenv-CMV-GFP infected 293TT cells, and AcHERVenv-CMV-GFP infected Sf9 cells

first: Ha

last: Shin

first: Hanul

last: Choi

first: Nahyun

last: Kim

first: Heesun

first: Jaebum

first: Young


title: Loss of extreme long-range enhancers in human neural crest drives a craniofacial disorder

city: Stanford

first: Hannah

middle: Katherine

last: Long

state: CA

address: Lokey Stem Cell Research Building

department: Chemical and Systems Biology

institute: Stanford University

summary: Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). In this study we utilise epigenomic profiling of histone modifications and coactivator binding using ChIP-seq and chromatin accessibility using ATAC-seq to map cis-regulatory enhancer elements within the PRS locus during differentiation of human embryonic stem cells to cranial neural crest and chondrocytes. Strikingly, these enhancers are located up to 1.45 Mb away from the SOX9 gene promoter. We further perform RNA-sequencing to determine gene expression changes during the differentiation and identify potential transcription factors that regulate enhancer activity during CNCC development, including TWIST1. We utilise Capture-C from the SOX9 promoter to profile long-range interactions with the distal PRS-associated enhancer elements, and we confirm these interactions using reciprocal Capture-C from the identified candidate enhancer elements. Finally, we phase the H9 human embryonic stem cell line using 10X genomics linked-read sequencing in order link genetically edited alleles to gene expresssion changes in cis. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and identify one factor that may contribute to enhancer function in a developmentally-regulated manner.

overall_design: Gene expression (RNA-seq), chromatin-modifications, transcription factor binding (ChIP-seq), chromatin accessibility (ATAC-seq) and long-range chromosomal interactions (Capture-C) were assayed during cranial neural crest cell (CNCC) differentiation from human embryonic stem cells (hESCs).

middle: K

first: Joanna

last: Wysocka


title: BAHCC1 couples H3K27me3 to gene silencing and tumorigenesis via a conserved BAH module [Jurkat BAHCC1_H3Ac_ChIPseq]

first: Gang

last: Wang

overall_design: Examination of genome-wide binding for wild-type (WT) BAHCC1 in Jurkat T-ALL cells with knockin (KI) of a 3xFlag tag into C-terminus of endogenous BAHCC1 gene locus; parental Jurkat cells without KI of tag were used as negative control for Flag-BAHCC1 ChIP-seq. The same 3xFlag tag KI strategy was used for examining genome-wide binding of a BAH-mutated (Y2533A) form of BAHCC1 in Jurkat cells. We also examined genome-wide H3 acetylation (H3Ac) levels in the Jurkat cells with either WT BAHCC1 or the homozygous mutations of the BAHCC1 BAH domain (i.e., W2554G). We also sequenced the input chromatin sample of parental Jurkat cells (kindly provided by Drs. D Schuermann and P Schär) that matches the GSM2279072 H3K27me3 dataset used in the study.

first: Huitao

last: Fan

first: Yiran

last: Guo

first: Greg


title: BAHCC1 couples H3K27me3 to gene silencing and tumorigenesis via a conserved BAH module [GW760_K27me3_ChIPseq]

overall_design: Examination of the genome-wide distribution of H3K27me3 in the E2a-Pbx1-transformed murine acute leukemia cell line.


title: Single cell RNA seq of mouse bladder and bladder assembloids

status: Public on Sep 27 2020

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: To investigate whether the bladder assembloids recapitulate cell compositions, in addition to the gene expression patterns of each cell type in the adult bladder, we performed single-cell RNA-seq of bladder assembloids and mouse adult bladders, and compared the transcriptional profiles between them at the single-cell level.

overall_design: Mouse bladders from C57BL/6 mice (a pool of 8 bladders), 1-day bladder assembloids (a pool of 3 assembloids), and 7-days bladder assembloid (a pool of 3 assembloids) were analyzed by single-cell RNA-seq.

first: Hyo-Min

first: Byunghee

last: Kang

first: Kunyoo

first: Eunjee


title: Highly-motile versus unsorted bulk primary Glioblastoma cells from two patients (GBM965 and GBM897)

city: Baltimore

first: Konstantinos

last: Konstantopoulos

state: MD

address: 3400 N Charles St

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

summary: Glioblastoma (GBM) is the most aggressive form of brain cancer, characterized by high recurrence and dismal prognosis. Presently, there is no effective in vitro platform that can rapidly measure complex cellular phenotypic traits and predict patient-specific clinical outcomes. Here, we fabricated and evaluated an in vitro testing platform, Microfluidic Assay for Quantification of Cell Invasion (MAqCI), by screening a panel of 28 patient-derived primary GBM specimens in a blinded multi-institutional retrospective cohort study. We quantified the ability of GBM cells to navigate and squeeze through confined microenvironments that mimic tight perivascular conduits and white matter tracts in the brain parenchyma in vivo, as well as the proliferative capacity of highly motile subpopulations. By combining migratory- and proliferative-based indices, MAqCI correctly categorized patients into short- or long-term survival groups with high sensitivity (84%), specificity (89%), and accuracy (86%), and predicted time to recurrence. In a pilot prospective study, MAqCI classified all 5 patients accurately based on their survival outcomes. Overall, our study suggests that invasive growth is intimately linked with GBM progression and patient outcomes, and reveals the translational potential of MAqCI for personalized GBM care.

overall_design: RNA was isolated from samples of ~1000 migratory or unsorted cells in duplicate for GBM897 or triplicate for GBM965

first: Bin

last: Wong

first: Sagar

last: Shah

first: Christopher

middle: L

last: Yankaskas

first: Vivek

last: Bajpai

first: Deborah

last: Chin

first: Karim

last: ReFaey

first: Paula

last: Schiapparelli

first: Stuart

last: Martin

first: Xiaobin

last: Zheng

first: Chen-Ming

first: Alfredo

last: Quiñones-Hinojosa


title: RNA-seq data of PHF8 wild-type and PHF8 knockout TRAMP mouse

status: Public on Sep 26 2020

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

summary: RNA-seq analysis were applied to elucidate the transcriptional differences of PHF8 wild-type and PHF8 knockout TRAMP mouse. A total of 2,092 differentially expressed genes (Fold Change > 2, or Fold Change＜0.5; FDR < 0.05) with 623 down- and 1469 up-regulated genes were identifed in Phf8-KO TRAMP mice.

overall_design: Total RNA was extracted from tumor tissues derived from either Phf8-KO TRAMP mice or the control TRAMP mice at week 37 using Trizol reagent (Invitrogen). And RNA-Seq was performed by Shanghai NovelBio Bio-Pharm Technology Co., Ltd (Shanghai, China). A pooled RNAs from 3 mice were mixed with an equal mass of RNA to minimize variation across samples. RNA-Seq reads were filtered and mapped to Mouse genome (GRCm38, NCBI) utilizing HISAT2. HTSeq was used to calculate the gene count. Differentially expressed genes analysis was applied utilizing DESeq2 under following criteria: Fold Change > 2, or Fold Change＜0.5; FDR < 0.05.

first: Qiuli

last: Liu


title: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans.

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

summary: Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation and fertility. Here we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in altered replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.

overall_design: Characterization of replication timing and replication origins in C. elegans. Analysis of differences between wild type and H3.3 null mutants. ChEC-seq, Repli-Seq, EdU-seq data done in C. elegans with different replicates. Free MNase and gDNA for control

first: Maude

last: Strobino


title: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts [RNA-seq]

first: Tae-Young

last: Roh

summary: Consistent with the previous study, we showed that tumor molecular subtypes switched between the luminal subtype and the basal subtype during long-term maintenance of conventional tumor organoids in the absence of stroma in vitro, indicating the important role of tumor stroma in maintaining the tumor phenotype. Interestingly, genomic alterations seen in parental tumors are preserved well in both conventional tumor organoids and tumor assembloids, implying that the determination of tumor phenotypes may rely on epigenetic changes in tumor stroma-dependent ways, particularly through stromal BMP signals, elicited by Hh expression in tumor cells. We performed extensive epigenomic analyses including RNA-seq, ATAC-seq, and ChIP-seq with genetically manipulated tumor assembloids, in which genetic manipulations were applied independently to tumor organoids and tumor stroma in a combinatorial manner. Using this system, we identified FOXA1 as a master pioneering factor that drives enhancer reprogramming during the molecular switching of tumor subtypes. We have also obtained new evidence that FOXA1 is induced by stromal BMP signals and identified the HH-BMP-FOXA1 signaling feedback between urothelial tumors and stromal fibroblasts as a critical signaling axis in the FOXA1-mediated enhancer reprogramming of tumor phenotypes in the determination of urothelial carcinomas.

overall_design: FOXA1 was overexpressed or knocked out in human bladder tumor organoids. BMP4 and BMP5 were overexpressed or knocked out in cancer-associated fibroblasts (CAF). Genetically manipulated tumor assembloids were created by reconstituting the resulting tumor organoids and CAF, and cultured for 7 days. After CAF elimination, the tumor organoids were analyzed by RNA-seq. Two biological replicates for each sample were analyzed.

first: Hyo-Min

first: Byunghee

first: Kunyoo

last: Shin

first: Eunjee

last: Kim


title: A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in embryonic stem cells (sgRNA-seq)

city: Clayton

first: Partha

last: Das

state: VIC

address: 15 innovation walk

country: Australia

institute: Monash Biomedicine Discovery Institute, Monash University

summary: Regulatory elements (REs) consist of enhancers and promoters that occupy a significant portion of the non-coding genome and control gene expression programs either in –cis or in –trans. Putative REs have been identified largely based on their regulatory features (co-occupancy of ESC-specific transcription factors, enhancer histone marks and DNase hypersensitivity) in mouse embryonic stem cells (mESCs). However, less has been established regarding their regulatory functions in their native context. We deployed cis- and trans-regulatory elements scanning through saturating mutagenesis and sequencing (ctSCAN-SMS) to target elements within the ~12kb cis-region of the Oct4 gene locus, as well as genome-wide 2,613 high-confidence trans-REs (TREs), in mESCs. The ctSCAN-SMS identified 10 CREs and 12 TREs, as novel candidate REs of the Oct4 gene in mESCs. Furthermore, deletion of these REs confirmed that the majority of the CREs and TREs are functionally active, and involved in regulating Oct4 gene expression. Additionally, a subset of the functional CREs and TREs physically interact with the Oct4 promoter to varying degrees through intra- and inter-chromosomal interactions, respectively. Comparative genomics analysis reveals that functional CREs are more conserved in terms of their regulatory sequence conservation between mouse and primates (including humans) than TREs. Notably, a few active CREs are devoid of canonical regulatory features. Taken together, our work demonstrates the reliability and robustness of ctSCAN-SMS screening to identify critical REs, and probe their roles in the regulation of transcriptional output of a target gene (in this case Oct4).

overall_design: Deep sequencing of sgRNAs from GFP-negative/low and pre-sort cell populations of REs CRISPR-Cas9 pool screen

first: Yogesh

last: Kumar


title: A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in embryonic stem cells

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

overall_design: Refer to individual Series


title: A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in embryonic stem cells (ATAC-seq)

overall_design: ATAC-seq from 0, 8, 24, 96hr time points (undifferentiated to differentiated state) of wild-type (Zhbt-Oct4) mESCs; ATAC-seq from wild-type (J1) mESCs


title: Thermoneutral housing regulates intestinal tissue tolerance

status: Public on Sep 25 2020

city: San Francisco

first: Kevin

last: Man

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California, San Francisco

summary: Purpose: Tissue tolerance is a host defense strategy that protects tissues from damage cuased by pathogens or the immune system.  Here, we provide a framework for investigating the mechanisms of tissue tolerance in experimental models of colitis. We find that the program of tissue tolerance is preferentially expressed in thermoneutral mice, which protects them from injury-induced colitis and inflammation-induced colon cancer. The expression of intestinal tissue tolerance is mediated by an unexpected crosstalk between thermogenic adipocytes and intestinal epithelial cells.

overall_design: Large intestine epithelial cells were isolated for RNA sequencing

first: Ajay

last: Chawla


title: Gene expression in classes of adult hippocampal precursor cells defined by ROS content

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Regulating the cell cycle entry of neural stem cells (NSCs) is critical for continued adult neurogenesis and is extensively shown to be subject to environmental modulation. Here we demonstrate that pro-proliferative stimulation by physical activity is achieved by activating quiescent hippocampal precursors. Using independent approaches, we show that differential enrichment of endogenous ROS distinguishes this pool of activatable, quiescent cells. Endogenous ROS content clusters Nestin (Nes)-GFP+ precursor cells into heterogeneous cell populations with unique transcriptional identities and significant changes in ROS content precede gene expression changes and neurogenic commitment. A sub-optimal physical activity triggers a ROS surge exclusively in cells with high intracellular ROS content underpinning their recruitment into active growth cycle. These ROS dynamics are independent of mitochondrial function and are driven by the activity of NADPH oxidising enzyme Nox2. While baseline neurogenesis is unaffected, ROS fluctuations and the pro-neurogenic response to physical activity was abolished in Nox2-deficient mice.

overall_design: 14 samples in 3 experimental groups with 4/5 replicates per group

first: Vijay

last: Adusumilli

first: Rupert

last: Overall


title: Lung cell lines grown in 2D and 3D

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary:
Comparison of gene expression data between cell lines grown on 2D tissue culture plastic or 3D matrigel
A427, A549, H23, H358, H460, H661, H1437, and H1703 cells were compared

overall_design: Cells were cultured at similar density and growth media on either tissue culture plastic (2D) or in matrigel (3D)

middle: C


title: Herpes simplex encephalitis in a patient   with a new form of  inherited IFNAR1 deficiency

status: Public on Sep 24 2020

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

country: France

institute: INSERM, Institut Imagine

summary: Inborn errors of TLR3-dependent IFN-α/β- and -λ-mediated immunity in the central nervous system (CNS) can underlie herpes simplex virus 1 (HSV-1) encephalitis (HSE). The respective contributions of IFN-α/β- and -λ are unknown. We report a child homozygous for a genomic deletion of the entire coding sequence and part of the 3’UTR of the last exon of IFNAR1, who died from HSE at the age of two years. An older cousin died following vaccination against measles, mumps and rubella at 12 months of age, and another 17-year-old cousin homozygous for the same variant has had other viral illnesses. The encoded IFNAR1 protein is expressed on the cell surface but is truncated and cannot interact with the tyrosine kinase TYK2. The patient’s fibroblasts and EBV-B cells did not respond to IFN-α2b or IFN-β, in terms of STAT1, STAT2 and STAT3 phosphorylation, or the induction of IFN-stimulated genes (ISGs). Transcriptome analysis revealed a complete abolition of genome-wide ISG induction in response to IFN-α2b in IFNAR1-deficient fibroblasts from the patient. These fibroblasts were susceptible to viruses, including HSV-1, even in the presence of exogenous IFN-α2b or IFN-β. HSE is therefore a consequence of inherited complete IFNAR1 deficiency. This experiment of Nature indicates that IFN-α/β are essential for anti-HSV-1 immunity in the CNS.

overall_design: Total RNA profiles from primary fibroblasts of the HSE IFNAR1 patient, a previously validated IFNGR1 patient, a previously validated IFNAR1 patient, and three healthy controls. Each library was sequenced twice.

first: Paul

last: Bastard

first: Shen-Ying

last: Zhang


title: Profiling of CD8+T cells upon treatment with extracellular vesicles derived from colorectal cancer and normal patients with different body mass index

city: Kuala Lumpur

first: NADIAH

last: ABU

state: Kuala Lumpur

address: UKM Medical Molecular Biology, UMBI, UKM MEDICAL CENTER

country: Malaysia

institute: UKM MEDICAL MOLECULAR BIOLOGY INSTITUTE (UMBI)

summary: To determine the changes in the CD8+T cells upon treatment with different types of extracellular vesicles

overall_design: Freshly isolated CD8+T cells from healthy individuals were co-cultured for 24 hours with the following groups of extracellular vesicles: 1) healthy individuals with BMI (≥ 18.5 kg/m2 - ≤ 23.0 kg/m2) 2)healthy individuals with BMI >25 kg/m2. 3) Colorectal cancer patients with BMI  (≥ 18.5 kg/m2 - ≤ 23.0 kg/m2) 4) Colorectal cancer patients with BMI >25 kg/m2 and 5) PBS

first: Abu

last: Nadiah


title: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts [H3K27ac ChIP-seq]

first: Tae-Young

overall_design: FOXA1 was overexpressed or knocked out in human bladder tumor organoids. BMP4 and BMP5 were overexpressed or knocked out in cancer-associated fibroblasts (CAF). Genetically manipulated tumor assembloids were created by reconstituting the resulting tumor organoids and CAF, and cultured for 7 days. After CAF elimination, the tumor organoids were analyzed by ChIP-seq. Two biological replicates for each sample were analyzed.

first: Hyo-Min

last: Kang


title: Transcriptional Changes during T cell development following conditional loss of Bcl6

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

institute: UCL

summary: In this study we investigated the changes during T cell development in Rag knockout Bcl6 conditional knockout E16.5 thymi compared to Control E16.5 thymi.  We measured the transcription changes by RNA seq in three different populations including CD25+, CD8+CD4- (ISP) and CD8+CD4+ (DP) thymocytes.

overall_design: Embryonic day (E16.5) thymi from Rag knockout Bcl6 conditional knockout (Ragfl/flBcl6LckCre) embryos were used for this study. CD25 positive thymocytes were isolated from Control (RagKOBclfl/flLckCre-) and RagKOBcl6coKO (RagKOBcl6fl/flLckCre+). Some RagKOBcl6coKO thymi were treated with anti-CD3 for 2days to promote differentiation following a TCR mimicking stimulus. CD8+CD4- (ISP) cells and CD8+CD4+ (DP) cells were isolated from these treated thymi. RNA-Seq was carried out on the CD25 positive, ISP and DP populations from Control and RagKOBcl6coKO samples.

first: Anisha

last: Solanki


title: Regulatory elements with preferential activity in cortical interneurons identified by histone modification ChIP-seq

first: Kenneth

last: Lim

department: Psychiatry

institute: UCSF

summary: Cortical interneuron (CIN) dysfunction is thought to play a major role in neuropsychiatric conditions like epilepsy, schizophrenia and autism. It is therefore essential to understand how the development, physiology and functions of CINs influence cortical circuit activity and behavior in model organisms such as mice and primates. We sought to discover gene regulatory enhancer elements (REs) that can be used in AAV viral vectors to drive expression in CINs through systematic genome-wide identification of putative REs (pREs) that are preferentially active in immature CINs by histone modification ChIP-seq. We evaluated two novel pREs in AAV vectors, alongside the well-established Dlx I12b enhancer, and found that they drove CIN-specific reporter expression in adult mice.

overall_design: FAC-sorted GFP-positive CINs and GFP-negative non-CINs from microdissected cerebral cortical tissue from P2 Gad67-GFP mice were used in histone modification ChIP-seq experiments. We performed two independent replicate experiments with antibodies against H3K27ac and H3K27me3 with matched input controls.

first: Anna

middle: N

last: Rubin

middle: J

first: Susan

last: Lindtner

first: John

last: Rubenstein


title: Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics

status: Public on Sep 23 2020

city: Cambridge

first: Dylan

last: Kotliar

state: MA

address: 4 Garnder Rd, Apt 2

department: Viral genomics

institute: Broad Institute

summary: Ebola virus (EBOV) causes epidemics with high mortality, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, providing insight into pathogenesis: e.g., immature, proliferative monocyte-lineage cells with reduced antigen presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV down-regulates STAT1 mRNA and interferon signaling, and up-regulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response, and provides a framework for characterizing host-virus interactions under maximum containment.

overall_design: Examination of an ex vivo Ebola infeciton model of PBMCs from rhesus macaque

first: Aaron

middle: E

last: Lin


title: Epstein-Barr Virus episome physically interacts with active regions of the host genome in lymphoblastoid cells

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

summary: Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently the high-resolution chromatin interaction capture (Hi-C) assays in lymphoblastoid cells have become available enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. Using available Hi-C data at 10kb resolution, we have identified nearly 15000 reproducible contacts between EBV episome and human genome. These contacts are highly enriched in chromatin regions denoted by typical or super enhancers and active marks including histone H3 K27ac, K4me1, K79me2 and K4me2. Additionally, these contacts are highly enriched at loci bound by host transcription factors that regulate B cell growth (e.g. IKZF1 and RUNX3), factors that enhance cell proliferation (e.g. HDGF) or factors that promote viral replication (e.g. NBS1 and NFIC). EBV contacts show nearly two-fold enrichment in host regions bound by EBV EBNA2 and EBNA3B transcription factors. Chromosome conformation capture coupled with sequencing (4C-seq) using the EBV oriP as a “bait” loci in lymphoblastoid cells further confirmed contact with active chromatin regions. Collectively, our analysis supports the interaction between EBV episome(s) and active regions of human genome in lymphoblastoid cells.

overall_design: Epstein-Barr virus (EBV) genomes persist in latently infected cells as extrachromosomal molecules that attach to host chromosomes through a viral encoded sequence-specific DNA binding protein. We employed circular chromosome conformation capture (4C) analysis to identify genomewide associations between EBV episomes and host chromosomes.

first: Luopin

last: Wang


title: Functional analysis of the NucS/EndoMS of the hyperthermophilic archaeon Sulfolobus islandicus REY15A

city: Jimo, Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhai Road

department: Microbial Technology Institute

institute: Shandong University

summary: We report Over-expression of the wild type SisEndoMS in S. islandicus resulted in retarded growth and abnormal cell morphology. Transcriptomic analysis revealed that SisEndoMS overexpression led to upregulation of distinct sets of genes including the CRISPR-Cas IIIB system, methytransferases, and glycosyltransferases, which are mainly localized to a specific segment in the chromosome.

overall_design: RNA Seq/Transcriptomics analysis of SisEndoMS wild type overexpression strain and SisEndoMS catalytic and DNA binding mutant overexpression strain

first: Sohail

last: Ahmad

first: Yulong

last: Shen


title: Long-term expansion with germline potential of human primordial germ cell-like cells in vitro [aCGH]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

type: Genome variation profiling by genome tiling array

summary: Human germ cells perpetuate human genetic and epigenetic information. However, the underlying mechanism remains elusive, due to a lack of appropriate experimental systems. Here, we show that human primordial germ cell‐like cells (hPGCLCs) derived from human‐induced pluripotent stem cells (hiPSCs) can be propagated to at least ~10^6‐fold over a period of 4 months under a defined condition in vitro. During expansion, hPGCLCs maintain an early hPGC‐like transcriptome and preserve their genome‐wide DNA methylation profiles, most likely due to retention of maintenance DNA methyltransferase activity. These characteristics contrast starkly with those of mouse PGCLCs, which, under an analogous condition, show a limited propagation (up to ~50‐fold) and persist only around 1 week, yet undergo cell‐autonomous genome‐wide DNA demethylation. Importantly, upon aggregation culture with mouse embryonic ovarian somatic cells in xenogeneic‐reconstituted ovaries, expanded hPGCLCs initiate genome‐wide DNA demethylation and differentiate into oogonia/gonocyte‐like cells, demonstrating their germline potential. By creating a paradigm for hPGCLC expansion, our study uncovers critical divergences in expansion potential and the mechanism for epigenetic reprogramming between the human and mouse germ cell lineage.

overall_design: array Comparative Genome Hybridization analysis of human iPSC and expanded PGCLC.

first: Yusuke

last: Murase

first: Hiroshi

last: Ohta

first: Chika

last: Yamashiro

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Pogz deficiency leads to abnormal behavior, transcription dysregulation and impaired cerebellar physiology

city: Jerusalem

first: Reut

last: Suliman

address: Givat ram campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: As part of characterizing the novel pogz deficiency mouse model, we performed RNA-Seq from cerebellum and hippocampus of adult mice to discover Pogz targets and changes in gene expression that might explain the phenotypes we see in those mice

overall_design: Cerebellar and hippocampal mRNA profiles of control (WT), pogz+/- and pogz-/- mice, both males and females, in triplicates, using Illumina NextSeq 500

last: Suliman Lavie

first: Sagiv

last: Shifman


title: Long-term expansion with germline potential of human primordial germ cell-like cells in vitro

type: Methylation profiling by high throughput sequencing


title: Effects of pE66L missing on ASFV

city: Wuhan

first: Zhou

address: 1 Shi-zi-shan Street

institute: Huazhong agriculture university

summary:
Identify the function of pE66L
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-- Retinal Transcriptomes

overall_design: 2 groups in triplicates


title: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts [FOXA1 ChIP-seq]

city: Seoul

first: Tae-Young

last: Roh

address: 52 Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

first: Hyo-Min

last: Kim

first: Byunghee

last: Kang

first: Kunyoo

last: Shin

first: Eunjee


title: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts [ATAC-seq]

overall_design: FOXA1 was overexpressed or knocked out in human bladder tumor organoids. BMP4 and BMP5 were overexpressed or knocked out in cancer-associated fibroblasts (CAF). Genetically manipulated tumor assembloids were created by reconstituting the resulting tumor organoids and CAF, and cultured for 7 days. After CAF elimination, the tumor organoids were analyzed by ATAC-seq. Two biological replicates for each sample were analyzed.


title: Therapeutic Responses to Roseomonas mucosa in Atopic Dermatitis Involve Lipid-Mediated TNF-related Epithelial Repair

city: Bethesda

first: Ian

middle: A

last: Myles

address: 9000 Rockville Pike, BLD 29B, Rm 5NN24

department: NIAID

institute: NIH

summary: Dysbiosis is increasingly implicated as a targetable contributor to the pathogenesis of atopic dermatitis (AD).  We previously reported first-in-human safety and clinical activity results from topical application of commensal R. mucosa for the treatment of AD in ten adults and five children older than 9 years of age.  However, both mechanism of action and impacts on the most common age range for AD patients (less than 7 years of age) remained unexplored.  We now show in patients as young as three years, R. mucosa treatment was associated with significant improvements in disease severity, barrier function, S. aureus burden, topical steroid requirements, and quality of life without any related adverse events.  Our observed response rates were significantly greater than those seen in the placebo control groups of prior AD studies and similar to responses seen during open-label testing phase for currently approved topical treatments.  Improvements and colonization persisted up to 8 months after cessation of treatment.  Production of lipids in the sphingolipid pathway, cholinergic signaling, and flagellin expression accounted for modeled therapeutic impacts via induction of TNFR2-related epithelia-to-mesenchymal transition.  These results support conduct of a placebo-controlled trial and suggest a role of commensals in maintenance of the epithelial barrier.

overall_design: Two atopic dermatitis-causing species of bacteria (Roseomonas mucosa and Staphyloccus aureus) and two species of bacteria from healthy volunteers (Roseomonas mucosa and coagulase negative Staphylococci) were incolulated in three human cell types (dendritic cells, primary fibroblasts, and primary keratinocytes). Each cell type also had a diluent control. RNA-seq samples from each were collected in triplicate.

first: Tovah

last: Markowitz


title: Long-term expansion with germline potential of human primordial germ cell-like cells in vitro [Bisulfite-seq]

first: Yukihiro

overall_design: WGBS (PBAT method) analysis of human PGCLC, and expanded PGCLC.


title: Reprogramming to recover youthful epigenetic information and restore vision

first: Yuancheng Ryan

last: Lu

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

type: Methylation profiling by genome tiling array

summary: Epigenetic reprogramming via a combination of three Yamanaka factors, Oct4, Sox2, and Klf4 (OSK), provides an effective way to promote axon regeneration in chemical- or injury-damaged neurons and improve neuronal function in aged mice. DNA methylation landscape is remodeled during this reprogramming process. This study was designed to examine DNA methylation age in differentiated human neurons post axonal damage with or without OSK expression. Differentiated SH-SY5Y neurons were transduced with AAV.DJ vectors to induce OSK expression for five days, followed by 24-hr treatment with 100nM vincristine (VCS) to induce neurite degeneration. Neurons were harvested at either day 1 or day 9 after VCS treatment. The Illumina Infinium DNA methylation EPIC array was used to obtain DNA methylation profiles. The skin & blood clock from Horvath 2018 (PMID: 30048243 PMCID: PMC6075434) was used for DNA methylation age analysis.

overall_design: The study was designed to examine DNA methylation profile of differentiated human SH-SY5Y neurons post vincristine induced axonal injury with or without OSK treatment.

first: Steve

last: Horvath

first: Xiao

last: Tian

first: Yuancheng

first: David

last: Sinclair


title: Single-cell RNAseq profiling of HeLa cells after stimulation with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: HeLa cells were treated with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL: 10, 25 or 40ng/ml) or with the drug vehicle ("Control"), for 50 minutes or 2 hours prior to analyses by single-cell RNA sequencing. The objective was to study the extent of gene expression variability in resting cells and to evaluate the effect of time and dose of TRAIL treatments on gene expression variability.

overall_design: HeLa cells from the different conditions were processed following standard cell hashing protocol with Hashtag oligonucleotide (HTO), pooled, and single cell RNAseq profiling was performed using the 10x Genomics single-cell 3' V2 chemistry. Correspondence between the Hashtags and conditions was: A0251: control; A0252: Trail 25ng/ml for 50mn; A0253: Trail 10ng/ml for 120mn; A0254: Trail 25ng/ml for 120mn; A0255: Trail 40ng/ml for 120mn.

first: Jeremie

last: Roux

first: Marie-Jeanne

last: Arguel

first: Agnes

last: Paquet

first: Pascal

last: Barbry


title: RNA sequencing of zbtb46+ conventional dendritic cells in the mediastinal lymph nodes of naïve and previously influenza infected memory mice

city: New York

first: Daniel

last: Paik

state: NY

address: 650 W 168th Street

department: Microbiology and Immunology

institute: Columbia University Medical Center

summary:
Purpose: The goal of this study was to compare the transcriptome of conventional dendritic cells (cDC) isolated from the mediastinal lymph nodes (medLN) of mice that were uninfected (naïve) or had been infected 25 days previously with X31 (memory)
Methods: medLN cDC were isolated from naïve and memory mice in biological triplicates and RNA was sequenced using Illumina Novaseq 6000.  Reads were mapped to mouse genome using Kallisto and differential gene expression determined by DESeq2
Results: 61 differentially expressed genes were found between naive and memory medLN cDC after a workflow that filtered out the bottom third of genes by number of reads and had a padj ≤0.05 and fold change ≥2.

overall_design: RNA profiles of  zbtb46+ medLN cDC of uninfected mice and mice previously infected with X31 influenza virus 25 days prior

first: Donna

last: Farber


title: Radiotherapy and IFNγ treatment effect on transcriptome in HT1080 cells

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher PI

institute: University of Michigan

summary: Immune checkpoint blockade is a powerful oncologic treatment modality for a wide variety of human malignancies. Randomized clinical trials are assessing how best to interdigitate this treatment modality with traditional therapies including radiotherapy. A challenge in oncology is to rationally and effectively integrate immunotherapy with traditional modalities including radiotherapy. Here, we demonstrate that radiotherapy induces tumor cell ferroptosis. Ferroptosis agonists augment and ferroptosis antagonists limit radiotherapy efficacy in tumor models. Immunotherapy sensitizes tumors to radiotherapy by promoting tumor cell ferroptosis. Mechanistically, IFN derived from immunotherapy-activated CD8+ T cells and radiotherapy-activated ATM independently, yet synergistically repress SLC7A11, a unit of the glutamate-cystine antiporter xc-, resulting in reduced cystine uptake, enhanced tumor lipid oxidation and ferroptosis, and improved tumor control. Thus, ferroptosis is an unappreciated mechanism and focus for the development of effective combinatorial cancer therapy.

overall_design: Following Illumina’s TruSeq RNA protocol, mRNA profile was got from HT1080 cells, treated with IFNγ, radiation or combination.

first: Michael

last: Green

first: Xueting

last: Lang


title: siQ-ChIP: A reverse-engineered quantitative framework for ChIP-sequencing

city: Grand Rapids

first: Scott

last: Rothbart

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

summary: Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution and relative abundance of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge regarding the ability to quantitatively plot ChIP-seq data, and as such, approaches making use of exogenous additives, or “spike-ins” have recently been developed. Relying on the fact that the IP step of ChIP-seq is a competitive binding reaction, we present a quantitative framework for ChIP-seq analysis that circumvents the need to modify standard sample preparation pipelines with spike-in reagents. We also introduce a visualization technique that, when paired with our formal developments, produces a much more rich characterization of sequencing data.

overall_design:
Examination of H3K27me3 in a wild-type cell line and one treated with the EZH2 inhibitor (EPZ6438).
Examination of H3K9me3 in a wild-type cell line.

first: Bradley

middle: M

last: Dickson

first: Rochelle

last: Tiedemann

first: Alison

last: Chomiak

first: Robert

last: Vaughan

first: Evan

last: Cornett

middle: B


title: 2-year Longitudinal Analyses of Peripheral Blood RNA in Huntington's Disease gene-positive and control subjects

city: Leicester

first: Christopher

last: Mitchell

address: University Road

department: Neuroscience, Psychology & Behaviour

institute: University of Leicester

summary:
Samples collected in the course of the TRACK HD study and used to analyse association between gene expression in blood and symptomatic progression of Huntington's disease
Longitudinal analysis of UHDRS TMS versus gene expression in individual subjects followed by cross-sectional comparisons across phenotype groups at each timepoint

overall_design:
Year 1: 24 Controls, 17 Huntington's mutation-positive presymptomatic far from age of predicted onset (Pre-A), 18 Huntington's mutation-positive presymptomatic near to age of predicted onset (Pre-B), 18 Manifest Huntington's disease Stage 1 (zHD1), 19 Manifest Huntington's disease Stage 2 (zHD2); Year 3: 20 Controls, 15 pre-A, 15 pre-B, 16 zHD1, 16 zHD 2
contributor: TRACK-HD Investigators

first: Irina

last: Krier

first: Alberto

last: Capurro

first: Jamshid

last: Arjomand

first: Beth

last: Borowsky

first: Ruth

last: Luthi-Carter


title: Gene expression in adult neural precursor cells from the hippocampus or subventricular zone

city: Dresden

first: Gerd

last: Kempermann

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Regulating the cell cycle entry of neural stem cells (NSCs) is critical for continued adult neurogenesis and is extensively shown to be subject to environmental modulation. Here we demonstrate that pro-proliferative stimulation by physical activity is achieved by activating quiescent hippocampal precursors. Using independent approaches, we show that differential enrichment of endogenous ROS distinguishes this pool of activatable, quiescent cells. Endogenous ROS content clusters Nestin (Nes)-GFP+ precursor cells into heterogeneous cell populations with unique transcriptional identities and significant changes in ROS content precede gene expression changes and neurogenic commitment. A sub-optimal physical activity triggers a ROS surge exclusively in cells with high intracellular ROS content underpinning their recruitment into active growth cycle. These ROS dynamics are independent of mitochondrial function and are driven by the activity of NADPH oxidising enzyme Nox2. While baseline neurogenesis is unaffected, ROS fluctuations and the pro-neurogenic response to physical activity was abolished in Nox2-deficient mice.

overall_design: 9 samples in 2 experimental groups with 4/5 replicates per group

first: Tara

last: Walker

first: Rupert

middle: W

last: Overall


title: Genome wide ChIP-Seq of two histone marks in primary myoblasts

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: ChIP-Seq analysis of H4K4me1 and H3K4me3 on cultured primary myoblasts

overall_design: Examination of two regulatory histone marks in primary myoblasts

first: Vahab

middle: D

last: Soleimani


title: Anergic CD8+ T cells with lower levels of IL-7 receptor α

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

institute: Seoul National University College of Medicine

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

overall_design: Refer to individual Series


title: Anergic CD8+ T cells with lower levels of IL-7 receptor α (Illumina)

summary: We investigated the entity of IL-7Rα low effector memory (EM) CD8+ T cells in healthy individuals and finally uncovered that they were unable to proliferate and produce IL-2 in response to TCR stimulation

overall_design: Total RNA obtained from human IL-7Rα high and low effector memory (EM) CD8+ T cells in fresh or IL-2 reversed state.


title: Whole genome transcriptome profiling of P. falciparum sexually comitted ring stage parasite from malaria patient's peripheral blood

first: Surendra

middle: Kumar

last: Prajapati

state: Maryland

address: 4301 Jones Bridge Road

institute: Uniformed Services University of the Health Sciences

summary:
Malaria is spread by the transmission of sexual stage parasites, called gametocytes. However, with Plasmodium falciparum, gametocytes can only be detected in peripheral blood when they are mature and transmissible to a mosquito, which complicates control efforts. Here, we identify the set of genes overexpressed in patient blood samples with high levels of gametocyte-committed ring stage parasites. Expression of all 18 genes was regulated by transcription factor AP2-G, which is required for gametocytogenesis. We selected three genes, not expressed in mature gametocytes, to develop as biomarkers.
All three biomarkers were validated in vitro using 6 different parasite lines and an algorithm developed that predicted gametocyte production in ex vivo samples and volunteer infection studies. The biomarkers were also sensitive enough to monitor gametocyte production in asymptomatic P. falciparum carriers allowing early detection and treatment of infectious reservoirs, as well as the in vivo analysis of factors that modulate sexual conversion.

sample_organism:
Plasmodium falciparum
Homo sapiens

overall_design: We selected a subset of High and Low gametocyte conversion rate (GCR) blood samples (GCR>5.5% and 0%, respectively) collected on day zero (D0) prior to treatment (n=8 each group) in the 2016 study cohort for transcriptome analysis. Samples with High and Low GCR also had high and low transcript levels of mature gametocyte specific genes pfs25 and pfs230 in D8 ex vivo parasite RNA, respectively. For control, we have included parasite lines that produces high (NF54 with shield, NF54 without shield and C9 with shield) or low to no gametocytes (C9 without shield and RCM47).

first: Kim

last: Williamson


title: Transcriptome of liver extracts issue from mice treated with Diphenyl Phosphate (DPhP)

status: Public on Sep 22 2020

city: Lyon

first: Arnaud

last: Vigneron

address: 28 rue Laënnec

department: INSERM UMR1052, CNRS UMR5286

institute: Centre de recherche en cancérologie de Lyon

summary: We reports transcriptomic changes observed in the liver of mice treated by 3 concentration of DPhP through drinking water (0.1 mg/L (C1), 1mg/L (C2), 10mg/L(C3)). Mice were treated from 5 to 17 weeks.

overall_design: 4 groups of animals were untreated, or treated with the 3 different concentrations C1, C2, C3. Livers from a same group were pooled and a crude extract was performed before RNA quantification. Four analytical replicates were performed for each group.

first: Jessica

last: Garcia


title: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts

first: Tae-Young

last: Roh

department: Life Sciences


title: Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics (InVivo scRNA-seq)

first: Dylan

last: Kotliar

address: 4 Garnder Rd, Apt 2

institute: Broad Institute

summary: Ebola virus (EBOV) causes epidemics with high mortality, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, providing insight into pathogenesis: e.g., immature, proliferative monocyte-lineage cells with reduced antigen presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV down-regulates STAT1 mRNA and interferon signaling, and up-regulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response, and provides a framework for characterizing host-virus interactions under maximum containment.

overall_design: Single-cell RNA-Seq analysis of circulating immune cells transcriptomes in a rhesus macaque in vivo Ebola infection model at multiple days post innoculation.

first: Aaron

last: Lin


title: PD-L1 blockade in combination with inhibition of MAPK oncogenic signaling in patients with advanced melanoma

city: Los Angeles

first: Antoni

last: Ribas

address: 9-954 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

summary: Combining PD-L1 blockade with inhibition of oncogenic mitogen-activated protein kinase (MAPK) signaling may result in long-lasting responses in patients with advanced melanoma. This phase 1, open-label, dose-escalation and -expansion study (NCT02027961) investigated safety, tolerability and preliminary efficacy of durvalumab (anti–PD-L1) combined with dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor) for patients with BRAF-mutated melanoma (cohort A, n=26), or durvalumab and trametinib given concomitantly (cohort B, n=20) or sequentially (cohort C, n=22) for patients with BRAF-wild type melanoma. Adverse events and treatment discontinuation rates were more common than previously reported for these agents given as monotherapy. Objective responses were observed in 69.2% (cohort A), 20.0% (cohort B) and 31.8% (cohort C) of patients, with evidence of improved tumor immune infiltration and durable responses in a subset of patients with available biopsy samples. In conclusion, combined MAPK inhibition and anti–PD-L1 therapy may provide treatment options for patients with advanced melanoma.

overall_design: Melanoma biopsy mRNA profiles at baseline and following MAPKi/PD-1 blockade treatment.

first: Katie

last: Campbell


title: Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics (ExVivo scRNA-seq)

city: Cambridge

overall_design: Examination of an ex vivo Ebola infeciton model of PBMCs from rhesus macaque


title: Expression data for hTERT-immortalized human Sertoli cell line versus original primary human Sertoli cells

city: Tucson

first: Nathan

middle: J.

last: Cherrington

state: AZ

address: 1703 E. Mabel St.

department: Pharmacology & Toxicology

institute: The University of Arizona

summary:
Primary human Sertoli cells (hSerCs) were immortalized by transducing human TERT into the genome to produce human TERT-immortalized human Sertoli cells (hTERT hSerCs). Total RNA was isolated from both primary hSerCs and hTERT hSerCs and submitted for Affymetrix gene analysis.
Gene expression differences of common Sertoli cell marker genes and xenobiotic transporters was preferentially assessed between each cell type.

overall_design: Two pooled RNA samples from each cell type were analyzed and data was exported with log2 quantitative signals for further fold-change analysis.

first: Raymond

last: Hau

first: Siennah

middle: R

last: Miller

first: Stephen

middle: H

last: Wright


title: NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation [ingSVF RNA-seq]

city: Tokyo

first: Hironori

last: Waki

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

summary: The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation. Here we show that the C-terminal 17 amino acid residues of NFIA (which we named pro#3 domain) is required for transcriptional activity of NFIA. Full-length NFIA, but not deletion mutant lacking pro#3 domain rescued impaired Pparg expression and adipogenesis in NFIA-knockout cells. Mechanistically, the ability of NFIA to increase chromatin accessibility is mediated through pro#3 domain. However, the deletion mutant still binds to Myod1 enhancer to decrease chromatin accessibility and represses Myod1 as well as proximally transcribed non-coding RNA called DRReRNA, leading to suppression of myogenic gene program. Therefore, the negative effect of NFIA on myogenic gene program is, at least in part, independent from the positive effect on Pparg expression and its downstream adipogenic gene program. These results uncover multiple ways of action of NFIA to ensure optimal regulation of brown adipocyte differentiation.

overall_design: ChIP-seq , FAIRE-seq and RNA-seq analysis of control-, full-length NFIA and Δpro#3 mutant-expressing C2C12 myoblasts and RNA-seq analysis of NFIA-KO ingSVF cells

first: Yuta

last: Hiraike

first: Misato

last: Oguchi

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Toshimasa

last: Yamauchi

first: Takashi

last: Kadowaki


title: Intestinal FGF15/19 physiologically represses hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

summary: Hepatic lipogenesis is normally tightly regulated but is aberrantly elevated in obesity. Fibroblast Growth Factor-19 (FGF19, mouse FGF15) is a late fed-state gut hormone that decreases hepatic lipid levels by unclear mechanisms. We examined whether FGF15/19 and FGF15/19-activated Small Heterodimer Partner (SHP/NR0B2) have a role in transcriptional repression of lipogenesis. Comparative genomic analyses reveal that most of the SHP cistrome, including lipogenic genes repressed by FGF19, have overlapping CpG islands. FGF19 treatment or SHP overexpression in mice inhibits lipogenesis in a DNA methyltransferase-3a (DNMT3A)-dependent manner. FGF19-mediated activation of SHP via phosphorylation recruits DNMT3A to lipogenic genes, leading to DNA methylation and gene repression. In non-alcoholic fatty liver disease (NAFLD) patients and obese mice, occupancy of SHP and DNMT3A and DNA methylation at lipogenic genes are low, with elevated gene expression. These results demonstrate that FGF15/19 represses hepatic lipogenesis by activating SHP and DNMT3A physiologically, which is likely dysregulated in NAFLD.

overall_design: Deep sequencing generated liver mRNA profiles in C57BL/6 mouse liver which was treated by vehicle or FGF19 for 6 hr after fasting overnight.

first: Sunmi

last: Seok

first: Yang

last: Zhang

first: Jian

last: Ma

first: Bo

last: Kong

first: Grace

last: Guo

first: Byron

last: Kemper

first: Jongsook


title: Rescuing over-activated microglia by acetaminophen treatment restores cognitive performance in the Dp(16) mouse model of Down syndrome.

city: Genova

first: Laura

last: Cancedda

state: Genova

address: Via Morego, 30

department: Brain Development and Disease

institute: Italian Institute of Technology

summary: Microglia are the resident immune cells of the brain and have been implicated in mechanisms essential for cognitive functions. Down syndrome (DS), the most frequent cause of genetic intellectual disability, is caused by the presence of a supernumerary chromosome 21, which contains genes essential for the function of the immune system. Here, we investigated the presence of microglial alterations and their implication for cognitive impairment in the Dp(16) mouse model of DS. In the hippocampus of Dp(16) mice and individuals with DS, we found microglial morphology indicative of an activated state. Accordingly, we found an electrophysiological profile typical of activated microglia, increased levels of pro-inflammatory cytokines, and altered interferon signaling in Dp(16) mice. In addition, DS mice showed decreased neuronal spine density and neuronal activity, as well as cognitive behavioral deficits. Remarkably, depletion of defective microglia by PLX3397 treatment or rescue of the microglia activated state by the commonly used anti-inflammatory drug acetaminophen rescued the neuronal deficits and cognitive impairment in Dp(16) mice. Our data suggest an involvement of microglia in the cognitive impairment of DS animals and identify a new therapeutic approach for the potential rescue of cognitive disabilities in individuals with DS.

overall_design: 4 Down syndrome and 5 neurologically normal control samples from post-mortem human subjects

first: Bruno

last: Pinto

first: Mohit

last: Rastogi

first: Andrea

last: Contestabile