title: The landscape of global long-range interactions in human erythroid cells mediated by GATA1 and CTCF during differentiation

city: Irvine

first: Weihua

last: Zeng

state: CA

address: 2300E Bio Sci III

department: Dev & Cell Biology

country: USA

institute: UCIrvine

summary: A network of long-range interactions between functional DNA elements regulates gene expression in a precise spatio-temporal pattern during development. We carried out anti-RNA polymerase II and cohesin ChIA-PET and DNase-seq in Mouse Erythroleukemia (MEL) cells to capture genome-wide changes between open chromatin elements in chromatin interaction graphs (CIGs) during DMSO-induced hemoglobin activation. We found that the change of interaction strength in CIGs is positively correlated to expression changes in corresponding genes as measured by RNA-seq. DNaseI footprints and ChIP-seq data indicate that these long-range interactions are controlled through distinct combinations of transcription factors before and after differentiation, with CTCF or cohesin only mediating half of these interactions, with GATA1, PU.1 and/or other transcription factorsYY1 interactions accounting for an additional 40% of detected interactions. Strikingly, while CTCF and GATA1–mediated interactions were enriched in genes involved in erythrocyte differentiation and mitochondrial regulation, PU.1YY1-mediated interactions were enriched for genes involved in RNA processing, cell cycletranslation, and chromatin organizationhistone remodeling.  We further found that two-thirds of MEL DNA elements with long-range interactions as well as 35% of their interactions are conserved in human K562 cells and they show similar combinations of factor occupancy in both species. Our study highlights the importance of quantitative analysis of changes in long-range interaction strengths in quantifying changes in gene expression.

overall_design:
MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. Biological replicates of anti-SMC1 (subunit of cohesin complex) ChIA-PET libraries for uninduced (MEL) and induced (MEL+DMSO) MEL were constructed.

Please note that the processed data *new.txt files were generated from both replicates (i.e. R1 and R2 samples) and are linked to the corresponding R1 sample records.

first: Ricardo

last: Ramirez

first: Camden

last: Jansen

first: Marissa

last: Macchietto

first: Shan

last: Jiang

first: Ana

last: Conesa

first: Ali

last: Mortazavi


title: L1CAM is a marker for isolating corticospinal motor neurons in the developing brain

status: Public on Feb 29 2020

city: Kyoto

first: Bumpei

last: Samata

address: 53 Kawahara-cho, Shogoin

country: Japan

institute: Kyoto university

summary: The cerebral cortical tissue of murine embryo and pluripotent stem cell-derived neurons can survive in adult brain and extend axons to the spinal cord. These features suggest that cell transplantation can be a strategy to reconstruct the corticospinal tract (CST). It is unknown, however, which cell population makes for safe and effective donor cells. To address this issue, we grafted the cerebral cortex of E14.5 mouse to the brain of adult mouse and found that the cells in the graft extending axons along the CST expressed CTIP2. By using CTIP2:GFP knockin mouse embryonic stem cells, we identified L1CAM as a cell surface marker to enrich CTIP2+ cells. We sorted L1CAM+ cells from E14.5 mouse brain and confirmed that they extended a larger number of axons along the CST compared to L1CAM- cells. Our results suggest that sorting L1CAM+ cells from the embryonic cerebral cortex enriches subcortical projection neurons to reconstruct the CST.

overall_design: Differentiated mouse ESC-derived cortical progenitors just after sorting (CTIP2:GFP+ versus CTIP2:GFP-) were subjected to RNA extraction and hybrdization on Affymetrix microarray.

first: Jun

last: Takahashi


title: The distribution of individual miRNA species between high-molecular weight and low-molecular weight RISC complexes by small RNA sequencing in thyroid cancer cell lines

status: Public on Feb 28 2020

city: Baltimore

first: Bonita

middle: H

last: Powell

state: MD

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Thyroid cancer is the most prevalent malignancy of the endocrine system. We and others have  shown that several microRNAs, which are ~21-24nt post-transcriptional gene regulators, are  aberrantly expressed in anaplastic thyroid cancer (ATC) and papillary thyroid cancer (PTC)  tissues and cell lines. In the cell, miRNAs are bound to Argonaute (AGO) proteins as low  molecular weight RNA Induced Silencing Complexes (LMW-RISCs) that can then assemble into  high molecular weight RISCs (HMW-RISCs) that also include additional proteins and mRNA. In  this study, we sought to analyze the association of miRNAs across RISC complexity in ATC and  PTC. For both ATC and PTC lines, miRNAs were enriched in HMW-RISC and LMW-RISC  fractions compared with intermediate fractions or very low molecular weight (AGO-poor)  fractions. Furthermore, 60% of all miRNAs were more abundant in LMW-RISC versus HMW-  RISC fractions by ~2-4 fold. Surprisingly, miR-21-5p, one of the most abundant miRNAs in  both ATC and PTC lines, was consistently one the least abundant miRNAs in HMW-RISC and  the most enriched miRNA in LMW-RISC fractions. These findings suggest that miR-21 may be  uniquely distributed in RISCs relative to other miRNAs. Furthermore, the methodology  described here is a useful way to assess the relative magnitude of miR-21association with HMW  and LMW-RISCs and may help to reveal the true roles of this miRNA in thyroid cancer  development, progression, and treatment.

overall_design: Total RNA was extracted from SW1736 and TPC-1 cell line fractionated lysates. HMW-RISC and LMW-RISC fractions. Input, Medium Molecular weight (MMW-RISC), and RISC-poor fractions were included as controls.

first: Kenneth

middle: W

last: Witwer

first: Andrey

last: Turchinovich


title: RNA-seq analysis of WT and HDAC1f/f HDAC2f/+ x CD4cre deficient activated helper T cells

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

type: Expression profiling by high throughput sequencing

summary: CD4+ T cells have the potential to differentiate into effector cells with cytotoxic activity (CD4+ CTLs), however molecular mechanisms regulating CD4+ CTL induction are poorly understood. By analyzing mice with graded deletion of Hdac1 and Hdac2 alleles in T cells, we observed an HDAC1-HDAC2 dose-dependent induction of CD4+ CTLs. A transcriptome analysis of activated CD4+ T cells carrying a combined deletion of two Hdac1 and one Hdac2 alleles (HDAC1f/f-HDAC2f/+) revealed enrichment of gene signatures similar to CD8+ T cells and CD4+ CTLs.

overall_design:
mRNA expression profiles of activated CD4+ T cells isolated from WT and HDAC1f/f HDAC2f/+ (CD4-cre) mice were generated by deep sequencing.
mRNA expression profiles of activated CD4+ T cells isolated from WT and HDAC1f/f (CD4-cre) mice were generated by deep sequencing.

first: Teresa

last: Preglej

first: Lisa

last: Goeschl


title: microRNA expression in innate lymphoid cells from human decidua

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary:
Innate lymphoid cells are a heterogeneous subset of lymphocytes deeply implicated in the innate immune responses to different pathogens, in lymphoid organogenesis and in the maintenance of tissue homeostasis. Group 3 innate lymphoid cells (ILC3) have been detected in human decidua, where they play a role in the early inflammatory phase favoring implantation and tissue remodeling as well as in the subsequent regulatory phase preventing fetal rejection and supporting neoangiogenesis. A balance between inflammation and immune tolerance is required to maintain pregnancy, thus maternal immune system must be controlled by finely tuned mechanisms.
MicroRNAs (miRNAs) are small non-coding RNAs with important regulatory roles in immune cells, but their function in decidual ILC3 (dILC3) and decidual NK (dNK) cells is still undefined. Here, we examined the miRNome by microarray in these cells during the first trimester of pregnancy and compared with miRNA profiles of peripheral blood NK (pbNK) cells from pregnant women. We show that distinct miRNA profiles could clearly distinguish dILC3 from NK cells. Correlation analyses revealed that dNK and pbNK miRNome profiles are more similar to each other as compared to dILC3. Overall, our data identified specific miRNA signatures distinguishing dILC3, dNK and pbNK cells.

overall_design: NCR+ dILC3 and dNK cells were isolated from decidua basalis of healthy pregnant women undergoing voluntary termination of pregnancy in the first trimester of gestation, applying a multi-parametric cytofluorimetric gating strategy. In order to perform an Affymetrix microRNA microarray analysis, three samples of sorted dILC3 were analyzed (pool #1: three patients; pool #2: five patients; pool #3: three patients). Further, five samples of sorted dNK were included in the microarray: three samples derived from the same pools used for dILC3, plus two additional non-pooled dNK samples. Finally, the microarray analysis included four samples of pbNK isolated from peripheral blood of four healthy pregnant women undergoing voluntary termination of pregnancy in the first trimester of gestation.

first: Paola

last: Vacca

first: Lorenzo

last: Moretta


title: Vγ6+ γδ T cells play a critical role in protection against infection by Escherichia coli

city: Fukuoka

first: Tun

last: Xin

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: γδ T cells producing interleukin 17A (IL-17A), which are mainly Vγ4 and Vγ6 subsets, are involved in protection against infection by extracellular bacteria. Using a new Vγ6-specific monoclonal antibody (mAb) (1C10-1F7) which we recently developed, we found that IL-17A+ Vγ6+ γδ T cells increased predominantly in the peritoneal cavity compared with IL-17A+ Vγ4+ γδ T cells during intraperitoneal Escherichia coli infection. The number of IL-17A+ Vγ6+ γδ T cells, which rapidly became CD69+ from CD69-, peaked at 12 h after infection. In vivo treatment with 1C10-1F7 mAb significantly inhibited the accumulation of neutrophils and hampered the resolution of E. coli infection. These results suggest that rapid activation of IL-17A+ Vγ6+ γδ T cells contributed to host defence against E. coli infection.

overall_design: Microarray analysis of gene expression in Vγ6+ γδT cells from the peritoneal cavity of mice before or 3 h after E. coli infection (1 replicate of cells from 20 mice per sample).

first: Yasunobu

last: Yoshikai

first: Xin

last: Tun

first: Shinya

last: Hatano

first: Keiichiro

last: Mine

first: Naoto

last: Noguchi

first: Yoichiro

last: Iwakura

first: Sun

last: Xun


title: RNASeq analysis of gene expression in effector Treg cells from Nrn1+/- and Nrn1-/- mice

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

summary: Nrn1-/- and Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+ were sorted from Nrn1-/- and Nrn1+/- mice on Foxp3DTRgfp background and subjected to RNASeq analysis.

overall_design: The gene expression patterns in effector Treg cells from Wild type and NRN1 KO mice were assessed and compared using RNASeq. Sequencing was performed using a Illumina NextSeq500.

first: Fan

last: Pan

first: Zhiguang

last: Li

first: Xuehong

last: Zhang


title: transcriptional profiling of H9 human embronic stem cells (hESC) and hESC derived retinal pigment epithelium (RPE)

city: Dresden

first: Seba

last: Almedawar

address: Fetscherstrasse 105

country: Germany

institute: CRTD- TU Dresden

summary: RPE was derived from hESC based on the protocol described in Zhu et al. PlosOne. 2013.

overall_design: RNA was purified from three consecutive RPE and hESC preps


title: Sex-specific adipose tissue imprinting of regulatory T cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Lamin B2 controls nuclear envelope permeability and regulates cardiomyocyte regeneration

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

summary: Heart muscle cells, cardiomyocytes, are highly differentiated cells that usually do not proliferate . During the non-proliferative state, extracellular signals control cardiomyocyte contractile function. However, during development and regeneration, cardiomyocytes enter the cell cycle and divide. It is unknown how cardiomyocytes modify their intracellular signaling to direct the cell cycle program.  Here, we show that the nuclear lamina protein Lamin B2 (Lmnb2) regulates cardiomyocyte cell cycle activity using a gatekeeper mechanism. We identified Lmnb2 as a candidate for regulating intracellular signaling with deep transcriptional profiling of single cardiomyocytes. Lmnb2 was sufficient and necessary for cardiomyocyte cycling in the presence of serum. Lmnb2 increased the nucleoporin NUP98 and permeability of the nuclear membrane for phosphorylated ERK1/2. In vivo, the Lmnb2 gene was required for cardiomyocyte cell cycle activity during development. Increasing the expression of Lmnb2 in neonatal mice promoted cardiomyocyte M-phase and cytokinesis. LmnB2 gene transfer in neonatal mice that received a myocardial injury increased cardiomyocyte division and myocardial function in the injury border zone, indicating that the regenerated cardiomyocytes were functionally integrated.  We propose a gatekeeper function of Lmnb2 that can be targeted to increase cardiomyocyte regeneration without the administration of exogenous growth factors.

overall_design: The cardiomyocytes were isolated from embryonic (E14.5) and postnatal (P19) mouse (FUCCI) hearts, then the single cardiomyocytes were collected through FACS. The cycling cardiomyocytes were identified through Azami Green-Geminin (mAG-hGem) signal. The mRNA was amplified using the antisense RNA (aRNA) amplification method.

first: Sangita

last: Choudhury

first: Balakrishnan

last: Ganapathy

first: Niyatie

last: Ammanamanchi

last: Suresh

first: Brian

middle: D

last: Polizzotti

first: Mugdha

last: Khaladkar

first: Jennifer

last: Singh

first: Rene

last: Maehr

first: James

last: Eberwine

first: Yijen

last: Wu

first: Bernhard

last: Kühn


title: Sex-specific adipose tissue imprinting of regulatory T cells (ATAC-seq)

summary: Visceral adipose tissue (VAT) is a metabolically active endocrine organ that plays a critical role regulating organismal metabolism. Regulatory T (Treg) cells restrain VAT inflammation, and preserve insulin sensitivity and organismal metabolism. Here we report pronounced sexual dimorphism in VAT Treg cells, which were enriched specifically in males and differed strikingly from their female counterparts in phenotype, transcriptional landscape and chromatin accessibility. These differences were imprinted by the adipose tissue in a manner dependent on sex hormones. Male VAT was characterized by heightened inflammation, which resulted in CCR2-dependent recruitment of Treg cells. Sex hormones also regulated the differentiation of unique IL-33-producing stromal cell populations specific to the male VAT, which paralleled the local expansion of Treg cells and the induction of a transcriptional program controlled by transcription factor Blimp1. Overall our findings reveal a novel multi-layered feedback circuit depending on Treg cells and regulated by sex hormones to limit VAT inflammation.

overall_design: ATACseq was performed to assess the chromatin accessibility in male and female spleen and VAT resident Tregs to understand sexual dimorphism

first: Ajithkumar

last: Vasanthakumar

first: David

last: Chisanga

first: Jonas

last: Blume

first: Renee

last: Gloury

first: Nicholas

last: Collins

first: Tom

last: Sidwell

first: Li

last: Chaoran

first: Sebastian

last: Liene

first: Santiago

middle: V

last: Torres

first: Yifan

last: Zhan

first: Darren

last: Henstridge

first: Paul

last: Beavis

first: Thomas

last: Gebhardt

first: Kara

last: Britt

first: Stephen

last: Nutt

first: Jeffrey

last: Zajac

first: Rachel

middle: A

last: Davey

first: Mark

last: Febbraio

first: Diane

last: Mathis

first: Axel

last: Kallies


title: Liver transcriptome profile in geese with different phenotypes of weight

city: Rongchang

first: Jie

last: Zhang

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

institute: Southwest University

summary: The unique fat storage and metabolic characteristics of goose liver is an important model for studying lipid metabolism in animals or humans. In this study, RNA sequencing technology was used to obtain the liver transcriptome of Sichuan white goose with significant weight difference in the same population, and differentially expressed genes and their pathways were identified, which may help to understand the mechanism of goose weight change. In addition, the identified candidate genes may be useful for molecular breeding of geese.

overall_design: Liver mRNA profiles of 70-day-old goose with high (H), middle (M) and low (L) weight were generated by deep sequencing, in triplicate, using Illumina High-seq 2000.


title: Differential Regulation of Alcohol Consumption and Reward by the Transcription Cofactor LMO4

city: Austin

first: Rajani

last: Maiya

state: TX

address: 1601B Trinity St., Stop Z0700 HDB 5.322

department: Neuroscience

institute: The University of Texas at Austin

summary:
The goal of this study is to identify and validate transcriptional targets of LMO4 in the Basolateral Amygdala (BLA) and the Nucleus Accumbens (NAc)
We mapped about 15-25 million reads per sample to the mouse genome (mm9) . We identified about 16,000 transcripts per sample.

overall_design: Methods: Transcriptome data from the BLA and NAc of 11 WT and 9 Lmo4gt/+ (Lmo4 genetrap) mice were compared to identify putative transcriptional targets of LMO4

first: Robert

middle: O

last: Messing


title: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [ChIP-seq]

status: Public on Feb 27 2020

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

summary: The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of the independent and interdependent functions of these two isoforms in gene expression using endogenously-tagged isoform. RNA-Seq analysis following depletion of either isoform or both together in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Our data revealed that the two isoforms have similar or antagonistic function depending on the gene. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, PHF14 and associated proteins for H2A.Z.1 and the histone deacetylase SIRT1 for H2A.Z.2. Moreover, we show that PHF14 and SIRT1 mediate the functional antagonism between H2A.Z.1 and H2A.Z.2. In conclusion, we propose a model in which the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression and depends on the recruitment of specific proteins. Our work thus provides an additional layer of complexity to the control of gene expression by histone variants.

overall_design: H2A.Z1 and H2A.Z2 ChIP-seq datasets in U2OS Flag-Z1 and U2OS Flag-Z2 cells.

first: Assala

last: Lamaa

first: Marion

last: Aguirrebengoa

first: Didier

last: Trouche


title: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [WI38_siPHF14-siSIRT1 RNA-seq]

overall_design: Strand-specific RNA-seq datasets in WI38 hTERT RAF1-ER cells treated with siPHF14 or siSIRT1 (2 replicates).


title: MicroRNAs secreted by human embryos are potential biomarkers for clinical outcomes of assisted reproductive techniques

city: Wuhan

first: Zili

last: Li

state: Hubei

institute: HuaZhong Science and Technology University

summary: MicroRNAs (miRNAs) are important regulators of many biological functions, including embryo implantation and development. Recently, it is reported that miRNAs in biofluids are predictive for physiological and pathological processes. In this study, we aim to investigate whether the miRNAs secreted by human embryos in culture medium can be used as embryonic biomarkers. The culture media were prospectively collected from embryos of patients who underwent routine in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) at reproductive medicine center with informed consent. A high-throughput miRNA sequencing method was applied to detect the miRNAs profiles in culture media of embryos with different reproductive outcomes. Compared with embryos with failed pregnancy, the embryos with successful pregnancy secreted different miRNA profiles into the culture media. These differentially expressed miRNAs were predicted to be involved in multiple biological processes, cellular components and molecular functions. After bioinformatics analysis, 18 miRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR) and droplet digital PCR (ddPCR). We found that the cleavage embryos with successful pregnancy presented decreased expression of hsa-miR-26b-5p and hsa-miR-21-5p in the culture media. Moreover, the Receiver Operating Characteristic (ROC) curve analysis indicated that hsa-miR-26b-5p and hsa-miR-21-5p could serve as potential biomarkers for reproductive outcomes. Together, our findings highlight the important predictive potential of miRNAs secreted by human embryos in culture media, which is meaningful for noninvasive embryo selection during IVF cycles.

overall_design: The culture media were prospectively collected from embryos of patients who underwent routine in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) at reproductive medicine center with informed consent. A high-throughput miRNA sequencing method was applied to detect the miRNAs profiles in culture media of embryos with different reproductive outcomes (15 samples were mixed for each group). After bioinformatics analysis and screening of differentially expressed miRNAs, quantitative real-time polymerase chain reaction (qRT-PCR) assay was subsequently performed to further confirm the sequencing results with mixed samples. Furthermore, we performed droplet digital PCR (ddPCR) to verify the target miRNAs at single sample level (100 cleavage samples in total, 50 with successful pregnancy and 50 with failed pregnancy). Receiver operating characteristic (ROC) analyses were performed for differentially expressed miRNAs.

first: Fang

last: Fang

first: Yuting

last: Long

first: Qian

last: Zhao

first: Xiaofang

last: Ding

first: Li

last: Wu

first: Shumin

last: Shao

first: Ling

first: Wenpei

last: Xiang


title: Hyperacetylated Chromatin Domains Mark Cell Type-Specific Genes and Suggest Distinct Modes of Enhancer Function

city: Rochester

first: Michael

last: Bulger

state: NY

address: 601 Elmwood Ave.

department: Pediatrics

institute: University of Rochester

summary: Stratification of enhancers by relative signal strength in ChIP-seq assays has resulted in the establishment of “super-enhancers” as a widespread and useful tool for identifying cell type-specific, highly expressed genes and associated pathways.  We have examined a distinct method of stratification that focuses on peak breadth, and use it to classify broad regions exhibiting histone modifications associated with gene activation as “hyperacetylated chromatin domains” (HCDs).  We find that application of this analysis to multiple datasets serves to identify genes that are both more highly expressed and more closely aligned to cell identity than “super-enhancer” analysis does.  Moreover, genetic manipulations of selected gene loci suggest that at least some HCDs harbor enhancers that work by distinct mechanisms, and in turn reveal that the “super-enhancer” concept can obscure important functions of constituent elements.

overall_design: ATAC-Seq of mouse proeyrthorblasts and ChIP-seq (H3K4Me1, H3K4Me2, H3K4Me3, H3K27Ac) analysis of mouse 14.5 fetal liver

first: Sierra

last: Fox

first: Jacquelyn

last: Lillis


title: Ibrutinib blocks YAP1 activation and reverses BRAFi resistance in melanoma cells

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

summary: Most BRAF-mutant melanoma tumors respond initially to BRAFi/MEKi therapy, although few patients have durable long-term responses to these agents. The goal of this study was to utilize an unbiased computational approach to identify inhibitors which reverse an experimentally derived BRAFi resistance gene expression signature. Using this approach, we predicted that ibrutinib, a BTK inhibitor, effectively reverses this signature, and we demonstrate experimentally that ibrutinib re-sensitizes a subset of BRAFi-resistant melanoma cells to vemurafenib. Ibrutinib is used clinically as a BTK inhibitor; however, neither BTK deletion nor treatment with acalabrutinib, an analog of ibrutinib with reduced off-target activity, re-sensitized cells to vemurafenib. These data suggest that ibrutinib acts through a BTK-independent mechanism in vemurafenib re-sensitization. To better understand this mechanism, we analyzed the transcriptional profile of ibrutinib-treated BRAFi-resistant melanoma cells and found that the transcriptional profile of ibrutinib was highly similar to that of multiple SRC kinase inhibitors. Since ibrutinib, but not acalabrutinib, has significant off-target activity against multiple SRC family kinases, it suggests that ibrutinib may be acting through this mechanism. Furthermore, genes either upregulated or downregulated by ibrutinib treatment are enriched with YAP1 target genes and we experimentally demonstrate that ibrutinib, but not acalabrutinib, reduces YAP1 activity in BRAFi-resistant melanoma cells. Taken together, these data suggest that ibrutinib, or other SRC family kinase inhibitors, may be useful for treating some BRAFi/MEKi-refractory melanoma tumors.

overall_design: This study contains 6 different treatment conditions (DMSO, Vemurafenib, Ibrutinib, Acalabrutinib, Vemurafenib + Ibrutinib, and Vemurafenib + Acalabrutinib. There are three biological replicates per treatment condition.

first: Bin

last: Chen

first: Richard

middle: R

last: Neubig


title: Senataxin, the helicase mutated in AOA2 and ALS4, plays a role in autophagy regulation

status: Public on Feb 26 2020

city: Bridgewater

first: Wencheng

state: NJ - New Jersey

institute: PTC Therapeutics


title: Senataxin, the helicase mutated in AOA2 and ALS4, plays a role in autophagy regulation [microarray]

summary: Senataxin (SETX) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response, through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of ALS (amyotrophic lateral sclerosis) named ALS4, while recessive mutations are responsible for an ataxia called AOA2 (ataxia with oculomotor apraxia type 2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX depleted cells. Importantly, we discovered a strong connection between SETX and the autophagy pathway, reflecting a direct effect on the transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2.

overall_design: U87 cells treated with SETX siRNA or control siRNA in triplicates

first: Mainul

last: Hoque

first: Patricia

last: Richard

first: Shuang

last: Feng

first: Yueh-Lin

last: Tsai

first: Ubayed

last: Muhith

first: Juan

last: Irizarry-Cole

first: Katharine

last: Stolz

first: James

middle: L

last: Manley

last: Tian


title: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [U2OS_siZ1-siZ2 RNA-seq]

first: Estelle

last: Nicolas

overall_design: Strand-specific RNA-seq datasets in U2OS cells treated with siH2A.Z1 and/or siH2A.Z2 (2 replicates).

first: Assala

last: Lamaa

first: Marion

last: Aguirrebengoa

first: Didier

last: Trouche


title: Genome-wide Methylation Profiles of femoral bones

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of femoral bones obtained from young and old individuals. The Illumina Infinium HumanMethylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850K CpGs from human femoral bones.

overall_design: Bisulfite converted DNA from 32 samples were hybridised to the Illumina Infinium HumanMethylation EPIC BeadChip

first: Hwan

middle: Y


title: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [WI38_siZ1-siZ2 RNA-seq]

overall_design: Strand-specific RNA-seq datasets in WI38 hTERT RAF1-ER cells treated with siH2A.Z1 and/or siH2A.Z2 (2 replicates).


title: The Myb domain of TbRAP1 plays an important role in subtelomeric gene expression

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

summary: We examine the function of the TbRAP1 Myb domain in gene expression regulation in Trypanosoma brucei that causes human African trypanosomiasis. TbRAP1 is required for normal VSG monoallelic expression, a key aspect of antigenic variation that is used by T. brucei to evade the host immune response.

overall_design: High-throughput paired-end RNA sequencing on the Illumina platform was performed. Mutant T. brucei strain has one WT TbRAP1 allele flanked by two loxP repeats (floxed) and an FLAG-HA-HA tagged TbRAP1∆Myb allele. Control T. brucei strain has one floxed and a WT TbRAP1 allele. Both mutant and control cells were induced for Cre induction for 30 hrs (to remove the floxed TbRAP1 allele) before total RNA was isolated. Three independent induction were performed for both cells. RNA samples were sent to Novogene for subsequent experiments. Poly(A) RNA was purified for generating cDNA library and paired-end sequencing was done using Illumina. Gene expression profiles were compared between the mutant and control cells by differential gene expression analysis.

first: Marjia

last: Afrin


title: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation


title: ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin-STAG1 from WAPL

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

institute: IMP - Research Institute of Molecular Pathology

summary: The human genome folds to create thousands of loops connecting sites that are bound by the insulator protein CTCF and the ring-shaped cohesin complex. It is thought that most of these loops emerge through a process whereby cohesin extrudes chromatin, forming an initially small loop that grows larger and larger until the loop’s expansion is arrested by CTCF. Cohesin rings comprise four proteins: SMC1, SMC3, SCC1, and, in higher eukaryotes, either STAG1 or STAG2. We explore differential roles of especially STAG1, STAG2 and ESCO1 proteins in chromatin organization.

overall_design: We combine Hi-C and ChIP-Seq data with FRAP and physical simulations to dissect the roles of these two forms of cohesin - STAG1 and STAG2 - in G1 phase.

first: Gordana

last: Wutz

first: Wen

last: Tang

first: Stefan

last: Schoenfelder

first: Miroslav

last: Ivanov

first: Cilla

last: Varnai

first: Brian


title: Fc receptor-like 6 (FCRL6) defines pre-BCR dependent and independent pathways of natural antibody selection

city: Birmingham

first: Randall

middle: S

last: Davis

state: AL

address: 1825 University Blvd SHEL402

institute: UAB

summary:
B-1a cells produce ‘natural’ antibodies (Abs) to neutralize pathogens and clear neo self-antigens, but the fundamental selection mechanisms that shape their polyreactive repertoires are poorly understood. Here, we identified a B cell progenitor subset defined by Fc receptor-like 6 (FCRL6) expression, harboring innate-like defense, migration, and differentiation properties conducive for natural Ab generation
Compared to FCRL6- pro B cells, the repressed mitotic, DNA damage repair, and signaling activity of FCRL6+ progenitors, yielded VH repertoires with biased distal Ighv segment accessibility, constrained diversity, and hydrophobic and charged CDR-H3 sequences. Beyond nascent autoreactivity, VH11 productivity, which predominates phosphatidylcholine-specific B-1a B cell receptors (BCRs), was higher for FCRL6+ cells as was pre-BCR formation, which was required for Myc induction and VH11, but not VH12, B-1a development.
Thus, FCRL6 revealed unexpected heterogeneity in the developmental origins, regulation, and selection of natural Abs at the pre-BCR checkpoint with implications for autoimmunity and lymphoproliferative disorders.

overall_design: FCRL6+ and FCRL6- pro B (AA4.1+Lin-CD43+B220+CD19-IgM-) cells derived from the fetal livers of embryonic day 18 and bone marrow of adult 8-12 week old mice were sorted by flow cytometry from BALB/cJ strain mice. Single cell suspensions from leg bones were pooled from 5-10 adult male and female mice and 7-10 fetal livers were pooled from embryonic day 18 fetuses isolated from pregnant mothers according to the timing of vaginal plug formation. Data are from a total of eight samples that were isolated in duplicate from four independent sorts. Each sort yielded two samples per cell type (FCRL6+ and FCRL6- pro B cells).

first: Kazuhito

last: Honjo

first: Woong-Jai

last: Won

first: Rodney

middle: G

last: King

first: Lara

last: Ianov

first: David

middle: K

last: Crossman

first: Juliet

last: Easlick

first: Mikhail

last: Shakhmatov

first: Mohamed

last: Khass

first: Andre

middle: M

last: Vale

first: Robert

middle: P

last: Stephan

first: Ran


title: Murine MDSCs: Mock vs Epigenetic drug treated

city: Beijing

first: Shuang

last: Li

address: Haidian District

institute: Peking University Cancer Hospital

summary: Genome-wide gene expression analysis of mouse MDSCs comparing control group  with epigenetic drugs treated group.

overall_design: Mock vs. treated. From lung and bone marrow. Biological replicates: 3 control replicates, 3 treated replicates.

first: Zhihao

last: Lu

first: Malcom

last: Brock


title: Trem2 effects on brain resident myeloid cells in PS2APP model

status: Public on Feb 25 2020

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Comparing Trem2-KO;PS2APP and Trem2-WT;PS2APP CD11b+ cells reveals
the role of Trem2 in microglial gene expression in amyloid-laden brains.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0014430

overall_design: RNA from purified CD11b+ CD45+ Ly6g- Ccr2- cells from Trem2-KO and Trem2-WT PS2APP brains at 14-15 months of age.

first: Karpagam

last: Srinivasan

last: Hansen


title: RNA-seq analysis of VV-iPDL1/GM-infected MC38 cells at 2, 4, 8, 16, and 24 h postinfection

city: los angeles

first: Guan

last: Wang

state: ca

address: 1450 biggy st, NRT7509

institute: University of southern california

summary: TNF signaling genes and protein processing genes in VV-iPDL1/GM-infected tumor cells were upregulated.

overall_design: Compare genes expression level of 2, 4, 8, 16, or 24 h postinfected tumor cells to those of uninfected cells.

first: Si-Yi

last: Chen


title: Analysis of transcriptome in dorsal hippocampus in response to over-expression of hepatic leukemia factor (Hlf) in dentate gyrus neurons

city: Zurich

first: Lukas

last: Rambousek

address: Winterthurerstrasse 161

country: Switzerland

institute: University of Zurich

summary: We report differential gene expression analysis of brain tissue (dorsal hippocampus) in adult mice over-expressing mouse hepatic leukemia factor (AAV-2/8-hSyn1-mHLf) in dentate gyrus neurons.

overall_design: Differential gene expression analysis of dorsal hippocampus in mice overexpressing hepatic leukemia factor in dentate gyruse neurons generated by NGS.

first: Tilo

last: Gschwind

first: Carlos

last: Lafourcade

first: Jean-Charles

last: Paterna

first: Linda

last: Dib

first: Jean-Marc

last: Fritschy

first: Adriano

last: Fontana


title: Integrating Next Generation Sequencing with Morphology Improves Prognostic and Biologic Classification of Spitz Neoplasms [RNA-Seq]

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

institute: Northwestern University

summary: The newest WHO classification suggests eliminating cases with BRAF and NRAS mutations from the categories of Spitz tumors (ST) and Spitz melanoma (SM). We aimed to better characterize the genomics of Spitz neoplasms and assess whether integrating genomic data with morphologic diagnosis improves classification and prognostication. We performed DNA and RNA sequencing on 80 STs, 26 SMs, and 22 melanomas with Spitzoid features (MSF).  NGS data was used to reclassify tumors by moving BRAF/NRAS-mutated cases to MSF. Eighty-one percent of STs harbored kinase fusions/truncations. Of SMs, 77% had fusions/truncations, 8 involving MAP3K8. Novel fusions identified were MYO5A-FGFR1, MYO5A-ERBB4, and PRKDC-CTNNB1. The majority of MSFs (84%) had BRAF, NRAS, or NF1 mutations, and 62% had TERT promoter mutations.  Only after reclassification, the following was observed: 1) mRNA expression showed distinct clustering of MSF; 2) 6/7 cases with recurrence and all distant metastases were MSFs; 3) RFS was worse in MSF than ST and SM groups (p=0.0073); 4) classification incorporating genomic data was highly predictive of recurrence (OR 13.20, p=0.0197). The majority of STs and SMs have kinase fusions as primary initiating genomic events.  Eliminating BRAF/NRAS-mutated neoplasms from these categories results in improved classification and prognostication of melanocytic neoplasms with Spitzoid cytomorphology.

overall_design: We performed sequencing on 75 Spitz Tumors, 24 Spitzoid Melanomas, and 20 melanomas with Spitzoid features (MSF) to better characterize the genomics of Spitz neoplasms and assess whether integrating genomic data with morphologic diagnosis improves classification and prognostication.

first: Victor

last: Quan

first: Bin

last: Zhang

first: Yongzhan

first: Lauren

last: Mohan

first: Katherine

last: Shi

first: Annette

last: Wagner

first: Lacey

last: Kruse

first: Timothy

last: Taxter

first: Nike

last: Beaubier

first: Kevin

last: White

first: Lihua

last: Zou


title: Calibrated ChIP-seq for meiotic-specific cohesin (Rec8) and mitotic-specific cohesin (Scc1) in budding yeast cells arrested in metaphase of mitosis

status: Public on Feb 24 2020

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Purpose: The goal of this study is to look at differences in genome wide localization of cohesin when budding yeast, Saccharomyces cerevisiae, is forced to use the meiosis-specific cohesin, Rec8, instead of its mitotic counterpart, Scc1, during the mitotic cell cycle.

first: V

last: Makrantoni


title: H2A.Z ChIP seq datasets of Trypanosoma brucei in WT cells and 2T1 cells, which were depleted of HAT1 or HAT2 over a time period up to 72 h

city: Planegg-Martinsried

first: T.

middle: Nicolai

last: Siegel

address: Großhaderner Str. 9

department: Department of Physiological Chemistry

institute: Ludwig-Maximilians-Universität

summary: Analysis of the genome-wide distribution of the histone variant H2A.Z following depletion of HAT1 or HAT2 over a time period up to 72 h and in WT cells

overall_design: H2A.Z-ChIP-seq analyses in T. brucei

first: Amelie

middle: J

last: Kraus

first: T

middle: N


title: 2'O-methylation profile of ribosomal RNA in Kasumi-1 SNORD42A knock out cells by RiboMethSeq

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: Non-coding RNAs including small nucleolar RNAs (snoRNAs) play important roles in leukemogenesis but the relevant mechanisms remain incompletely understood. We performed snoRNA focused CRISPR-Cas9 knockout library screenings which targeted the entire snoRNAnome and corresponding host genes. The C/D box containing SNORD42A was identified as an essential modulator for AML cell survival and proliferation in multiple human leukemia cell lines. In line, SNORD42A was consistently expressed at high levels in primary AML patient samples. Functionally, knockout of SNORD42A reduced colony formation capability and inhibited proliferation. The SNORD42A acts as a C/D box snoRNA and directs 2´-O-methylation at Uridine 116 of 18S rRNA. Deletion of SNORD42A decreased 18S-U116 2´-O-methylation which was associated with a specific decrease in the translation of ribosomal proteins. In line, the cell size of SNORD42A deletion carrying leukemia cells was decreased. Taken together, these findings establish that high level expression of SNORD42A with concomitant U116 18S rRNA 2´-O-methylation is essential for leukemia cell growth and survival.

overall_design: We used RiboMethSeq to determine 2'O-methylation profile Kasumi-1 samples in SNORD42A KO conditions. This series includes RiboMethSeq samples for SNORD42A_KO and CTRL_KO Kasumi-1 cells.

first: Yi

last: Liu

first: Carsten

last: Müller-Tidow


title: KLF4 knockdown in human keratinocytes

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with pooled siRNAs targeting KLF4, or non-targeting control siRNA (siCon)

overall_design: N/TERT2G keratinocytes were transduced with siRNAs and harvested 48hs after transduction

first: Iglesias-Bartolome

last: Ramiro

first: Yuan

last: Yao


title: TY1-RPB9 ChIP seq datasets of Trypanosoma brucei in 2T1 cells, which were depleted of HAT1 or HAT2 over a time period up to 48 h

status: Public on Feb 22 2020

summary: Analysis of the genome-wide distribution of RNA Pol II subunit RPB9, endogenously tagged with 2 x TY1, following depletion of HAT1 or HAT2 over a time period up to 48 h and in WT cells

overall_design: TY1-RPB9-ChIP-seq analyses in T. brucei


title: Functional Mature Human Microglia Developed in Human iPSC Microglial Chimeric Mouse Brain

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Microglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under homeostatic states. We developed a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage precursors into neonatal mouse brains. The engrafted human microglia widely disperse in the brain and replace mouse microglia in corpus callosum at 6 months post-transplantation. Single-cell RNA-sequencing of the microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the engrafted hPSC-derived microglia exhibit dynamic response to cuprizone-induced demyelination and species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a novel tool to study the role of human microglia in brain development and degeneration.

overall_design: RNA sequencing was performed on replicate cultures of iPSC-derived primitive macrophage progenitors (PMPs)

first: Ranjie

last: Xu

first: Andrew

last: Boreland

first: Anthony

last: Posyton

first: Kelvin

last: Kwan

first: Peng

last: Jiang


title: TY1-H2A-ChIP-seq datasets of Trypanosoma brucei

status: Public on Feb 21 2020

summary: Analysis of the genome-wide distribution of the histone H2A, using TY1-H2A as a Proxy

overall_design: TY1-H2A-ChIP-seq analyses in T. brucei


title: Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes

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

overall_design: Refer to individual Series


title: YAP1 and TAZ knockdown in human keratinocytes

summary: RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with pooled siRNAs targeting YAP1 and TAZ (WWTR1), or non-targeting control siRNA (siCon)

first: Yao

last: Yuan


title: RNA-seq datasets of Trypanosoma brucei WT cells and 2T1 cells, which were depleted of HAT1 or HAT2 for 48 h

summary: To analyze the effect of HAT1 or HAT2 depletion on transcript levels, we performed RNA-seq analyses comparing the transcript levels after 48 h of HAT1 or HAT2 depletion to WT levels.

overall_design: Transcriptome analyses in T. brucei

first: Benedikt

last: Brink


title: Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

summary:
Background: The historically recent domestication of fishes has been essential for mankind due to the overexploitation of natural stocks and the increasing protein demand to meet the needs of a growing human population. Selection for relevant traits, such as growth, during domestication is a complex process whose epigenetic basis is poorly understood.
Results: We have determined changes that occur in the muscle transcriptome after a single generation of Nile tilapia (Oreochromis niloticus) domestication. There was a downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated.
Methods:  RNA was extracted and ribosomal RNA was removed using the Ribo-Zero gold rRNA removal kit. RNA libraries were prepared using the NEBNext Ultra II directional RNA library prep kit for Illumina. In total, we obtained 480 million 150 bp paired-end reads.
Conclusion: Taken together, our data indicate that thousands of genes were differentially expressed within a single generation of fish domestication.

overall_design: Fast muscle RNA-Seq from rRNA depleted libraries of 5-month old Wild type (W) and first generation of fish undergoing domestication (D) females in six replicates. W and D samples are genetically paired (i.e., each D sample corresponded to a W progenitor) and at the same ontogeny stage. The pairs are grouped according to their numbers (i.e. W53 - D53, W63 - D63)

first: Pål

last: Sætrom

first: Robin

last: Mjelle

first: Artem

last: Nedoluzhko

first: Diego

last: Robledo

first: Jorge

last: Fernandes


title: Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects

status: Public on Feb 20 2020

city: Indianapolis

first: James

last: Marrs

state: IN

address: 723 West Michigan Street

institute: Indiana University-Purdue University Indianapolis

summary: Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.

overall_design: control vs. ethanol treated embryos

first: Swapnalee

last: Sarmah


title: RNA-Seq analysis of Candida glabrata wild-type and Cghhf1Δhhf2Δ mutant in the presence and absence of methyl methanesulfonate (MMS).

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary: To determine the effect of lack of two Histone H4 genes, CgHHF1 and CgHHF2, on global transcriptional profile, and on transcriptional response towards MMS exposure, RNA-Seq analysis was conducted on log-phase grown Candida glabrata wild-type and Cghhf1∆2∆ cells in the presence and absence of MMS. Comparative transcriptome analysis of wild-type and Cghhf1∆2∆ cells displayed deregulation of 303 genes due to the loss of CgHHF1 and CgHHF2 genes.  C. glabrata responded to MMS by upregulating genes involved in transmembrane transport and invasive growth in response to glucose limitation, and by downregulating the aerobic respiration and ergosterol biosynthetic process genes.

overall_design: The study was designed to profile the transcriptomes of C. glabrata wild-type and Cghhf1Δhhf2Δ strains grown under normal (YPD medium) and DNA damage stress (MMS treatment) conditions via RNA-Sequencing approach. The experiment was performed with two biological replicates.

first: Kundan

last: Kumar

first: Romila

last: Moirangthem


title: ChIP-seq analysis of dCas9 chromatin occupancy in K562 cells by CAPTURE2.0

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: The spatiotemporal control of 3D chromatin structure is fundamental for gene regulation, yet it remains challenging to obtain high-resolution chromatin interacting profiles at cis-regulatory elements (CREs) by chromatin conformation capture (3C)-based methods. Here, we describe the redesigned dCas9-based CAPTURE method for multiplexed, high-throughput and high-resolution analysis of locus-specific chromatin interactions. Using C-terminally biotinylated dCas9, endogenous biotin ligase and pooled sgRNAs, the new system enables quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling systematic comparisons across CREs within and between gene clusters. Multiplexed analyses of erythroid super-enhancers (SEs) reveal SE hierarchical structure and distinct modes of SE-gene interactions. Multiplexed capture of temporal dynamics of promoter-centric interactions establishes the instructive function of enhancer-promoter looping in transcriptional regulation during lineage differentiation. These applications illustrate the ability of multiplexed CAPTURE for decoding the organizational principles of genome structure and function.

overall_design: ChIP-seq was performed to determine the chromatin occupancy of biotinylated dCas9 in cells expressing target-specific sgRNAs or the non-targeting sgRNA (sgGal4).

first: Xin

last: Liu

first: Yuannyu

last: Zhang


title: TEAD inhibition in human keratinocytes

first: Ramiro

last: Iglesias-Bartolome

summary: RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with TEAD inhibitor protein (TEADi) or control GFP for 12, 24 and 48 hs

overall_design: N/TERT2G keratinocytes were transduced in triplicate with adenoviruses expressing  GFP (control) or TEADi and harvested 12hs, 24hs and 48hs after transduction


title: Graphene oxide nanoparticles induce hepatic dysfunction through the regulation of innate immune signaling in zebrafish (Danio rerio)

city: Ji'an

first: Guanghua

last: Xiong

address: No. 28 Xueyuan Road, Qingyuan District

institute: Jinggangshan University

summary:
Purpose: The goals of this study are to investigate the toxic effects and molecular mechanisms of GO exposure in adult zebrafish liver by transcriptome profiling (RNA-seq)
Methods: Liver mRNA profiles of three-month-old control (CK) and GO-exposed (GO) zebrafish were generated by deep sequencing, in triplicate, using Illumina Hiseq X ten. The sequence reads that passed quality filters were analyzed at the gene level with two methods: RSEM and HISAT followed by Ballgown. qRT-PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the zebrafish genome (GRCz11) and identified 43,106 genes in the livers of CK and GO zebrafish with RSEM and HISAT2 workflow. RNA-seq data confirmed stable expression of 10 known housekeeping genes, and 6 of these were validated with qRT-PCR. Approximately 0.7% of the genes showed differential expression between the CK and GO liver, with a fold change ≥1.5 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several genes that may contribute to function in liver inflammation and lipid disorder.
Conclusions: Our study represents the detailed analysis of zebrafish liver transcriptomes after GO exposure, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that steroid hormone biosynthesis, lipoprotein metabolic process and PPAR signaling pathway were signifificantly enriched. Most of the lipid metabolism genes were down-regulated while majority of the immune genes were up-regulated after GO treatment.

overall_design: Liver mRNA profiles of three-month old control (CK) and GO-exposed (GO) adult zebrafish were generated by deep sequencing, in triplicate, using Illumina Hiseq X Ten.

first: Huiqiang

last: Lu


title: RNA-seq transcriptonal profiling in human K562 cells and G1E-ER4 cells with or without dCas9 and sgRNAs

summary: The spatiotemporal control of 3D chromatin structure is fundamental for gene regulation, yet it remains challenging to obtain high-resolution chromatin interacting profiles at cis-regulatory elements (CREs) by chromatin conformation capture (3C)-based methods. Here, we describe the redesigned dCas9-based CAPTURE method for multiplexed, high-throughput and high-resolution analysis of locus-specific chromatin interactions. Using C-terminally biotinylated dCas9, endogenous biotin ligase and pooled sgRNAs, the new system enables quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling systematic comparisons across CREs within and between gene clusters. We reveal the hierarchical structure of super-enhancers (SEs) and distinct modes of SE-gene interactions. Multiplexed capture of temporal dynamics of promoter-centric interactions establishes the instructive function of enhancer-promoter looping in transcriptional regulation during lineage differentiation. These applications illustrate the ability of multiplexed CAPTURE for decoding the organizational principles of genome structure and function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq was performed to determine the effects on global gene expression in K562 or G1ER-ER4 cells stably expressing dCas9-CBio and sgRNAs, or erythroid differentiation of G1ER-ER4 cells.

first: Yong

last: Chen


title: ATAC-seq analysis in G1E-ER4 cells during erythroid differentiation

overall_design: ATAC-seq was performed to determine the chromatin accessibility in G1E-ER4 without (0 hour) or with β-estradiol treatment for 2, 6, 12, and 24 hours


title: CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells

overall_design: We combined the chromatin interaction assays (Chromatin Conformation Capture or 3C) with the high affinity dCas9 purification approach to unbiasedly identify single genomic locus-associated long-range interactions (CAPTURE-3C-seq).


title: Analysis of CRE-mediated chromatin interactions by CAPTURE2.0


title: Tracing tumorigenesis in a solid tumor model at single-cell resolution

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterise tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment and emphasizes the power of using defined genetic model systems.

overall_design: Single cell transcriptome and epitope profiling of mouse salivary glands using Drop-seq and CITE-seq

first: Samantha

middle: D

last: Praktiknjo

first: Qionghua

last: Zhu

first: Liang

last: Fang

first: Haiyue

first: Hazel

last: Quinn

first: Marlon

last: Stoeckius

first: Christine

last: Kocks

first: Walter

last: Birchmeier

first: Nikolaus

last: Rajewsky


title: Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination

city: Nanjing

first: Rong

last: Zhou

address: 50 Zhongling Street

institute: Jiangsu Academy of Agricultural Sciences

summary: Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. Of these miRNAs, 32, 74 and 61 miRNAs were responsive to drought, heat and their combination, respectively. Following degradome sequencing, 50 sequences were identified as targets of 34 miRNAs in tomatoes at combined stress. Moreover, 467 circRNAs were identified in the 12 samples.

overall_design: Methods: Tomato seedlings were treated at control, single heat, drought and their combination. Leaves from the tomato seedlings at four treatments were collected, frozen in liquid nitrogen and stored at -80 degrees Celsius before sequencing. Afterwards, the sRNA libraries of samples were constructed and sequenced with Illumina Hiseq2500 (LC-BIO, Hangzhou, China).


title: ASO-mediated RNA Suppression through Targeted Epigenetic Reprogramming of the Hdac2 Gene

city: La Jolla

first: Shane

middle: Gary

last: Poplawski

state: CA

address: 4120 Capricorn Lane

institute: JCVI

summary: We elicited ASO-mediated knockdown of mRNAs in the nervous system by targeting the memory-repressor gene Histone deacetylase 2 (Hdac2) in vitro and in vivo. We observed that an Hdac2-targeted ASO not only triggered a reduction in mRNA levels, but also a direct transcriptional suppression of the Hdac2 gene in neurons in vitro. In further in vivo studies, we observed that a single dose of the Hdac2-targeted ASO delivered by intracerebroventricular injection into the central nervous system (CNS) achieved steady-state diminution of Hdac2 mRNA levels that lasted more than 6 months in vivo. Knockdown of this factor resulted in memory enhancement. ASO administration also caused a prolonged alteration of steady-state levels of a set of known memory-associated mRNAs and triggered secondary changes in the epigenome at sites outside of the primary target gene.

overall_design: 3 scrambled ASO and 3 HDAC2 ASO mice were sacrificed and at 9 timepoints (3d, 2w, 4w, 8w, 16w, 32w, 40w, 48w, 52w) after ASO injection. Cortex, hippocampus and cerebellum were analyzed for total RNA expression. expression.

first: Celeste

middle: B

last: Greer

first: Krassimira

last: Garbett

first: Rebekah

last: McMahon

first: Holly

last: Kordasiewicz

first: S

middle: T

last: Motley

first: Eric

middle: E

last: Swayze

first: David

last: Ecker

first: Slavina

last: Goleva

first: Teresa

middle: H

last: Sanders

first: Andrew

last: Kennedy

first: Todd

last: Michael

first: J

last: Sweatt


title: RNAseq analysis on e9.5 mutant mouse hearts

status: Public on Feb 19 2020

city: Boston

first: Abir

last: Yamak

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: We report RNAseq analysis on RNA from e9.5 hearts of Asb2 mutant and Asb2.Flna double mutants with controls. The goal of this study is to identify Asb2 downstream targets in the heart as well as targets that are corrected in the Asb2.Flna double mutant vs the Asb2 singe mutants.

overall_design: RNA was extracted from hearts of Asb2 single, Asb2.Flna double mutants and two control samples with n=3 for each.

first: Ibrahim

last: Domian


title: RNA-seq on periodontal tisuues of  susceptible and resistant collaborative cross mice after periodontal infection

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We assessed alveolar bone changes of Collaborative cross (CC) lines in response to a mixed oral infection with a well-known periodontal pathogen. The CC lines showed significant variation in their response to the mixed infection. We then carried out RNA-seq analysis on periodontal tisuues of resistant CC lines, susceptible CC lines and two CC lines that showed bone formation after oral bacterial infection.

overall_design: We assessed alveolar bone changes of Collaborative cross lines after periodontal infection with P.g. (strain 381) and F.n. (strain PK1594) using micro–computed tomography (µCT) (control groups were treated with PBS and 2% Carboxymethycellulose). The CC lines showed significant variation in their response to the mixed infection. We then carried out RNA-seq analysis on periodontal tisuues of two resistant CC lines (TAU-IL188, TAU-IL111), two susceptible CC lines (TAU-IL785, TAU-IL551) and two CC lines that showed bone formation after oral bacterial infection (TAU-IL2124, TAU-IL2126).

first: Aysar

last: Nashef

first: Yael

last: Haddad

first: Fuad

last: Iraqi


title: Long heat stress induced RNA dynamics in Arabidopsis

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

summary: Heat stress is a common stress for plants. Long heat stress can triger a series of biological responses. RNA-seq is a useful method to profile RNA dynamics in creatures. Here we profiles the RNA dynamics in heat stressed Arabidopsis. These data will help us understanding the stress response mechanism in plants.

overall_design: Total RNA-seq of Arabidopsis 7-day-old seedlings. LHS (long heat stress) samples were treated by 37°C 30 hours. LHSR12 (long heat stress recovery 12 hours) samples recovered under normal condition (22°C) for 12 hours after long heat stress. LHSR84 (long heat stress recovery 84 hours) samples recovered under normal condition (22°C) for 84 hours after long heat stress.

first: Quancan

last: Hou

first: Kuan

last: Li

first: Wei

last: Xu

first: Qianwen

last: Sun


title: Transcriptional profiling of lung cancer cell expressing MET wt and its variant

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Lung cancer cells expressing polymorphic MET-N375S demonstrated enhanced oncogenic phenotype. The transcriptional profile of isogenic lung cancer cells overexpressing each MET isoform were compared to elucidate mechanisms leading to the observed phenotype.

overall_design: RNAseq analyses of H2170 cells overexpressing METwt and MET-N375S variant.

first: Li

middle: R

last: Kong


title: R-loop landscapes in Arabidopsis

summary: The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas during Arabidopsis development and in response to various environmental factors.

overall_design: ssDRIP-seq in Arabidopsis

first: Shuai


title: The role of a glucosinolate-derived nitrile in plant immune responses

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

summary: To investigate the processes affected when plants are exposed to 3-butenenitrile (3BN; allyl cyanide ACN), we performed a genome scale transcriptional profiling of Arabidopsis thaliana Col(0) and the nia1nia2 double mutant after 24 hour treatment with 3BN.

overall_design: 21-day-old Arabidopsis thaliana plants (Col-0 and nia1nia2) were exposed to 3BN vapour for 24 hours. Rosette tissue used for each biological replicate were harvested separately and immediately flash-frozen in liquid N2. Each sample consists of three biological replicas from 3BN-treated and mock control plants.

first: Hieng-Ming

last: Ting

first: Ralph

last: Kissen

first: Atle

last: Bones

first: Torfinn

last: Sparstad

first: Ane

last: Vie


title: Evaluation of transcriptomic regulations behind metabolic syndrome in obese and lean subjects

status: Public on Feb 18 2020

city: Bialystok

first: Magdalena

last: Paczkowska-Abdulsalam

address: M. Sklodowskiej-Curie 24A

country: Poland

institute: Medical University of Bialystok

summary: The study aimed to investigate molecular signatures in peripheral blood of individuals affected by metabolic syndrome (MetS) and different degrees of obesity. Metabolic health of 1204 individuals was assessed, and 32 subjects were recruited to four study groups: MetS lean, MetS obese, “healthy obese” and healthy lean. Whole-blood transcriptome next generation sequencing with functional data analysis was carried out.

overall_design: Whole-blood transcriptome next generation sequencing of 32 human samples, with the use of Illumina NextSeq500.

last: Niemira

first: Agnieszka

last: Bielska

first: Anna

last: Szałkowska

first: Edyta

last: Adamska-Patruno

first: Adam

last: Krętowski


title: Transcriptome analysis of Suaeda salsa under salt stress

status: Public on Feb 17 2020

city: Jinan

first: Luoyan

last: Zhang

address: wenhuadong 88

institute: shandong normal university

summary: To understand the molecular mechanisms of Suaeda salsa under salt stress, RNA-seq analysis was used to identify genes expressed in Suaeda salsa during salt stress response.

overall_design: SRA  submission (SRP189945) and BioProject accession  (PRJNA527358)

first: Xuejie

first: Yan

last: Yao

first: Shoujin

last: Fan


title: GeneChip Expression Array

city: Sendai

first: Tsuyoshi

last: Shirai

state: Miyagi

address: 1-1 Seiryomachi

institute: Tohoku University

summary:
Gene expression analysis to compare control cells and sorted cells
We transfected cDNA of human umbilical vein endothelial cells into rat myeloma cells, and sorted cells bound to patient IgG. Sorted cells were analyzed using the Affymetrix Human Genome U133 Plus 2.0 Array to investigate the cDNA inserted into the sorted cells. Array data was processed by Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software.  No techinical replicates were performed.

overall_design: Control cells and sorted cells, one sample each was analyzed.


title: Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling: HP scRNA-seq

city: San Francisco

first: Qin

last: Zhu

address: 600 Minnesota Street

institute: UCSF

summary: RUNX1 is frequently mutated in myeloid and lymphoid malignancies. It has been shown to negatively regulate Toll-like receptor 4 (TLR4) signaling through nuclear factor kappa-B (NF-κB) in lung epithelial cells. Here we show that RUNX1 regulates TLR1/2 and TLR4 signaling and inflammatory cytokine production by neutrophils. Hematopoietic-specific RUNX1 loss increased the production of pro-inflammatory mediators, including tumor necrosis factor α (TNF-α), by bone marrow (BM) neutrophils in response to TLR1/2 and TLR4 agonists. Hematopoietic RUNX1 loss also resulted in profound damage to the lung parenchyma following inhalation of the TLR4 ligand lipopolysaccharide (LPS). However, neutrophils with neutrophil-specific RUNX1 loss lacked the inflammatory phenotype caused by pan-hematopoietic RUNX1 loss, indicating that dysregulated TLR4 signaling is not due to loss of RUNX1 in neutrophils per se, and single cell RNA sequencing indicates the dysregulation originates in a neutrophil precursor.  Enhanced inflammatory cytokine production by neutrophils following pan-hematopoietic RUNX1 loss correlated with increased degradation of the inhibitor of NF-κB signaling (IκBα), and RUNX1-deficient neutrophils displayed broad transcriptional upregulation of many of the core components of the TLR4 signaling pathway.  Hence early, pan-hematopoietic RUNX1 loss de-represses an innate immune signaling transcriptional program that is maintained in terminally differentiated neutrophils, resulting in their hyper-inflammatory state. We hypothesize that inflammatory cytokine production by neutrophils may contribute to leukemia associated with inherited RUNX1 mutations.

overall_design: 12 samples were analzyed including 3 replicates each of Control and Runx1 KO neutrophils treated with vehicle or 100 ng/mL LPS. The Control sample includes LKS- cells of pooled BM from 1 Runx1f/f and 1 Runx1f/- mouse (i.e. with a monoallelic germline Runx1 mutation).

first: Dana

middle: C

last: Bellissimo

first: Chia-hui

last: Chen

first: Sumedha

last: Bagga

first: Chung-Tsai

last: Lee

first: Bing

last: He

first: Gerald

last: Wertheim

first: Martha

last: Jordan

first: Kai

last: Tan

first: G

last: Worthen

first: D

last: Gilliland

first: Nancy

middle: A

last: Speck


title: ChIP-seq analysis of H3K4me3, H3K27ac and CTCF in undifferentiated and differentiated G1E-ER4 cells

first: Jian

last: Xu

summary: Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

overall_design: ChIP-seq was performed to determine H3K4me3, H3K27ac and CTCF chromatin occupancy in G1E-ER4 cells (0 hour) treated without or with β-estradiol for 2, 6, 12, or 24 hours.

first: Xin

last: Liu

first: Yuannyu

first: Yuxuan


title: Transcriptomic profiling of CXCL9/10-overexpressing (OE) MDA-MB-231 breast cancer cells upon treatment with CXCR3i or DMSO vehicle

city: Heidelberg

first: Maren

last: Pein

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

summary: Cancer-associated fibroblasts promote the development of many primary malignancies, but their function in metastatic progression is poorly understood. Here, we demonstrate that colonization of the lungs by metastatic breast cancer cells induces an inflammatory phenotype in lung fibroblasts. CXCL9 and CXCL10 are induced in an NFκB-dependent manner in metastasis-associated fibroblasts in response IL-1α and IL-1β secreted by disseminated breast cancer cells. We find that the chemokine receptor CXCR3, that binds CXCL9/10, is expressed in a small subset of breast cancer cells that exhibits greater tumor-initiating ability when co-transplanted with fibroblasts. CXCR3-expressing cancer cells maintain JNK signaling that drives IL-1A/B expression, and thus rendering this subpopulation efficient in both inducing CXCL9/10 in lung fibroblasts and responding to the chemokines. Importantly, disruption of the CXCL9/10-CXCR3 axis significantly reduces metastatic colonization in xenograft and syngeneic mouse models suggesting an essential role of this paracrine crosstalk in metastatic progression and a potential therapeutic vulnerability for the treatment of metastatic breast cancer.

overall_design: For profiling of CXCR3 inhibitor (CXCR3i)-treated or vehicle-treated breast cancer cells, 500,000 MDA-MB-231 (MDA) cells overexpressing CXCL9 and CXCL10 were seeded into ultra-low attachment cell culture flasks in 20 ml Onco2 medium, consisting of HuMEC-medium (Invitrogen) supplemented 50 U/ml penicillin (Sigma-Aldrich), 50 μg/ml streptomycin (Sigma-Aldrich), 10 ng/ml basic fibroblast growth factor (bFGF, Invitrogen), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml human insulin (Sigma-Aldrich) and 2 % vol/vol B27 (Life Technologies) and incubated at 37 °C for 7 days. Cells were stimulated with 1 µM AMG-487 or 0.001% DMSO vehicle daily for 7 days. RNA from three biological replicates was analyzed using Affymetrix Gene Chip human U133 Plus 2.0 Arrays.

first: M

first: T

last: Oskarsson


title: Transcriptomic profiling of fibroblasts at different stages of lung colonization by MDA-MB-231 or MDA-MB-231-LM2 cells

overall_design: For profiling of fibroblasts at different metastatic stages, NSG mice (6-8 weeks of age) were injected with MDA-MB-231 (MDA) or highly metastatic MDA-MB-231-LM2 (MDA-LM2) breast cancer cells via the tail vein. At week 1 and 3 post cancer cell injection (representing micro- and macrometastatic stages, respectively), lungs from mice with similar metastatic burden were harvested. Lungs from age-matched healthy mice were used as control group. Fibroblasts were isolated from whole lungs by fluorescence-activated cell sorting (FACS) using a panel of negative selection markers and CD140a/b as positive fibroblast markers. For each time point and metastasis group, 3 biological replicates were analyzed, and each biological replicate encompasses 1-3 mice.


title: Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay pathways [RNA-seq]

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

summary: In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs. Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs were identified. We also found that PROMPTs become sources of 21-22 nt small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPT production. In addition, we found ~200 transcription start sites within 3’-UTR-encoding regions that produce long unspliced, exosome-sensitive antisense RNAs. The previously characterized non-coding (nc) RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of ncRNAs. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

overall_design: RNA-seq sequencing in triplicates of 12 days-old Arabidopsis thaliana whole seedlings (Col-0) for different genotypes: wild type, rrp4-2 mutant, lsm8-2 mutant and lsm8-2 rrp4-2 double mutant.

first: Jette

last: Bornholdt

first: Maxim

last: Ivanov

first: Peter

last: Brodersen

first: Albin

last: Sandelin

first: Maria

last: Vigh


title: Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

summary: Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachón cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab‐raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.

overall_design: Comparison of transcriptomes of livers from wild-caught and lab-reared river and cave-dwelling Astyanax mexicanus. 12 samples comprised of 3 replicates for each group were used.

first: Jaya

last: Krishnan

first: Jenna

middle: L

last: Persons

first: Robert

last: Peuß

first: Alexander

last: Kenzior

first: Shaolei

last: Xiong

first: Luke

last: Olsen

first: Ernesto

last: Maldonado

first: Nicolas

last: Rohner


title: Loss of mitochondrial proline catabolism depletes FAD, impairing sperm function, and male reproductive advantage

city: Los Angeles

first: Sean

last: Curran

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

summary: Exposure to environmental stress has a clinically established influence on male reproductive health, but the impact of normal cellular metabolism on sperm quality and function is less well-defined.  Here we show that homeostatic changes in mitochondrial dynamics driven by defective mitochondrial proline catabolism result in pleiotropic consequences on sperm quality and competitive fitness. Disruption of alh-6, which converts 1-pyrroline-5-carboxylate (P5C) to glutamate, results in P5C accumulation that drives oxidative stress, activation of the cytoprotective transcription factor SKN-1, and a reduction of energy-storing flavin adenine dinucleotide (FAD) levels. These molecular changes lead to premature male reproductive senescence by reducing sperm quality.  These sperm-specific defects are suppressed by abating P5C metabolism, by treatment with antioxidants to combat reactive oxygen species (ROS), or by feeding diets that restore FAD levels. Our results define a role for mitochondrial proline catabolism and FAD homeostasis on sperm function and specify strategies to pharmacologically reverse unintended outcomes from SKN-1/Nrf transcriptional activation.

overall_design: Our study aim to look at transcriptional signatures that define the physiological changes in alh-6 mutant animals as young and old animals. 12 RNA samples in total are turned in for high-throughput sequencing. N2 (WT) and lax105 (alh-6) worms are collected in triplicates at two time points: L4 and day 3 adults.

first: C

last: Yen

first: S


title: Circadian rhythms in the absence of the clock gene Bmal1

status: Public on Feb 14 2020

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

summary: Circadian clocks exist in almost all levels of living organisms and play elementary roles in the persistence of regular physiological and behavioural processes. Canonical transcription/translation feedback loop models portray BMAL1 (ARNTL) as one of the principal drivers of circadian periodicity in mammalian systems. In this integrated multi-omics study, we demonstrate, for the first time, 24 hr circadian oscillations in the expression levels of several transcripts and proteins in dexamethasone-synchronized Bmal1-/- mouse fibroblast cells and liver tissue slices. Intriguingly, daily oscillations were also observed in phosphoproteome profiles in the absence of this core clock gene. Our findings reveal that Bmal1 knockout radically alters the expression and phosphorylation patterns of mice hepatic proteome, which possibly attributes to considerably different sets of rhythmic candidates compared to wild-type. It is, therefore, reasonable to accentuate that circadian rhythms are not obliterated in mammalian systems due to deletion of the core clock genes.

overall_design: Wild-type and Bmal1-/- MSF cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% (v/v) HyClone III Serum (Analab; Cat # SH30109.03), 1/100  Glutamax-I (Invitrogen; Cat # 35050-038), 1/100 Penicillin-Streptomycin (SIGMA; Cat # P4333) and 1/500 MycoZap™ (Lonza; Cat # VZA-2022) in multiple six-well plates until complete confluency (n=3, per time-point, per genotype). The confluent MSF cells were treated with 100nM (final concentration) of dexamethasone (DEX) for 15 min to synchronize the cells [Balsalobre et al. Science 2000]29. MSF cells were then washed three times with PBS (37°C) and were incubated in HEPES-buffered Medium; 1X DMEM powder (SIGMA; Cat # D5030), 0.35mg/mL sodium bicarbonate, 5mg/mL glucose, 0.01M HEPES, 10% (v/v) HyClone III Serum, 1/100 Glutamax-I, and 1/500 MycoZap™, pH 7.3 (adjusted with HCl) and osmolality 320 mOsm (adjusted with NaCl) at 37°C under DD cycle. 48 hrs after DEX treatment, MSF cells were harvested at every three or two hours interval for three days for transcriptomics analyses.

first: Utham

middle: K


title: Transcriptome analysis of Dunaliella salina on carotenoid biosynthesis under red and blue light induction

status: Public on Mar 01 2020

city: Qingdao

first: Yuanxiang

last: Li

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of sciences

summary: Light quality is an important abiotic factor that affects growth and development of photosynthetic organism. In this study, D. salina was exposed to red (660 nm) and blue light (450 nm), and cell growth, pigments, and transcriptome were analyzed. The RNA of D. salina was sequenced and transcriptomic response of algal cells after transitioning from white light to red and blue light was investigated. Genes encoding for enzymes involved in photosynthesis were down-regulated, whereas genes involved in the metabolism of carotenoid were up-regulated. Genes encoding for photoprotective enzymes related to reactive oxygen species scavenging were up-regulated under both red and blue light. The present transcriptomic study would assist in the comprehensive understanding of carotenoid biosynthesis of D. salina.

overall_design: 9 biological samples, each condition in triplicates

first: Guangce

last: Wang


title: Organismal Benefits of Transcription Speed Control at Gene Boundaries

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

institute: University of Copenhagen

summary: We modulate RNAPII transcription speed by point mutations in the second largest subunit of Arabidopsis RNAPII, NRPB2. Nascent transcription profiling revealed that accelerated RNAPII complexes clear stalling sites at both gene ends, resulting in read-through transcription. Accelerated nascent RNAPII transcription increased the association with 5'SS intermediates and improved splicing efficiency, supporting tight connections between transcription speed and co-transcriptional pre-RNA processing.

overall_design: Plant native elongating transcripts sequencing (plaNET-Seq) was used to determine the genomic positions of transcriptionally engaged RNAPII in wild type and nrpb2-Y732F seedlings.

first: Xueyuan

last: Leng

first: Peter

last: Kindgren

first: Ryan

last: Ard

first: Indranil

last: Malik

first: Axel

last: Thieffry

last: Brodersen

first: Albin

first: Craig

last: Kaplan

first: Sebastian

last: Marquardt


title: Microarray profiling analysis of miRNAs expression in relapse melanoma post-radiation

status: Public on Feb 13 2020

city: Shenyang

first: Peng

last: Shen

state: Liaoning

address: 36 Sanhao street

institute: Shengjing Hospital of China Medical University

summary:
Recent development of integrative therapy against melanoma combines surgery, radiotherapy, targeted therapy, and immunotherapy; however, the clinical outcomes of advanced stage and recurrent melanoma are poor. As a skin cancer, melanoma is generally resistant to radiotherapy. Hence, there is an urgent need for evaluation of the mechanisms of radioresistance. The present study identified miR-335 as one of the differential expression of miRNAs in recurrent melanoma biopsies post-radiotherapy. The expression of miR-335 declined in melanoma tissues compared to the adjacent tissues. Moreover, miR-335 expression correlated with advanced stages of melanoma negatively. Consistent with the prediction of STARBASE and miRDB database, miR-335 targeted ROCK1 via binding with 3’-UTR of ROCK1 directly, resulting in attenuation of proliferation, migration and radioresistance of melanoma cells. The authors validated that overexpression of miR-335 enhanced X-ray-induced tumor regression by B16 mouse models. Briefly, the present findings gained insights into miR-335/ROCK1-mediated radiosensitivity and provided a promising therapeutic strategy for improving radiotherapy against melanoma.
miRNAs profiling by array

overall_design: Three recurrent melanoma patients who underwent complete resection without pre- or postoperative immunotherapy were recruited in the present study. Microarray based miRNAs expression profiles were obtained with Qiagen custom RT2 PCR Arrays.


title: An exon DNA element modulates heterochromatin spreading in the master regulator for sexual commitment in malaria parasites

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

summary: Heterochromatin is essential in all eukaryotic systems to maintain genome integrity, long-term gene repression and to help chromosome segregation during mitosis. However, heterochromatin regions must be restricted by boundary elements to avoid its spreading over actively transcribed loci. In Plasmodium falciparum, facultative heterochromatin is important to regulate parasite virulence, antigenic variation and transmission, but the underlying molecular mechanisms that regulate repressive regions remain unknown. To investigate this topic, we chose the ap2-g gene, that forms a strictly delimited heterochromatin island of 10 kb with no adjacent repressive chromatin. Using electrophoretic motility shift assay (EMSA) we identified an ap2-g exon element at the 3? end that shifts in the presence of nuclear extracts. Upon replacement of this region by a gfp gene, we observed a shift in the heterochromatin boundary, resulting in HP1 to spread over ~2 additional kb downstream. We used this DNA element to affinity purify candidate proteins followed by liquid-chromatography tandem mass-spectrometry (LC-MS/MS). The identified complexes are enriched in RNA-binding proteins, pointing to a potential role of RNA in the regulation of the ap2-g heterochromatin 3? boundary. Our results provide insight into the unexplored topic of heterochromatin boundary biology in P. falciparum and identifies a DNA element in the master regulator of sexual commitment that modulates heterochromatin spreading.

overall_design: Examination of HP1 distribution in wild type and 2 clones from a mutant line.

first: Anna

last: Barcons-Simon

first: Christine

last: Scheidig-Benatar

first: Aurelie

last: Claës

first: Valentin

last: Sabatet

first: Damarys

last: Loew

first: Artur

last: Scherf


title: Next generation sequencing of human monocyte derived dendritic cells stimulated with MGL-stimulating glycodendrimers in the absence or presence of LPS

city: Amsterdam

first: Anouk

last: Zaal

address: Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

summary: To investigate the effect of MGL ligation in monocyte-derived dendritic cell biology, we generated control dendrimers and two different glycodendrimers exposing the MGL ligands αGalNAc or GalNAcβ1-4Gal. αGalNAc and GalNAcβ1-4Gal glycodendrimers were validated in the corresponding manuscript. Monocyte-derirved dendritic cells were generated by culturing monocytes for 4 days with IL-4 and GM-CSF. To study the effect of MGL-ligation at the transcriptional level, next generation sequencing was performed on monocyte-derived dendritic cells from three independent donors, stimulated for 4 h with control, αGalNAc or GalNAcβ1-4Gal glycodendrimers in the absence or presence of LPS.

overall_design: 18 samples were included in next generation sequencing, including triplicates for control, αGalNAc and GalNAcβ1-4Gal glycodendrimers, all-in the absence or presence of LPS. The control dendrimers and control dendrimers in the presence of LPS serve as reference samples

first: Eveline

last: Li

first: Joyce

last: Lübbers

first: Sandra

last: van Vliet


title: Gene expression profiling of human CD11c+ CD19+ vs CD11C- CD19+ B-cells

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

summary: We aimed to characterize CD11c+ B cells from healthy humans by gene expression analysis. We report that CD11c+ B cells are a distinct subpopulation of B cells, even if their phenotype is heterogeneous, with overexpression of genes involved in B cell activation and antigen presentation.

overall_design: One-color technology, biological replicates : 5 paired samples (1-5), 2 conditions : CD11C- vs CD11C+ B cells

first: Marie-Laure

last: Golinski

first: Céline

first: Sébastien

last: Calbo


title: Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay pathways

first: Axel

last: Thieffry

overall_design: small RNA-seq sequencing of leaf and young flower bud tissues in wt, hen2-5 and rrp4-2 mutants

first: Maria

last: Vigh

first: Jette

last: Bornholdt

first: Maxim

last: Ivanov

first: Peter

last: Brodersen

first: Albin

last: Sandelin


title: Next Generation Sequencing of miRNA profile in HFD-induced diabetic ICR liver tissue treated by a Chinese formula

city: Beijing

first: Ying

last: Bai

state: Beijing

address: No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing

institute: Beijing University of Chinese Medicine

summary:
Objective: To investigate the impact of JTXK granule on the miRNA expression profiles in hepatic tissue of diabetic mice, and to explore the molecular targets and associated signaling pathways of JTXK granule in its anti-diabetic effect.
Methods: High fat diet was used to induce diabetic model, and mice were subsequently divided into JTXK-treated group and model group. After 8 weeks’ intervention we  screened the differentially expressed miRNAs between the two groups using microRNA sequencing analysis (3 mice in each group). Finally, miRNA target gene prediction, GO and KEGG analysis were applied to explore the function of DEMs.
Results: A total of 33 significantly differentiated miRNAs were detected in comparison between the two groups (|log2(fold change) |＞0.3, P<0.05). MiRNA-mRNA analysis showed that mmu-miR-30a-5p, mmu-miR-23b-5p, mmu-miR-199a-5p, mmu-miR-425-5p and mmu-miR-214-3p are closely related to inflammatory response, histological changes and insulin signal transduction in liver. In addition, KEGG analysis showed that the DEMs were closely related to Ras and insulin signaling pathway.
Conclusion: JTXK granule exerts anti-diabetic effect in hepatic tissue of diabetic mice by modulating miRNAs and mRNAs network.

overall_design: Liver miRNA profiles of 30-week old ICR mice were generated by NGS using Illumina HiSeq.

first: Fangfang

last: Mo


title: Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling: PMN bulk RNA-seq

first: Qin

last: Zhu

first: Dana

last: Bellissimo

first: Chia-hui

last: Chen

first: Sumedha

last: Bagga

first: Chung-Tsai

last: Lee

first: Bing

last: He

first: Gerald

last: Wertheim

first: Martha

last: Jordan

first: Kai

last: Tan

first: G

middle: S

last: Worthen

first: D

middle: G

last: Gilliland

first: Nancy

last: Speck