title: Expression profiles of satellite cells and alpha7Sca1 cells in mdxITGAM-DTR mice

status: Public on Sep 17 2019

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

summary: We took advantage of a dystrophic mouse model of transient macrophage-depletion, mdxITGAM-DTR mice, in order to analyze the role of macrophage in skeletal muscle regeneration. We generated the transcriptome of satellite cells (SCs) and alpha7Sca1 cells purified by cell sorting from mdxITGAM-DTR mice. The mice were treated, by intramuscular injection, with PBS, as vehicle, or with Diphtheria toxin (DT) in order to achieve the macrophage depletion form hind-limb muscle We described a shift in identity of muscle stem cells dependent on the crosstalk between macrophages and satellite cells. Indeed macrophage depletion determines an exacerbated dystrophic phenotype associated with adipogenic conversion of SCs and reduction of the SC pool.

overall_design: FACS isolation of primary satellite cells and alpha7sca1 cells from macrophage-depleted muscles of mdxITGAM-DTR mice at regenerative stage of dystrophy. Biological duplicates from control and DT-injected mdxITGAM-DTR mice were used

first: Marco

last: De Bardi

first: Giuseppe

last: Diaferia

first: Mattia

last: Pelizzola


title: Genome-wide Analysis and Functional Prediction of the Estrogen-Regulated Transcriptional Response in the Mouse Uterus

status: Public on Sep 16 2019

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

summary: The ovarian hormones estrogen and progesterone orchestrate the transcriptional programs required to direct functions of the uterus for initiation and maintenance of pregnancy. Estrogen, acting via estrogen receptor alpha (ERα), regulates gene expression by activating and repressing distinct genes involved in signaling pathways that regulate cellular and physiological responses including cell division, water influx, and immune cell recruitment. Historically, these transcriptional responses have been postulated to reflect a biphasic physiological response. In this study, we explored the transcriptional responses of the ovariectomized mouse uterus to 17β-estradiol (E2) by RNA-seq to obtain global expression profiles of protein coding transcripts (mRNAs) and long noncoding RNAs (lncRNAs) following 0.5, 1, 2 and 6 hours of treatment. The E2-regulated mRNA and lncRNA expression profiles in the mouse uterus indicate an association between lncRNAs and mRNAs that regulate E2-driven pathways and reproductive phenotypes in the mouse. The transient E2-regulated transcriptome is reflected in the time-dependent shifting of biological processes regulated in the uterus in response to E2. Moreover, high expression of some conserved lncRNAs that are E2-regulated in the mouse uterus are predictive of low overall survival in endometrial carcinoma patients (e.g., H19, KCNQ1OT1, MIR17HG, and FTX). Collectively, this study (1) describes a genomic approach for identifying E2-regulated lncRNAs that may serve critical function in the uterus and (2) provides new insights into our understanding of the regulation of hormone-regulated transcriptional responses with implications in pregnancy and endometrial pathologies.

overall_design: Using RNA-seq to evaluate transcriptional responses to estrogen in the ovariectomized adult uterus

first: Yasmin

middle: M

last: Vasquez

first: Tulip

last: Nandu

first: Andrew

last: Kelleher

first: Enrique

middle: I

last: Ramos

first: Shrikanth

last: Gadad

first: W

middle: L


title: Dissecting the dynamics of signaling events in the BMP,WNT and NODAL cascade during self-organized fate patterning in human gastruloids

city: Houston

first: Aryeh

last: Warmflash

address: 6100 Main St

institute: Rice University

summary: To determine the in vivo cellular identity of BMP-treated human embryonic stem cells (hESCs), we performed bulk RNA sequencing data of hESCs under pluripotency and  BMP-treated conditions. Our analyses show that BMP-treated hESCs resemble human trophoblast cells in vivo.

overall_design: mRNA profiles of four different samples, each with two biological replicates. Samples: 1) hESCs in mTeSR1 for 48h, 2) hESCs in mTeSR1+BMP4 for 48h, 3) hESCs in mTeSR1+BMP4+IWP2 for 48h, 4) hESCs in mTeSR1+BMP4+SB for 48h

first: Sapna

last: Chhabra

first: Lizhong

last: Liu

first: Ryan

last: Goh

first: Xiangyu

last: Kong


title: Transcriptome data of uterine and ovarian carcinosarcoma tissues derived from patients in the Cancer Institute Hospital of Japanese Foundation for Cancer Research

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation For Cancer Research

summary: We performed RNA-seq experiments for total RNA of uterin and ovarian carcinosarcoma tissues.

overall_design:
RNA-Seq analysis of 100 primary tumors of uterin and ovarian carcinosarcoma
The authors state the following:
Raw data is not provided.
Institutional Review Board (IRB) does not allow submitters to disclose raw data to the public.
Thus, this dataset is incomplete.

first: Seiichi

last: Mori


title: Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival fibroblasts

status: Public on Sep 12 2019

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

country: China

institute: Shandong university

summary: To better understand the global responses of GFs to F. nucleatum infection along the time sequence, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level

overall_design: 54 samples from 5 individuals (each individual involved 1 sample at time point 0h, 5 control samples at 2h 6h, 12h, 24h and 48h with no F. nucleatum treatment, and 5 experimental samples with F. nucleatum (F. nucleatum:cell=100:1) treatment at the same time point, one treated sample at time point 12h failed to extract sufficient RNA) were sequenced to analysis the whole gene expression level

first: Qiang

last: Feng


title: Sequencing short capped RNAs captures acute transcription initiation and identifies promoter and distal regulatory elements across eukaryotes from total RNA

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSS) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pre-miRNAs, antisense transcripts and promoter upstream transcripts in multicellular animals, plants and fungi spanning 1.6 million years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSS of stable transcripts, while H3K27ac marked nucleosomes downstream of all active TSS, suggesting an ancient role for post-translational histone modifications in transcription. Our findings demonstrate that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single nucleotide resolution in eukaryotes.

sample_organism:
Oryza sativa
Neurospora crassa
Homo sapiens
Mus musculus
Nematostella vectensis
Capsaspora owczarzaki

overall_design: Sequencing of short capped RNAs to identify transcription initiation sites

first: Sven

last: Heinz

first: Max

middle: W

last: Chang

first: Sascha

middle: H

last: Duttke


title: Tox4 Modulates Cell Fate Reprogramming

status: Public on Sep 19 2019

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Reprogramming to induced pluripotency induces the switch of somatic cell identity to induced pluripotent stem cells (iPSCs). However, the mediators and mechanisms of reprogramming remain largely unclear. To elucidate the mediators and mechanisms of reprogramming, we used a siRNA mediated knockdown approach for selected candidate genes during the conversion of somatic cells into iPSCs. We identified Tox4 as a novel factor that modulates cell fate, using reprogramming efficiency towards iPSCs as an assay. We found that Tox4 is needed early in reprogramming to efficiently generate early reprogramming intermediates, irrespective of reprogramming conditions used. Tox4 enables proper exogenous reprogramming factor expression and the closing and opening of putative somatic and pluripotency enhancers early during reprogramming, respectively. We show that TOX4 protein assembles into a high molecular form. Moreover, Tox4 is also required for the efficient conversion of fibroblasts towards the neuronal fate, suggesting a broader role of Tox4 in modulating cell fate. Our study reveals Tox4 as a novel transcriptional modulator of cell fate that mediates reprogramming from the somatic state to the pluripotent and neuronal fate.

overall_design: Bulk RNA sequencing of Tox4 knockdown and control condition early during reprogramming of mouse fibroblasts towards iPSCs

first: Lotte

last: Vanheer

first: Juan

last: Song

first: Natalie

last: De Geest

first: Adrian

last: Janiszewski

first: Irene

last: Talon

first: Caterina

last: Provenzano

first: Taeho

last: Oh

first: Joel

last: Chappell


title: TAF1 is critical for AE driven leukemogenesis [ChIP-seq]

status: Public on Sep 11 2019

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TAF1 is essential for AE driven leukemogenesis. Depletion of TAF1 impairs the recruitment of AE to its target genes, interfering with its control of gene expression. The bromodomains of TAF1 associate with K43 acetylated AE and this association plays a role in the proliferation of AE expressing AML cells.

overall_design: ChIP was performed on Kasumi-1 cells with antibodies targeting ETO, TAF1, H3K27ac, or H3K4me1.

first: Ye

last: Xu


title: Tox4 Modulates Cell Fate Reprogramming

overall_design: Bulk ATAC sequencing of Tox4 knockdown and control condition early during reprogramming of fibroblasts towards iPSCs


title: Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

summary: Liver tumors activate a regeneration-like genetic program in surrounding liver tissue akin to the regeneration program activated by toxic liver injury. Using genetically engineered mouse models we show that this program is regulated by the Hippo pathway. Our results identify a novel mechanism of non-autonomous tumor suppression where activation of a regeneration-like program in normal cells around liver tumors caused tumor cell death and tumor regression. Strikingly, deleting YAP specifically in peritumoral hepatocytes resulted in hepatocyte death and enhanced tumor growth, while hyperactivating YAP in peritumoral hepatocytes caused the elimination of tumor cells and tumor regression.

overall_design: RNA-seq from purified hepatocytes (wild type and peritumoral) and from livers exposed to toxic injury (24 and 48h after TAA).

first: G

last: Halder

first: I

last: Moya

first: J


title: Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ATAC-seq]

status: Public on Sep 10 2019

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

institute: Northwestern University

summary: Chromatin immunoprecipitation sequencing of H3K4me2, H3K27ac as well as, ATACseq and RNA-seq reveals regulatory landscapes across different muscle groups, as well as in response to chronic exercise or muscle PGC1a overexpression. This work defines the unique enhancer repetoire of skeletal muscle in vivo and reveals that highly divergent exercise-induced or PGC1a-driven epigenomic programs direct partially convergent transcriptional networks.

overall_design: Genome-wide maps of chromatin state in different muscles from sedentary mice

first: Krithika

last: Ramachandran


title: Intestinal tumor expression data from Apcmin/+ mice gavaged by feces from  healthy controls or colorectal cancer patients

city: Tianjin

first: Lu

last: Li

address: 154 Anshan Road in Heping District

department: Department of Gastroenterology and Hepatology

institute: General Hospital, Tianjin Medical University

summary: Colorectal cancer (CRC) is closely related to gut dysbiosis. We investigated the effects of imbalanced gut microbiota on the progression of intestinal adenoma in Apcmin/+ mice model using fecal microbiota transplantation (FMT). Administration of feces from CRC patients increased tumor proliferation and decreased apoptosis in tumor cells. Abnormal expression of genes related to Wnt-protein binding and lipid metabolic process was observed.

overall_design: There were 7 mice in the RNA-seq, which include four in the FMT-AH group (gavage of fecal samples from healthy controls) and three in the FMT-AC group (gavage of fecal samples from patients with CRC).

first: Bangmao

last: Wang

first: Kui

last: Jiang

first: Hailong

last: Cao

first: Xiaofei


title: Epigenome analysis of uterin and ovarian carcinosarcoma tissues

first: Osamu

last: Gotoh

summary: We performed genome-wide DNA methylation profiling of uterin and ovarian carcinosarcoma tissues derived from patients in the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

overall_design: DNA methylation status was analyzed using genomic DNA from each tumor on the Illumina Infinium HumanMethylation 450 BeadChip Arrays (n = 98) or MethylationEPIC BeadChip Arrays (n = 10), according to the manufacturer’s instructions.

first: Seiichi

last: Mori


title: Crosstalk between eIF2α and eEF2 phosphorylation pathways optimizes translational arrest in response to oxidative stress

status: Public on Sep 14 2019

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: The cellular stress response triggers a cascade of events leading to transcriptional reprogramming and a transient inhibition of global protein synthesis, which is thought to be mediated by phosphorylation of eukaryotic initiation factor-2α (eIF2α). Using mouse embryonic fibroblasts (MEFs) and the fission yeast S. pombe, we report that rapid translational arrest and cell survival in response to hydrogen peroxide-induced oxidative stress do not rely on eIF2a kinases and eIF2a phosphorylation. Rather H2O2 induces a block in elongation through phosphorylation of eukaryotic elongation factor 2 (eEF2). Kinetic and dose-response analyses uncovered crosstalk between the eIF2a and eEF2 phosphorylation pathways, indicating that, in MEFs, eEF2 phosphorylation initiates the acute shutdown in translation, which is maintained by eIF2a phosphorylation. Our results challenge the common conception that eIF2a phosphorylation is the primary trigger of translational arrest in response to oxidative stress and point to integrated control that may facilitate the survival of cancer cells.

overall_design: Examination of whole transcriptomes of 2 different cell lines under normal conditions and oxidative stress at 2 time points in duplicates

first: Marisa

last: Sanchez

first: Dieter

middle: A

last: Wolf


title: Investigsting the role of NF-ĸB p50 S80 phosphorylation in regulating TNFα-induced transcription in HEK293T cells

city: Glasgow

first: Emma

last: Smith

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary: Phosphorylation of the NF-ĸB p50 subunit is known to regulate target gene expression. Here, we investigate the role of the novel p50 S80 phosphorylation in regulating TNFα-induced transcription by utilising Wild type (WT) and NFKB1S80A HEK293T cells

overall_design: 12 samples in total (3 replicates of 4 conditions)

first: Domenico

last: Somma

first: David

last: Kerrigan

first: Zoe

last: McIntyre

first: John

middle: J

last: Cole

first: Patrick

last: Kiely

first: Karen

last: Keeshan

first: Ruaidhrí

last: Carmody


title: Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ChIP-seq, ATAC-seq]

first: Grant

last: Barish

overall_design: Genome-wide maps of chromatin state in skeletal muscle in exercise, sedentary and transgenic PGC1a conditions

first: Krithika

last: Ramachandran


title: TAF1 is critical for AE driven leukemogenesis [ATAC-seq]

first: Stephen

last: Nimer

summary: TAF1 is essential for AE driven leukemogenesis. Depletion of TAF1 impairs the recruitment of AE to its target genes, interfereing with its control of gene expression.   The bromodomains of TAF1 associate with K43 acetylated AE and this association plays a role in the proliferationof AE expressing AML cells.

overall_design: ATAC-seq was performed on Kasumi-1 cells with scramble control or TAF1 shRNA..

first: Ye

last: Xu


title: Single cell RNA-seq analysis for mouse melanocyte stem cells and melanoma tumors

status: Public on Sep 13 2019

city: New York

first: Qi

last: Sun

state: NY

address: 550 1st Avenue, Smilow 410

department: Dermatology

institute: New York University

summary: We compared the gene signatures of mouse melanocyte stem cells and the melanoma tumor derived from them upon Braf V600E mutation and loss of Pten, as well as the heterogeneity of the melanoma cells by single cell RNAseq

overall_design: Melanocyte stem cells isolated from 3 Tyr-CreER; R26R-Tomato mice were analyzed. 3 independent melanoma tumors derived from transplantation of melanocyte stem cells of Tyr-CreER; Braf V600E fl/+; Pten fl/fl; R26R-Tomato mice were analyzed

first: Mayumi

last: Ito


title: TAF1 is critical for AE driven leukemogenesis [RNA-seq]

overall_design: RNAseq of total RNA collected from Kasumi-1 acute myeloid leukemia cells after targeting TAF1 with lentiviral knockdown or with inhibitor.


title: Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate differentiation in Cryptococcus neoformans

city: Athens

first: Zachary

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

summary: Cellular differentiation is instructed by development regulators in coordination with chromatin remodeling complexes. Much information about their coordination comes from studies in the model ascomycetous yeasts. It is not clear, however, of the kind of information that can be extrapolated to species of other phyla in Kingdom Fungi. In the basidiomycete Cryptococcus neoformans, the transcription factor Znf2 controls yeast-to-hypha differentiation. Through a forward genetic screen, we identified the basidiomycete-specific factor Brf1 and discovered that it works together with Snf5 in the SWI/SNF chromatin remodeling complex in concert with existent Znf2 to execute cellular differentiation. We demonstrated that SWI/SNF assists Znf2 opening up the promoter regions of hyphal specific genes, including the ZNF2 gene itself. In addition, this complex supports Znf2 to fully associate with its target regions. Importantly, our findings revealed key differences in composition and biological function of the SWI/SNF complex in the two major phyla of Kingdom Fungi.

overall_design: This study involves ATAC and ChIP-Seq.

first: Xiaorong

last: Lin


title: Transcriptomic analysis of Tregs from RelB-dDC mice

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

country: Germany

institute: Helmholtz Center Munich

summary: We report here the effect of RelB ablation in CD11c+ cells on the Treg compartment accross various organs.This mice have been backcrossed to a Foxp3 reporter mouse line to enable cell sorting of Tregs with a high purity. Interestingly, RelB ablation in DCs leads to a substantial accumulation of Tregs and these Tregs show a 'tissue Treg' signature including high expression levels of KLRG1, I1LRL1 and Gata3 when compared to Tregs of littermate control mice.

overall_design: Bulk RNA_Seq analysisof sort-purified Tregs


title: Effects of human adipose tissue-derived and umbilical cord tissue-derived mesenchymal stem cells in a dextran sulfate sodium-induced mouse model

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

institute: Niigata University

summary: Background: Mesenchymal stem cells (MSCs) can be acquired from medical waste. MSCs are easily expanded and have multiple functions, including anti-inflammatory effects. We evaluated the effects of human adipose tissue-derived MSCs (AD-MSCs) and umbilical cord tissue-derived MSCs (UC-MSC) in a dextran sulfate sodium (DSS)-induced mouse model.    Methods: Human AD-MSCs and UC-MSCs (1 × 106 cells) were injected intravenously into a 7-day DSS-induced colitis model. The therapeutic effects of cell origin, injection timing, and supernatants obtained from MSC cultures were evaluated. We also analyzed mRNA expression in MSCs, tissues, and intestinal flora.    Results: AD-MSCs and UC-MSCs had strong anti-inflammatory effects when injected on day 3 in a mouse model. On day 11, mRNA levels of inflammatory factors in colon tissues were significantly decreased after injection of MSCs on day 3. Supernatants from MSCs culture decreased mRNA levels of tumor necrosis factor (Tnf)-α, but had reduced therapeutic effects compared with MSC cell injection. RNA sequencing using colon tissues obtained the day after cell injection revealed changes in the TNF-α/nuclear factor-κB and T-cell receptor signaling pathways. Additional analyses showed that several factors, including chromosome 10 open reading frame 54, stanniocalcin-1, and TNF receptor superfamily member 11b were increased in MSCs after adding serum from DSS colitis mice. Furthermore, both AD-MSCs and UC-MSCs maintained the balance of intestinal flora.    Conclusion: AD-MSCs and UC-MSCs showed therapeutic effects against inflammation after early cell injection while maintaining the intestinal flora. Although supernatants showed therapeutic effects, cell injection was more effective against inflammation.

overall_design: Examination of RNA expression of AD-MSC and UC-MSC with or without serum

first: Shunzo

last: Ikarashi

last: Tuchiya

first: Shuji

last: Terai


title: Nucleosome profiles in strains with different numbers of nucleosomes at HML and HMR

status: Public on Sep 06 2019

city: Berkeley

first: Daniel

middle: S

last: Saxton

address: 100 University Ave

department: MCB

institute: University of California Berkeley

summary: We report nucleosome positions by using native Mnase-seq. The results strongly suggest that nucleosome positions don't change at the heterochromatic locus HMR upon removal of adjacent nucleosomes via deletion of nucleosomal DNA. Positions of nucleosomes at HML are also quantified.

overall_design: Genome-wide analysis of nucleosome positions in strains of interest, with a particular focus on nucleosome positioning at HML and HMR.

first: Jasper

last: Rine


title: TAF1 is critical for AE driven leukemogenesis

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

overall_design: Refer to individual Series


title: Comparative transcriptomic analyses of Winter OilSeed Rape (WOSR) accessions during the germination process

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

country: Spain

institute: CBGP-INIA-UPM

summary: Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulators are conserved in B. napus suggesting a shared regulatory network with other plants species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable, not only to evaluate germination performance of B. napus accessions, but also to identify key targets for crop improvement in this important process.

overall_design: RNA sequencing (RNA-seq) on three selected accessions (C129, C032 and C033) at different stages of seed germination (0, 2, 12, 36 and 72 hours after imbibition).

first: M

last: Boter

first: J

last: Calleja-Cabrera

first: G

last: Carrera-Castaño

last: Wagner

first: S

middle: V

last: Hatzig

first: R

last: Snowdon

first: Laurie

last: Legoahec

first: Grégoire

last: Bianchetti

first: Alain

last: Bouchereau

first: Nathalie

last: Nesi

last: Pernas

first: L

last: Oñate-Sánchez


title: Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ChIP-Seq]

first: Grant

last: Barish

first: Krithika

last: Ramachandran


title: Transcriptome analysis of the hierarchical response of HDAC proteins that respond in an antagonistic manner to salinity stress

city: Yokohama

first: Minoru

last: Ueda

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: To understand the effect of HDA19 deficiency in hda5/14/15/18 (quad) under salinity stress conditions, hda19, quad, hda5/14/15/18/19 (quint) mutants and control (Col-0) plants were analyzed under normal and salinity stress conditions using Arabidopsis custom microarrays (GEO array platform: GPL22706).

overall_design: Microarray analysis was conducted using hda19, quad, quint and Col-0 plants subjected to non-stress and 125 mM NaCl salt-stress condition for 2 h.

first: Akihiro

last: Matsui

first: Shunsuke

last: Watanabe

first: Makoto

last: Kobayashi

first: Kazuki

last: Saito

first: Maho

last: Tanaka

first: Junko

last: Ishida

first: Miyako

last: Kusano

first: Mitsunori

last: Seo

first: Motoaki

last: Seki


title: RNAseq & Smad and Foxh1 ChIpseq in pluripotent mESC and EBs

status: Public on Sep 05 2019

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Smad2, Smad3, Smad4 and Foxh1 ChIPseq performed in pluripotent mESC and embryonic bodies (EBs). RNAseq were performed in WT mESCs and Ebs of WT, Smad2KO, Smad3KO and Smad2/3DKO.

overall_design: In this study, 10 RNA-Seq samples and 14 ChIP-Seq samples are included.

first: Q

last: Wang

first: Y

last: Zou

first: Joan

last: Massague


title: Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [RNA-seq]


title: Systematic identification of cell-cell communication networks in the developing brain

status: Public on Sep 09 2019

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

summary: In the current study, we describe Brain-FACS, a method to simultaneously isolate neural, microglial, mural and endothelial cells from the developing brain to more than 94% purity in around 4 hours. Utilising Brain-FACS, we isolate, transcriptionally analyse and build a cell-cell communication map of the mouse brain at embryonic day E14.5. Transcriptomic analyses on FACS-isolated cell populations provide a ~20-fold increase in sensitivity over single single-cell RNA sequencing methods and allow us to bioinformatically identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural and microglial cells including previously unidentified relationships. Together, this study provides a comprehensive map that reveals the richness of communication within the developing brain.

overall_design: Mouse E14.5 WT and Mof KO brains were dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.

first: Bilal

middle: N

last: Sheikh

first: Nadim

last: Aizarani

last: Sagar

first: Sukanya

last: Guhathakurta

first: Dominic

last: Grün

first: Lutz

last: Hein

first: Asifa

last: Akhtar


title: Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming

first: Grant

last: Barish


title: The time course of microRNA transcriptomes during C. elegans ageing

status: Public on Sep 03 2019

city: Shanghai

first: Yidong

last: Shen

state: Shanghai

address: 320 Yueyang Rd.

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: To obtain a global view of the microRNAs expression during ageing, the wild type worms of C. elegans at day 1, day 7 (around the end of reproductive period), day 14, and day 21 (around the mean lifespan)  were subjected to small RNA-Seq.

overall_design: MicroRNA profiles of wild type worms at day 1, 7, 14, and 21 of adulthood were generated by deep sequencing,  in triplicate.

first: Adam

last: Antebi

first: Christoph

last: Dieterich

first: Jorge

last: Boucas


title: GcrA binding pattern to Brucella abortus genome

city: Namur

first: Xavier

last: De Bolle

address: 61 rue de Bruxelles

institute: University of Namur

summary: ChIP-seq analysis of GcrA atypical transcription factor in Brucella abortus

overall_design: Rabbit antiserum was generated against recombinant GcrA from B. Abortus, and used to immunoprecipitate DNA fragments obtained from a B. Abortus culture, fixed with formaldehyde

first: Antonella

last: Fioravanti

first: Nayla

last: Francis

first: Emanuele

last: Biondi

first: Katy

last: Poncin


title: Identification of miRNAs and their targets regulated by LIF in trophoblastic cell lines

status: Public on Sep 01 2019

city: Jena

first: Diana

middle: Maria

last: Morales Prieto

address: Am Klinikum 1

department: Obstetrics

institute: Jena University Hospital

summary:
Aim of this study was to identify miRNAs which are regulated by LIF in different trophoblastic cell lines
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TaqMan Arrays. Quantitative real-time PCR was performed for 768 miRNAs. For each of two cards per sample (A and B), 9 ul of pre-amplified diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.

overall_design: miRNA profile of four trophoblastic cell lines was analyzed before and after LIF stimulation

last: Morales-Prieto

first: Ruby

last: Gutierrez-Samudio

first: Emanuel

last: Barth

first: Stephanie

last: Ospina-Prieto

first: Wittaya

last: Chaiwangyen

first: Manja

last: Marz

first: Udo

middle: R

last: Markert


title: Effect of Omomyc treatment on MYC mediated transcription

city: Boston

first: Mark

last: Demma

address: 33 Avenue Louis Pasteur

institute: Merck Research Laboratories

summary: Purpose: Identify MYC sensitive enes that are affected by treatment with Omomyc

overall_design: Treatemnt with two doses of Omomyc at 6 and 24 hours in two different cell lines

first: Sarah

last: Javid


title: Human bladder cancer cell line mRNA-seq

city: Wuhan

first: Feng

last: Liu

state: Hubei

address: Air Road 13

institute: Tongji Medical College, Huazhong University of Science and Technology

summary: Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. Our previous studies found that hundreds of circRNAs were aberrantly expressed in bladder cancer (BC) by high-throughput sequencing and we have confirmed that the downregulated circRNAs circHIPK3, BCRC3 and circNR3C1 played inhibitory roles in BC progression. However, the role of these upregulated circRNAs remain to be clarified.  In this study, we analyzed circRNA high-throughout sequencing from human tissues and focused on the upregulated circRNAs and identified a novel circular RNA, hsa_circ_0001361 (also named bladder cancer upregulated circRNA-1, BCUC-1), as a new candidate circRNA derived from FNDC3B gene. The expression levels of circRNA and miRNAs in BC tissues and cells were detected by qRT-PCR. Transwell migration, Matrigel invasion, CCK-8, EdU, cell cycle and in vivo tumor metastasis assays were preformed to evaluate the effects of circ0001361 on BC cells. Transcriptome analysis was performed to find the potential genes that could be regulated by BCUC-1. Luciferase reporter, RNA pull-down and fluorescence in situ hybridization (FISH) assays were applied to verify the interaction between BCUC-1 and miR-491-5p.

overall_design: In order to screen downstream genes regulated by BCUC-1 (hsa_circ_0001361), transcriptome analysis was performed in T24T and UMUC3 cells transfected with BCUC-1(has_circ_0001361) and compaired vector.

first: Fei

last: Xie


title: Phytoplasma SAP11 homologs differentially modulate development and defence in Arabidopsis and maize via destabilization of specific TCPs

status: Public on Sep 08 2019

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

summary: We report  SAP11AYWB destabilizes CIN and CYC/TB1 TCPs, whereas SAP11MBSP destabilizes primarily TB1 TCPs.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design: RNASeq exeperiment was desined to investigated  if  SAP11AYWB  and  SAP11MBSP  modulate  maize  processes  in  response  to  the  AY-WB  and  MBSP  insect  vectors  M.  quadrilineatus  and  D.maidis,  respectively.

first: Pascal

last: Pecher

first: Gabriele

last: Moro

first: Cristina

last: Canale

first: Sylvain

last: Capdevielle

first: Allyson

last: MacLean

first: Akiko

last: Sugio

first: Joao

last: Spotti-Lopes

first: Saskia

last: Hogenhout


title: Robust, long-term culture of endoderm derived hepatic organoids (eHEPOs) for disease modeling

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Many liver pathologies ranging from cancer to genetic metabolic diseases are amenable to cellular replacement therapies. One of the main difficulties associated with cellular therapy approaches is the generation and expansion of mature autologous hepatocytes. The ability to derive patient-specific induced pluripotent stem cells (iPSCs) have solved the problem of generating autologous cells but differentiation and expansion of mature hepatocytes remain a challenge. Here, we report the generation of human iPSC-derived hepatic organoid (eHEPO) culture system for producing functional hepatocytes using EpCAM-positive endodermal cells as an intermediate. eHEPOs can be produced within two weeks and expanded long-term without any lose of differentiation capacity to mature hepatocyte (>12 months with passage number 25) and are resilient to freeze-thaw cycles. The hepatic identity of eHEPOs was confirmed by morphological analyses, expression of mature hepatocyte markers and in vitro functional assays. Extensive global transcriptome analyses of all intermediate stages demonstrated the stepwise differentiation iPSCs to mature hepatocytes in endoderm-derived organoids. Finally, starting form patient-specific iPSCs, we created an organoid-based model of Citrullinemia type 1, an inherited urea cycle disorder caused by mutations in the argininosuccinate synthetase (ASS1) enzyme. The disease-related ammonia accumulation phenotype in eHEPOs could be reversed by the overexpression of the wild type ASS1 gene which also indicated that this model is amenable to genetic manipulation.  Our results demonstrate that iPSC-derived EpCAM-positive endodermal cells are excellent cell sources to generate patient-specific hepatic organoids in a fast and efficient manner.

overall_design:
We analysed the cell cultures at different stages of eHEPO differentiation from control and ASS1 mutant patients using RNA-sequencing. RNA from 26 samples including iPS, endoderm progenitors, organoids under expansion (EM) and differentiation (DM) conditions were isolated. Libraries were prepared using the Celseq2 method, which is originally designed for single cell sequencing, however these samples are bulk RNA. We aimed for low coverage sequencing (~2 million mapped to the coding regions) per sample to investigate the gross changes in the transcriptome during lineage specification and differentiation. Libraries (rpi small primer) were sequenced on an Illumina HiSeq 4000 using 151-bp paired-end sequencing at the Genomescan. All the samples were sequenced in a single run to an average depth of ~10 million reads per sample. Reads were mapped to the latest human coding transcriptome, normalized and analyzed using the standard DESEQ2 package

DK1 and DK3 are different citrullimenia patients with ASS1 mutation

first: Soheil

last: Akbari

first: Gulben

last: Gurhan Sevinc

first: Nevin

last: Ersoy

last: Basak

first: Erkin

last: Özel

first: Berke

last: Sengun

first: Eray

last: Enüstün

first: Burcu

last: Özçimen

first: Kübra

last: Kaplan

first: Alper

last: Bağrıyanık

first: Nur

last: Arslan

first: Tamer

last: Onder

first: Esra

last: Erdal


title: RNA-seq analysis of wt Metschnikowia pulcherrima cells and a spontaneous mutant (W8) in the snf2 gene that exhibited differential expression of the recently described pulcherrimin genes

city: Waedenswil

first: Christian

last: Ahrens

state: Zurich

address: Mueller-Thurgau Strasse 29

country: Switzerland

institute: Agroscope

summary: We analyzed differential gene expression in wt and a snf2 mutant (W8) cells; the pucherimin biosynthesis genes were among the top diff. regulated genes (reduced expression in the mutant). ABSTRACT: Metschnikowia pulcherrima synthesizes the pigment pulcherrimin, from cyclodileucine (cyclo(Leu-Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi. This yeast therefore has great potential for biocontrol applications against fungal diseases; particularly in the phyllosphere where this species is frequently found. To elucidate the molecular basis of the antifungal activity of M. pulcherrima, we compared a wildtype strain with a spontaneously occurring, pigmentless, weakly antagonistic mutant derivative. Whole genome sequencing of the wildtype and mutant strains identified a point mutation that creates a premature stop codon in the transcriptional regulator SNF2 in the mutant strain. Complementation of the mutant strain with the wildtype SNF2 gene restored pigmentation and recovered the strong antifungal activity. Mass spectrometry (UPLC HR HESI-MS) proved the presence of the pulcherrimin precursors cyclo(Leu-Leu) and pulcherriminic acid and identified new precursor and degradation products of pulcherriminic acid and/or pulcherrimin. All of these compounds were identified in the wildtype and complemented strain, but were undetectable in the pigmentless snf2 mutant strain. These results thus identify Snf2 as a regulator of antifungal activity and pulcherriminic acid biosynthesis in M. pulcherrima and provide a starting point for deciphering the molecular functions underlying the antagonistic activity of this yeast.

overall_design: Comparison of M. pulcherrima wt (2 replicates) and mutant W8 (3 replicates) which has a preliminary stop codon in the snf2 gene, leading to a truncated protein (420 instead of 1578 aa)

first: Florian

last: Freimoser

first: Kenneth

last: Wolfe


title: Systematic assessment of blood-borne microRNAs highlights molecular profiles of endurance sport and carbohydrate uptake

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

summary:
Multiple studies endorsed the positive effect of regular exercising on mental and physical health. However, the molecular mechanisms underlying training-induced fitness in combination with personal life-style remain largely unexplored. Circulating biomarkers such as microRNAs (miRNAs) offer themselves for studying systemic and cellular changes since they can be collected from the bloodstream in a low-invasive manner. In Homo sapiens miRNAs are known to regulate a substantial number of protein-coding genes in a post-transcriptional manner and hence are of great interest to understand differential gene expression profiles, offering a cost-effective mechanism to study molecular training adaption, and connecting the dots from genomics to observed phenotypes.
Here, we investigated molecular expression patterns of 2,549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of 8 weeks of endurance training, with several sessions per week, followed by 8 weeks of washout and another 8 weeks of running, using microarrays. Participants were randomly assigned to one of the two study groups, one of which administered carbohydrates before each session in the first training period, switching the treatment group for the second training period. During running sessions clinical parameters as heartbeat frequency and maximum load were recorded. This information was extended with four measurements of maximum oxygen uptake (VO2 max) for each participant.
We observed that multiple circulating miRNAs show expression changes after endurance training, leveraging the capability to separate the blood samples by training status. To this end, we demonstrate that most of the variance in miRNA expression can be explained by both common and known biological and technical factors. Our findings highlight six distinct clusters of miRNAs, each exhibiting an oscillating expression profile across the four study timepoints, that can effectively be utilized to predict phenotypic VO2 max levels. In addition, we identified miR-532-5p as a candidate marker to determine personal alterations in training performance on a case-by-case analysis taking the influence of a carbohydrate-rich nutrition into account. In literature, miR-532-5p is known as a common down-regulated miRNA in diabetes and obesity, possibly providing a molecular link between cellular homeostasis, personal fitness levels, and health in aging.
We conclude that circulating miRNAs expression can be altered due to regular endurance training, independent of the concentration of blood sugar levels. Further validation studies are required to confirm the role of exercise-affected miRNAs and the extraordinary function of miR-532-5p in modulating the metabolic response to a high availability of glucose.

overall_design: We profiled the miRNA repertoire of 90 blood samples, distributed over four timepoints (E1, A1, E2, A2), from two groups of participants that performed two rounds of endurance-training with 4x 45 min running each week. In the first interval (E1, A1) participants from the first group orally administered 50 g glucose monohydrate dissolved in 200 ml water, 15 minutes before each training session. For the second training period, participants assigned to the second group administered carbohydrates. Timepoints E1 and E2 correspond to samples taken before each training period (8 weeks), while A1 and A2 correspond to samples measured after the preceding training periods. All adjacent timepoints are 8 weeks apart from each other.

first: Nicole

last: Ludwig


title: Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain after the body plan is established in zebrafish

status: Public on Sep 07 2019

city: Nijmegen

first: Leonie

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

institute: Radboud University

summary: The goal of the ChIP-sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hours post-fertilization (hpf). The goal of RNA-sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0, 3.3, and 24 hpf and link these differences with the changes in epigenetic mark occupancy.

overall_design: RNAseq of 0 hph, 3.3hpf, and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 (MZezh2) mutant whole embyos (5 to 7 replicates); ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype (2 replicates) and MZezh2 mutant (2 sample) whole embryos (both second replicates, Drosophila spike in chromatin was used to assess ChIP and library quality);  ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype (2 replicates) and MZezh2 mutant (2 sample) whole embryos (both second replicates, Drosophila spike in chromatin was used to assess ChIP and library quality);  ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype (1 replicates) and MZezh2 mutant (2 sample) whole embryos;  ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype (2 replicates) and MZezh2 mutant (2 sample) whole embryos;  ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype (3 replicates) and MZezh2 mutant (3 sample) whole embryos;

first: Julien

last: Rougeot

first: Naomi

middle: D

last: Chrispijn

first: Marco

last: Aben

first: Karolina

last: Andralojc

first: Patrick

last: Murphy

first: Dei

last: Elurbe

first: Pascal

last: Jansen

first: Michiel

last: Vermeulen

first: Bradley

last: Cairns


title: Control ChIP-seq from HEK293 (ENCSR000EVA)

status: Public on Aug 30 2019

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Control ChIP-seq on human HEK293

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: MOWChIP-seq for low-input and high-throughput profiling of genome-wide histone modifications

status: Public on Aug 31 2019

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Epigenetic mechanisms such as histone modifications and DNA methylation form a critical layer of control that regulates gene activities. Histone modifications play critical roles in adaptive tuning of chromatin structures. Profiling various histone modifications at the genome scale using primary tissues from animal and human samples is an important step for functional studies of epigenomes and epigenomics-based precision medicine. Because the profile of a histone mark is highly specific to a particular cell type, isolation of a cell type of interest from primary tissues is often necessary to generate a homogeneous cell population and such operation tends to yield a low number of cells. In addition, high-throughput processing is desired in such effort due to the number of histone marks of interests and the potential volume of samples in a hospital setting. In this protocol, we describe detailed information on device fabrication, setup, and operation of microfluidic oscillatory washing-based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) for profiling histone modifications using as few as 30-100 cells per assay with a throughput as high as 8 assays in a run. The critical step of MOWChIP-seq operation involves flowing of chromatin fragments through a packed bed of antibody-coated beads followed by a vigorous microfluidic oscillatory washing. The ChIP process is semi-automated for reduced labor and improved reproducibility. We have used the protocol to study a number of histone modifications in various types of mouse and human tissue types ranging from isolated nuclei of brain cells to cell subtypes isolated from human breast tissues.

overall_design: We examined genome-wide H3K9me3, H3K36me3, H3K79me2 profiles of nuclei isolated from mouse prefrontal cortex, 1000 nuclei per assay. The ChIP experiment was performed using half of 8-unit MOWChIP device, which performed 2 replicat experments for H3K9me3, H3K36me3 and H3K79me2 in every run under the same operating conditions.

first: Bohan

last: Zhu


title: Xenograft-specific transcriptional profiling for the characterisation of human pluripotent stem cell-derived neural transplants in the rodent brain

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

summary: Here we aim to demonstrate a novel approach enabling standardised and rapid characterisation of transplanted xenografts in the rodent brain. The approach employs bulk tissue dissection, inclusive of the grafted human cells and surrounding host (rodent) tissue, and utilises differences in the RNA sequences between the species to discriminate the xenograft from host gene expression. To demonstrate and validate this technique, we assessed grafts of undifferentiated human stem cells, immature neural progenitors and mature neurons following transplantation into the rodent brain. Mixed species RNAseq was conducted on the bulk dissected tissue, and a high stringency analysis pipeline developed to discriminate the human reads. Xenograft-specific RNAseq allowed accurate profiling the complete transcriptome of the transplant with high sensitivity and accuracy. The profile allowed the identification of novel gene expression and an unbiased characterisation of graft composition, providing a valuable tool for the analysis of xenografts. This characterisation will be especially crucial for the characterisation of grafts in pre-clinical and batch testing of therapeutic cell preparations prior to translation to the clinic.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression profile of human xenografts transplanted into host mouse brains. Mixes species RNAseq with 3 biological replicates of 3 xenograft types (undifferentiated, immature and mature midbrain dopamine neurons differentated from embryonic stem cells).

first: Clare

last: Parish


title: Control ChIP-seq from CH12.LX (ENCSR000ERS)

summary:
Control ChIP-seq on mouse CH12 produced by the Snyder lab

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS of human retinal pigment epithelum

status: Public on Sep 04 2019

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

summary: We assessed the feasibility of transplanting a sheet of retinal pigment epithelial (RPE) cells differentiated from induced pluripotent stem cells (iPSCs) in a patient with neovascular age-related macular degeneration. The iPSCs were generated from skin fibroblasts obtained from two patients with advanced neovascular age-related macular degeneration and were differentiated into RPE cells. The RPE cells and the iPSCs from which they were derived were subject to extensive testing. A surgery that included the removal of the neovascular membrane and transplantation of the autologous iPSC-derived RPE cell sheet under the retina was performed in one of the patients.

overall_design: We conducted a series of genome and epigenome analysis, including RNA-sequencing and WGBS, for assessment of the iPSC-derived RPE, cultured RPE and RPE tissues.

first: Fumihito

last: Miura

first: Masayo

last: Takahashi

first: Shinya

last: Yamanaka

first: Takashi

last: Ito


title: Dietary-phytochemical mediated reversion of cancer-specific splicing inhibits Warburg effect in head and neck cancer

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary:
It’s a well-established fact that epigenetic changes regulate alternative splicing in a context-dependent manner, as well as the epigenetic modifying effect of curcumin, is known in cancer. In this study, we have investigated the role of curcumin in the regulation of alternative splicing through epigenetic alterations.
We performed Human Transcriptome Array 2.0 to understand the global changes in gene expression as well as alternative splicing upon curcumin-PEC treatment.

overall_design: The head and neck cancer cells, H157 cells were treated with curcumin-PEC and PEC-control at 0h and 24h. H157 cells were harvested at 48h and proceeded for RNA extraction

first: Sandhya

last: Yadav

first: Somnath

last: Bhagat

first: Amit

last: Gupta

first: Atul

last: Samaiya

first: Aasheesh

last: Srivastava


title: Control ChIP-seq from skeletal muscle myoblast (ENCSR000ANN)

summary:
Control ChIP-seq on human skeletal muscle myoblast

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from ES-E14 (ENCSR000ADJ)

summary:
Control ChIP-seq on mouse ES-E14 produced by the Snyder lab

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptional profiling of EPHA2-WT and EPHA2-KO pancreatic tumor cells

city: New York

first: Jinyang

last: Li

address: 1230 York Ave

institute: The Rockefeller University

summary: RNA-seq analysis of sorted EPHA2-WT and EPHA2-KO tumor cells from subcutaneously implanted mouse pancreatic tumors

overall_design: Compared EPHA2-WT vs EPHA2-KO in two parental pancreatic tumor cell clones

first: Ben

last: Stanger


title: The ChAHP complex counteracts chromatin looping at Ctcf sites that have emerged from recent SINE expansions

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Ctcf and cohesin are key players in the three dimensional organization of chromatin. Whereas genome-wide Ctcf binding has diverged substantially between species due to transposon-mediated motif expansions, demarcation of topologically associating domains (TADs) by Ctcf is remarkably well conserved. Yet, the Ctcf consensus motif poorly predicts TADs and the majority of Ctcf sites are not at TAD boundaries. Here we demonstrate that the ChAHP complex (Chd4, Adnp, HP1) competes with Ctcf for a common set of genomic binding sites. In absence of ChAHP, novel insulated regions are formed at ChAHP bound sites, whereas proximal canonical boundaries are weakened. These data reveal that Ctcf-mediated loop formation is modulated by a distinct zinc-finger protein complex. Strikingly, ChAHP bound loci are mainly situated within evolutionary young SINE B2 transposable elements. This further implicates ChAHP in maintenance of evolutionary conserved spatial chromatin organization by buffering novel Ctcf binding sites that emerged through SINE expansions.

overall_design: Ctcf, cohesin (Rad21) and H3K27ac ChIPs were performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. Hi-C was performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. For each biological Hi-C replicate, we performed a technical replicate for which the cells were grown and processed in parallel. 4C experiments were performed in biological duplicates using the same cell lines as for Hi-C.

first: Lucas

last: Kaaij

first: Marc

last: Bühler


title: UV-RIP experiments of ZNFX1 in VSV infected A549 cells

city: Guangzhou

first: Xin

last: Jia

state: Guangdong

address: 135 XinGangXi Road

department: College of Life Sciences

institute: Sun Yat-sen University

summary: UV-RIP-seq was used to identify VSV-RNA associated with endogenous ZNFX1 in VSV infected A459 cells.

overall_design: UV-RIP experiment was performed using endogenous anti-ZNFX1 antibody in VSV infected A549 cells, then the total RNAs of input and co-immunoprecipitated RNAs of ZNFX1 were analyzed using Illumina Xten.

first: Wang

last: Yao

first: Jia

last: Xin


title: Mitochondria-localized ZNFX1 functions as a dsRNA sensor to initiate antiviral responses via MAVS

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Genes expression profiles in ZNFX1 overexpression in Rig-I-/- cells with or without poly I:C stimulation

summary: Genes expression profiles in ZNFX1 overexpression in Rig-I-/- cells with or without poly I:C stimulation in A549 cells.

overall_design: mRNA profiles of  ZNFX1 overexpression in Rig-I-/- A549 cells with or without poly I:C stimulation .


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ZNFX1-overexpresed A549 Cells Transcriptomes

summary: Analysis of the pathways among genes significantly  up-regulated or down-regulated between ZNFX1 overexpressed cells and wild-type A549 cells.

overall_design: mRNA profiles of ZNFX1 overexpressed cells and wild-type A549 cells were generated by deep sequencing


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center


title: Combined inhibition of STAT3 and DNA repair in palbociclib-resistant ER-positive breast cancer

city: Houston

first: Khandan

last: Keyomarsi

address: 6565 MD Anderson Blvd

institute: UT MD Anderson Cancer Center

summary: The results from our study have identified two clinically relevant, divergent and druggable pathways (DNA repair and STAT3) that can be targeted in combination to effectively combat drug resistance. We also found that the same pathways that were deregulated in palbociclib-resistant cells were also altered in tumor samples obtained from patients who progressed while on palbociclib and endocrine therapy

overall_design: Palbociclib resistant T47D cells were generated in a step-wise dose-escalading fashion. Whole-exome sequencing, genome-wide expression analysis and proteomic analysis were performed in both resistant and parental (sensitive) cells. Pathway alteration was assessed mechanistically and pharmacologically. Biomarkers of altered pathways were examined in tumor samples from palbociclib treated breast cancer patients whose disease progressed while on treatment.

first: Smruthi

last: Vijayaraghavan

first: Nicole

last: Kettner

first: Min

last: Ha

first: Bin

last: Liu

first: Xiayu

last: Rao

first: Jing

last: Wang


title: Global analyses of the dynamics of miRNA metabolism

first: Elena

last: Kingston

state: Massachusetts

address: Nine Cambridge Center

institute: Whitehead Institute MIT

summary: Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell per min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with < 10 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3 termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together these results establish a framework for describing the dynamics and regulation of miRNAs throughout their lifecycle.

overall_design: Approach-to-equilibrium metabolic labeling of miRNAs in 3 different cell lines with replicates in all cell lines

first: David

middle: P

last: Bartel


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [10x Genomics Chromium]

summary: By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmental hierarchy of dynamic progenitor pools in murine sonic hedgehog-(SHH) MBs. We identified Olig2+ progenitors as transit-amplifying cells during initial tumorigenic phases. These cells are quiescent stem-like progenitors in full-blown tumors but enriched in therapy-resistant as well as recurrent medulloblastomas. Olig2 ablation or depletion of mitotic Olig2+ progenitors abrogated tumorigenesis. Transcriptome profiling and chromatin occupancy assays revealed that Olig2 activates oncogenic networks including HIPPO- Yap/Taz signaling and Aurora-A/MycN pathways. Co-targeting these oncogenic pathways induced sustained tumor growth arrest. Together, our single-cell analyses uncover unexpected glia-lineage-related Olig2+ progenitor pools critical for medulloblastoma initiation and suggest targeting Olig2-regulated oncogenic pathways as an avenue for therapy.

overall_design: one 10X genomics chromium sample from mice medullablastoma tumor cells

first: Liguo

last: Zhang

first: Xuelian

last: He


title: Control ChIP-seq from GM08714 (ENCSR000EUH)

first: ENCODE

last: DCC

state: CA

summary:
Control ChIP-seq on human GM08714

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Human iron status mediates mosquito susceptibility to Dengue infection

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

institute: Tsinghua University

summary: We report the RNA-seq based analyses of the transcriptional changes in the Aedes aegypti midguts transcriptome 24,48 hours after blood feeding with or without 250 um ferric ammonium citrate.

overall_design: Comparison of the midguts transcriptome of Aedes aegypti females at two blood feeding conditions (with or without 250 um ferric ammonium citrate) and two time points.

first: Cheng

last: Gong


title: Differential gene expression microarray analysis of Tregs and Teff cells expanded by TCR-dependent Vs independent methods

status: Public on Aug 29 2019

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

summary:
CD4+ cells from Foxp3.eGFP mice containing Foxp3- Teff and Foxp3+ Treg cells were treated with anti-CD3/CD28 monoclonal antibodies or soluble OX40L and JAG1 for 3 days to induce TCR-dependent vs TCR-independent Treg proliferation. Untreated fresh CD4+ T-cells used as control. Post treatment T-cell proliferation was confirmed by Cell Trace violet dilution and Foxp3+ (Treg) and Foxp3-(Teff) were sorted. Differential gene expression profiling between Tregs and Teff cells among control, anti-CD3/CD28 and OX40L-JAG1 treated cultured was performed using affymetrix mouse gene 2.0 ST micro array.
We used microarrays to detail the global programme of gene expression underlying Treg proliferation and identified distinct classes of up-regulated genes during this process under different methods of expansion.

overall_design: Sorted Foxp3- Teff and Foxp3+ Treg cells from fresh (control), anti-CD3/CD28 monoclonal antibodies or soluble OX40L and JAG1 treated cultures were used for RNA extraction followed by cDNA construction. Differential gene expression profiling between Tregs and Teff cells among control, anti-CD3/CD28 and OX40L-JAG1 treated cultured was performed using affymetrix mouse gene 2.0 ST micro array.

first: Zarema

last: Arbieva

first: Arden

middle: Z

last: Lei

first: Mark

last: Maienschein-Cline

first: Bellur

last: Prabhakar


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [ATAC-Seq]

first: Richard

last: Lu

overall_design: 2 ATAC-Seq samples from mice medulloblastoma tumor cells (ATAC_Olig2_GFP(-), ATAC_Olig2_GFP(+))


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [Drop-Seq]

overall_design: 2 Drop-Seq samples from mice medullablastoma tumor cells


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [ChIP-Seq]

overall_design: 4 ChIP-seq samples and 2 input samples from normal cerebellum and medulloblastoma tissues


title: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [RNA-Seq]

overall_design:
10 RNA-Seq samples from normal cerebellum and medullablastoma tissues (RNA_CB_1, RNA_CB_2, RNA_CB_3, RNA_Lats12cko_1, RNA_Lats12cko_2, RNA_Lats12cko_3, RNA_GFAP_Ptch_1, RNA_GFAP_Ptch_2, RNA_GFAP_Ptch_Olig2_1, RNA_GFAP_Ptch_Olig2_2)
6 RNA-Seq samples from Olig2-GFP+ cells and Olig2-GFP- cells sorted from tumor tissues of hGFAPcre;Ptchc/c;Olig2-GFP mice (RNA_Olig2-GFP+_1, RNA_Olig2-GFP+_2, RNA_Olig2-GFP+_3, RNA_Olig2-GFP-_1, RNA_Olig2-GFP-_2, RNA_Olig2-GFP-_3)


title: RNA-seq-based identification of StAR upregulation by islet amyloid formation

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: Aggregation of islet amyloid polypeptide (IAPP) into islet amyloid results in β-cell toxicity in human type 2 diabetes. To determine the effect of islet amyloid formation on gene expression, we performed RNA-seq analysis using cultured islets from either wild-type mice (mIAPP), which are not amyloid prone, or mice that express human IAPP (hIAPP), which develop amyloid. Comparing mIAPP and hIAPP islets, 5025 genes were differentially regulated (2439 upregulated and 2586 downregulated). When considering gene sets (reactomes), 248 and 52 pathways were up- and downregulated, respectively. Of the top 100 genes upregulated under two conditions of amyloid formation, seven were common. Of these seven genes, only steroidogenic acute regulatory protein AQ2 (Star) demonstrated no effect of glucose per se to modify its expression. We confirmed this differential gene expression using quantitative reverse transcription polymerase chain reaction and also demonstrated the presence of StAR protein in islets containing amyloid. Furthermore, Star is a part of reactomes representing metabolism, metabolism of lipids, metabolism of steroid hormones, metabolism of steroids and pregnenolone biosynthesis. Thus, examining gene expression that is differentially regulated by islet amyloid has the ability to identify new molecules involved in islet physiology and pathology applicable to type 2 diabetes.

overall_design: Here we applied RNA-seq to study the effect of high glucose and IAPP aggregation on the transcriptome. Aggregation was stimulated by transgenic replacement of the mouse IAPP gene sequence with the corresponding human IAPP sequence, as per Hiddinga et al (2011 DOI:10.1111/j.2040-1124.2011.00166.x).  To do this we profiled four sample groups with n=8 biological replicates: (1) wild type mouse islets cultured in 11.1 mmol/L glucose. (2) wild type mouse islets cultured in 16.7 mmol/L glucose. (3) transgenic hIAPP mouse islets cultured in 11.1 mmol/L glucose. (4) transgenic hIAPP mouse islets cultured in 16.7 mmol/L glucose

first: Meghan

middle: F

last: Hogan

first: Harikrishnan

last: KN

first: Hanah

last: Rodriguez

first: Antony

last: Kaspi

first: Nathalie

last: Esser

first: Andrew

middle: T

last: Templin

first: Assam

last: El-Osta

first: Steven

middle: E

last: Kahn


title: Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress dependent mRNAs

city: Valencia

first: Manuel

last: Martín-Expósito

state: Valencia

address: Jaume Roig 11

department: Gene Expression and RNA Metabolism

institute: Instituto de Biomedicina de Valencia (IBV-CSIC)

summary: RNA binding proteins (RBPs) participate in almost all steps of gene expression, underscoring their potential as key regulators of RNA homeostasis. We structurally and functionally characterized Mip6, a four-RNA Recognition Motif (RRM)-containing RBP, as a functional and physical interactor of the mRNA export factor Mex67. Mip6 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through tryptophan 442 of Mip6-RRM4, whose mutation leads to slow growth of yeast cells in vivo. Although Mip6-RRM4 binds to RNA in vitro, Mex67 UBA binding prevents Mip6-RRM4 interaction with RNA.  Mip6 shuttles between the nucleus and the cytoplasm in a Mex67-dependent manner and concentrates in cytoplasmic foci under several stressors. Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) experiments showed preferential binding of Mip6 to mRNAs regulated by the stress-response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affected their export and expression levels. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4 dependent transcripts by its direct interaction with Mex67 UBA domain.

overall_design: Yeast Mip6 RNA binding at 30 ºC and after 39 ºC for 20 minutes using Illumina HI-Seq

first: Jonathan

last: Merran

first: Jeffry

middle: L

last: Corden

first: Lorena

last: de la Fuente

first: Ana

last: Conesa

first: Susana

last: Rodríguez-Navarro


title: Proteasome subunit RPT2a promotes PTGS through repressing RNA quality control in Arabidopsis

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

country: South Korea

institute: DGIST

summary: RNA quality control (RQC) and post-transcriptional gene silencing (PTGS) target and degrade aberrant endogenous RNAs and foreign RNAs, contributing to homeostasis of cellular RNAs. In plants, RQC and PTGS compete for foreign and selected endogenous RNAs; however, little is known about the mechanism interconnecting the two pathways. Using a reporter system designed for monitoring PTGS, we revealed that the 26S proteasome subunit RPT2a enhances transgene PTGS by promoting the accumulation of transgene-derived short interfering RNAs without affecting their biogenesis. RPT2a physically associated with a subset of RQC components and downregulated the protein level. Overexpression of the RQC components interfered with transgene silencing, and impairment of the RQC machinery reinforced transgene PTGS attenuated by rpt2a. Overall, we demonstrate that the 26S proteasome subunit RPT2a promotes PTGS by repressing the RQC machinery to control foreign RNAs.

overall_design: Small RNA profiling in PORI and PORI/rpt2a was analyzed by small RNA-sequencing.

first: Myung-Hee

last: Kim

first: Jieun

last: Jeon

first: Seulbee

last: Lee

first: Jae-Ho

first: Lei

last: Gao

first: Byung-Hoon

first: Jeong

middle: M

last: Park

first: Yun

first: June

last: Kwak


title: NEEDLE1 (NDL1) ENCODES A MITOCHONDRIA LOCALIZED ATPase REQUIRED FOR THERMOTOLERANT MAIZE GROWTH

status: Public on Aug 28 2019

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

overall_design: RNA-seq was performed on 5-10mm maize tassels for a Bulked Segregant Analysis approach

first: Mary

last: Galli


title: Gene expression profile of transformed pancreatic ductal cells

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary:
We observed that upon the activation of the oncogene KRasG12D and the deletion of the tumour suppressor Fbw7 in pancreatic ducts (KFCkY model), not all ducts respond in the same way. Some ductal cells remain morphologically normal while others exhibit signs of transformation (cellular and nuclear enlargement) with the concomitant upregulation of CD44.
Here we wanted to understand the differences between the normal-looking and transformed cells at the transcriptional level.

overall_design: Control or transformed cells were recovered from the pancreases of fifteen mice by fluorescence-activated cell sorting. RNA was extracted for hybridisation to Affymetrix microarrays (GeneChip Mouse Gene 1.0 ST Arrays).

first: Rute

last: Ferreira

first: Axel

last: Behrens


title: Expression data from Toll-like receptor 4 (Tlr4)-deficient mice infected with respiratory syncytial virus (RSV)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
In airway epithelial cells, Tlr4 mediates both innate and adaptive immune responses to viral pathogens  through the surface fusion glycoprotein (RSV F), however the mechanism is not well characterized.
We used microarrays to identify Tlr4-mediated gene expression pathways induced by RSV infection.

overall_design:
Tlr4-normal and  Tlr4-mutant mice were infected intranasally with RSV19 (10^6 PFU) or vehicle.  Lungs were collected at 1 and 5 days post infection for RNA extraction and hybridization on Affymetrix arrays.
time course, gene variants

first: Jacqui

last: Marzec

first: Hye-Youn

last: Cho

first: Steven

last: Kleeberger


title: Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut

city: Durham

first: Michel

last: Bagnat

address: 333B Nanaline Duke Bldg. Box 3709 Duke University Medical Center

institute: Duke University

summary: The goal of this RNA-seq experiment was to compare gene expression profiles of two different intestinal cell populations (Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid-intestine) in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 days post fertilization (dpf) TgBAC(cldn15la-GFPpd1034) transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2, and gene counts were analyzed using HTSeq.

overall_design: mRNA profiles of 6 dpf cldn15la-GFP positive intestinal epithelial cells (IECs) and cldn15la-GFP, Alexa Fluor 568 double-positive lysosome rich enterocytes (LREs) were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples, with 3 replicates each.

first: Jieun


title: Smad2/3 binding regions in NMuMG cells

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

institute: University of Tokyo

summary: Smad2/3 binding regions in mouse mammary gland epithelial cells (NMuMG) treated with TGF-beta for 1.5 h were determined by ChIP-seq to evaluate the transcriptional mechanism of TGF-beta-Smad signaling.

overall_design: Smad2/3 binding regions in mouse mammary gland epithelial cells (NMuMG) treated with TGF-beta for 1.5 h were determined by ChIP-seq.

first: Yuka

last: Itoh

first: Tomohiro

last: Ogami

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono

first: Keiji

last: Miyazawa


title: Cell type-specific transcriptional programs in mouse prefrontal cortex  during adolescence and addiction

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Coordinated activity-induced transcriptional changes across multiple neuron subtypes of the prefrontal cortex (PFC) play a pivotal role in encoding and regulating major cognitive behaviors. Yet, the specific transcriptional programs in each neuron subtype remain unknown. Using single-cell RNA sequencing (scRNA-seq), here we comprehensively classified all unique cell subtypes in the PFC. We analyzed transcriptional dynamics of each cell subtype under a naturally adaptive and an induced condition. Adaptive changes during adolescence (between P21 and P60), a highly dynamic phase of postnatal neuroplasticity, profoundly impacted transcription in each neuron subtype, including cell type-specific regulation of genes implicated in major neuropsychiatric disorders. On the other hand, an induced plasticity evoked by chronic cocaine addiction resulted in progressive transcriptional changes in multiple neuron subtypes and became most pronounced upon prolonged drug withdrawal. Our findings lay a foundation for understanding cell type-specific postnatal transcriptional dynamics under normal PFC function and in neuropsychiatric disease states.

overall_design:
To generate a comprehensive cell map of mouse PFC, we dissect this brain region from acute coronal sections of young (3 weeks) and adult mouse brains (8-10 weeks). After cell dissociation, single cells are captured with the 10X Chromium platform (10X Genomics), followed by cDNA synthesis, library preparation and high-throughput sequencing. Adult mice were subject to cocaine self-administration, samples were collected a three time points: Maintance, 48h after cocaine withdrawal and 15 days after cocaine withdrawal. A total of 6 saline-treated adult mice samples (2 in each time point), 6 cocaine-treated adult mice samples (2 in each time point) and 3 young mouse (P21) samples were sequenced and analyzed.
Each sample represents mixed cell types (please refer to meta_data.csv).

first: Aritra

last: Bhattacherjee

first: Mohamed

first: Renchao

last: Chen

first: Wenqiang

first: Luis

last: Tuesta

first: Yi

last: Zhang


title: A nutritional memory impairs transcriptional, metabolic and survival response to dietary restriction in old mice

city: South San Francisco

first: Oliver

last: Hahn

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

summary: Dietary restriction (DR) during adulthood can greatly extend lifespan and improve metabolic health in diverse species. However, whether DR in mammals is still effective when applied for the first time at ¬old age remains elusive. Here, we conducted a late-life DR switch experiment employing 800 mice, by switching old animals from ad libitum (AL) to DR and vice versa. Strikingly, the switch from DR-to-AL acutely increased mortality, while the switch from AL-to-DR caused only a weak and gradual increase in survival, highlighting a memory of earlier nutrition. A significant association between fat preservation and survival response pointed to the adipose tissue as a potential memory source. Consistently, post-switch RNA-seq profiling in liver, brown (BAT) and white adipose tissue (WAT) demonstrated that the transcriptional and metabolic program of chronic DR remained largely refractory to the AL-to-DR switch in the two fat tissues, particularly in WAT. This loss of transcriptional flexibility coincides with a major proinflammatory signature in aged preadipocytes, which is prevented by chronic DR feeding. Integration of lipidomics confirmed impaired membrane lipogenesis and limited mitochondrial copy number increase under late-life DR as functional consequences of this memory effect. Together, our results provide evidence for a nutritional memory as a limiting factor for DR-induced longevity and metabolic remodeling of WAT in mammals.

overall_design:
Total RNA  of liver and white adipose tissue extracted from 26 months (old), control-fed(AL),  dietary-restricted (DR), AL-to-DR switched (ALDR) and DR-to-AL switched  (DRAL)  F1 hybrid mouse strain (C3B6F1) were generated by deep sequencing using Illumina sequencing. Total RNA of white adipose tissue extracted from 5 months young AL and AL-to-DR switched mice were additionally generated by deep sequencing using Illumina sequencing.
Liver and WAT samples (total RNA) were sequenced in paired-end mode with 2x100bp reads. BAT samples (mRNA; polyA-enriched) were sequenced in single-end mode with 1x150bp reads.

first: Lisa

last: Drews

first: An

last: Nguyen

first: Takashi

last: Tatsuta

first: Lisonia

last: Gkioni

last: Hendrich

first: Qifeng

first: Thomas

last: Langer

first: Scott

last: Pletcher

first: Andreas

last: Beyer

first: Michael

middle: J

last: Wakelam

first: Sebastian

last: Grönke

first: Linda

last: Partridge


title: Chronic Dengue Encephalitis in a Patient with Progressive Dementia

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Dengue virus is the most common arbovirus worldwide and represents a significant public health concern. To date, chronic Dengue infections have not been previously reported. While investigating the etiology of central nervous system (CNS) disease in a patient presenting with progressive dementia, we elucidated a chronic dengue infection within the CNS. Comprehensive viral immune responses in both serum and cerebrospinal fluid (CSF) were profiled by a phage-display assay (VirScan). Enrichment of Dengue viral antibodies were detected in the CSF as compared to the serum. No virus was detected in serum or CSF, but post-mortem analysis confirmed Dengue virus in the brain by quantitative polymerase chain reaction (PCR), immunohistochemistry, RNAscope and sequencing. Dengue virus was detectable by PCR and sequencing from brain biopsy tissue collected 33 months ante-mortem, confirming a chronic infection. Comprehensive antibody profiling assays can aid in the diagnosis of encephalitis of unknown etiologies. Our findings suggest that Dengue virus infections may persist in the CNS and should be considered in patients with progressive dementia in endemic regions or with relevant travel history.

overall_design: Microbe profiles for 1 postmortem human cortex clinical sample were generated via deep sequencing using the Illumina NovaSeq6000_S4 system and reagents.

first: Tory

first: H

middle: B

last: Larman

first: Myoung

middle: H

last: Lee

first: Stephen

middle: S

last: Whitehead

first: Jeffrey

last: Kowalak

first: Camilo

last: Toro

first: Juyun

last: Kim

first: Lauren

last: Reoma

first: Arline

last: Faustin

first: Carlos

last: Pardo

first: Sanjay

last: Kottapalli

first: Jonathan

last: Howard

first: Daniel

last: Monaco

first: James

last: Weisfeld-Adams

first: Craig

last: Blackstone

first: Steven

last: Galetta

first: Matija

last: Snuderl

first: William

middle: A

last: Gahl

first: Ilya

last: Kister

first: Avindra

last: Nath


title: Cardiomyocyte HIPK2 Maintains Basal Cardiac Function via ERK Signaling

status: Public on Aug 27 2019

city: South Birmingham

first: Hind

last: Lal

state: AL

address: 1720 2nd Ave South Birmingham, AL 35294-1913

department: Division of Cardiovascular Disease

institute: The University of Alabama at Birmingham

summary:
Background: Cardiac kinases play a critical role in the development of heart failure, and represent potential tractable therapeutic targets. However, only a very small fraction of the cardiac kinome has been investigated. To identify novel cardiac kinases involved in heart failure, we employed an integrated transcriptomics and bioinformatics analysis and identified Homeodomain-Interacting Protein Kinase 2 (HIPK2) as a novel candidate kinase. The role of HIPK2 in cardiac biology is unknown.  Methods: We used the Expression2Kinase algorithm for the screening of kinase targets. To determine the role of HIPK2 in the heart, we generated cardiomyocyte-specific HIPK2 knockout (CM-KO) and heterozygous (CM-Het) mice. Heart function was examined by echocardiography and related cellular and molecular mechanisms were examined. Adeno-associated virus serotype 9 (AAV9) carrying cardiac-specific constitutively active MEK1 (TnT-MEK1-CA) were administrated to rescue cardiac dysfunction in CM-KOs.
Results: To our knowledge, this is the first study to define the role of HIPK2 in cardiac biology. Using multiple HIPK2 loss-of-function mouse models, we demonstrated that reduction of HIPK2 in cardiomyocytes leads to cardiac dysfunction—suggesting a causal role in heart failure. Importantly, cardiac dysfunction in HIPK2 KOs developed with advancing age, but not during development. In addition, CM-KO and CM-Het exhibited a gene dose-response relationship of cardiomyocyte HIPK2 on heart function. HIPK2 expression in the heart was significantly reduced in human end-stage ischemic cardiomyopathy compared to non-failing myocardium, suggesting a clinical relevance of HIPK2 in cardiac biology. In vitro studies with neonatal rat ventricular cardiomyocytes corroborated the in vivo findings. Specifically, adenovirus-mediated overexpression of HIPK2 suppressed the expression of heart failure markers, NPPA and NPPB, at basal condition and abolished phenylephrine-induced pathological gene expression. An array of mechanistic studies revealed impaired ERK1/2 signaling in HIPK2 deficient hearts. In vivo rescue experiment with AAV9 TnT-MEK1-CA nearly abolished the detrimental phenotype of KOs suggesting that impaired ERK signaling mediated apoptosis as the key factor driving the detrimental phenotype in CM-KO hearts.   Conclusions: Taken together, these findings suggest that cardiomyocyte HIPK2 is required to maintain normal cardiac function via ERK signaling

overall_design: C57BL/6 male mice were subjected to transaortic constriction (TAC) to induce heart failure (n=4) or sham surgery (n=5).  At 6 weeks post-TAC or post-sham, RNA samples from the left ventricle were collected and subjected to microarray analysis

first: Yuanjun

last: Guo

first: Jennifer

middle: Y

last: Sui

first: Kyungsoo

first: Zhentao

last: Zhang

first: Xiaoyan

last: Qu

first: Young-Jae

last: Nam

first: Robert

middle: N

last: Willette

first: Joey

middle: V

last: Barnett

first: Bjorn

middle: C

last: Knollmann

first: Thomas

last: Force


title: Single-cell sequencing reveals the relationship between phenotypes and genotypes of Klinefelter syndrome

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

summary: One of the most common congenital disorders of male infertility is Klinefelter syndrome. Because of its extreme heterogeneity in clinical and genetic presentation, the relationship between transcriptome and the clinical phenotype and the associated co-morbidities seen in KS has not been fully clarified yet. We reported here a 47 XXY karyotype Chinese male (KS) with infertility and analyzed the differences in gene expression patterns of peripheral blood mononuclear cells (PBMCs) from a Chinese male and a female control with normal karyotype by single-cell sequencing. We analyzed a total of 24,439 cells and divided them into 5 immune cell types (including B cell, T cell, macrophage cell, dendritic cell, and natural killer cell) according to the marker genes. Using unsupervised dimensionality reduction and clustering algorithms, we identified molecularly distinct subpopulations of cells between KS and both controls. Gene ontology enrichment analyses yielded terms associated with well-known comorbidities seen in KS as well as an affected immune system, type I diabetes mellitus. Based on our data, we point towards several candidate genes, which may be implicated in the phenotype of KS. Overall, our analysis showed a comprehensive map of the cell types of the PBMCs of KS patient at the single-cell level, which will contribute to preventing comorbidity and improving the life quality of KS patients.

overall_design: sequenced PBMCs from a Chinese male with Klinefelter syndrome by using single-cell sequencing technology

first: Xiaohui

last: Liu

first: Donge

last: Tang


title: Analysis of local glucocorticoid receptor occupancy at glucocorticoid-repressed inflammatory enhancers in Beas-2B airway epithelial cells II

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

summary: This study combined ChIP-seq using two different GR antibodies and stable GR knockdown in Beas-2B airway epithelial cells to determine whether glucocorticoid-mediated repression of inflammatory enhancers requires local GR occupancy

overall_design: Duplicate samples of Beas-2B cells transduced with a control lentiviral-shRNA construct (shCtrl) were treated with vehicle (ethanol) or dexamethasone (100 nM) for 10 minutes prior to chromatin immunoprecipitation with a GR antibody (GR-356) and sequencing. Duplicate Input DNA samples from shCtrl-transduced cells were included as controls.

middle: K

first: Margaret

last: Gruca

first: Mary

last: Allen

first: Vineela

last: Kadiyala

first: Tengyao

last: Song

first: Fabienne

last: Gally

first: Arnav

last: Gupta

first: Miles

last: Pufall

first: Robin

middle: D

last: Dowell

first: Anthony

last: Gerber


title: Analysis of local glucocorticoid receptor occupancy at glucocorticoid-repressed inflammatory enhancers in Beas-2B airway epithelial cells

overall_design: Duplicate samples of Beas-2B cells transduced with lentiviral-shRNA against GR (shGR) or a control construct (shCtrl) were treated with vehicle (ethanol), TNF (20 ng/ml), dexamethasone (100 nM) or TNF+dex for one hour prior to chromatin immunoprecipitation with one of two GR antibodies and sequencing. Duplicate Input DNA samples, representing both shCtrl and shGR groups, were included as controls.


title: Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes

city: Charlottesville

first: Jason

last: Papin

state: VA

address: 415 Lane Rd

department: Biomedical Engineering

institute: University of Virginia

summary: Context-specific Genome-scale Metabolic Network Reconstructions (GENREs) provide a means to understand cellular metabolism at a deeper level of physiological detail. Here, we use transcriptomics data from chemically exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism and predict biomarkers of liver toxicity using the Transcriptionally Inferred Metabolic Biomarker Response (TIMBR) algorithm. We profiled alterations in cellular hepatocyte metabolism following in vitro exposure to three toxicants (acetaminophen, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six hours. TIMBR predictions were compared with paired metabolomics data from the same exposure conditions. Agreement between computational model predictions and experimental data led to the identification of specific metabolites and thus metabolic pathways associated with toxicant exposure; where predictions and experimental data disagreed, we identified testable hypotheses to reconcile differences between the model predictions and experimental data. The presented pipeline for using paired transcriptomics and metabolomics data provides a framework for interrogating multiple omics datasets to generate mechanistic insight of metabolic changes associated with toxicological responses.

overall_design: Examination of RNA from compound-treated primary rat hepatocytes for 5 conditions (including the control) with 3-4 replicates for each condition.

first: Kristopher

last: Rawls

first: Edik

last: Blais

first: Bonnie

last: Dougherty

first: Glynis

last: Kolling

first: Kalyan

last: Vinnakota

first: Venkat

middle: R

last: Pannala


title: Transcriptomic analysis reveals potential mechanisms of toxicity in a combined exposure to dibutyl phthalate and diisobutyl phthalate in zebrafish (Danio rerio) ovary

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

institute: jiangsu university

summary: Phthalate esters (PAEs), a notable plasticizer, could be prolific contaminants in the aquatic environment, and have been shown to induce reproductive toxicity. However, studies concerning the toxicity towards aquatic species are based upon individual chemicals and the combined toxicity of PAEs to aquatic organisms remains unclear. The aim of this study was to explore the potential toxic mechanism of combined exposure to dibutyl phthalate (DBP) and diisobutyl phthalate (DiBP) in adult female zebrafish ovarian. Zebrafish were exposed to DBP, DiBP and their mixtures for 30 days, and their effects on ovarian histology, plasma sex hormones and ovarian transcriptomics were investigated. The plasma estradiol (E2) levels were significantly decreased 38.9% for DBP-1133 exposure group and 41.0% for DiBP-1038 exposure group. The percentages of late/mature oocyte were also significantly decreased 17.3% in DBP-1133 exposure and 16.2% in DiBP-1038 exposure, while those in combined exposure were not significantly affected. Nonetheless, transcriptome sequencing discovered 2564 differential expressed genes (DEGs) in zebrafish ovary after exposure to the mixtures. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified that those DEGs were involved in the neuroactive ligand-receptor interaction, GnRH, progesterone-mediated oocyte maturation, oocyte meiosis and steroid hormone biosynthesis signaling pathways. These results revealed that combined exposure showed potential reproductive toxicity at the molecular level.

overall_design: Ovarian mRNA sequencing of adult female zebrafish after single and combined exposure to DBP and DiBP for 30 days

first: Weiwei

last: Feng

first: Kun

first: Xuchun

last: Qiu

first: Hai

last: Xu

first: Guanghua

last: Mao

first: Ting

last: Zhao

first: Yangyang

last: Ding

first: Xiangyang

last: Wu


title: Synchronized HES7 Oscillation In Human Embryonic Stem Cell-Derived Presomitic Mesoderm

city: Madison

first: Li-Fang

last: Chu

address: 330 N. Orchard St.

institute: Morgridge Institute for Research

summary: Little is known about human segmentation clock during somitogenesis. Human embryonic stem (ES) cell differentiation towards PSM and somite cells provide a window of opportunity to probe for the dynamics of oscillatory gene expression. Using high temporal RNA-seq, we captured a transcriptional signature highly reminiscent of segmentation clock during somite differentiation. Our study provides a novel in vitro system to model human segmentation clock that is otherwise inaccessible during development.

overall_design: Human ES differentiation to PSM and somite cell fate, profiled by RNA-seq. Daily profiling, total 12 samples, triplicate for each day of sampling. 30 mins profiling, total 46 samples, replicates for each time points.