title: Identification of the KDM4B regulated transcriptome in the ER positive breast cancer cell line MCF-7

status: Public on Aug 06 2019

summary: To elucidate the KDM4B regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM4B-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. Differentially expressed genes were compared with KDM3A and FOXA1 regulated transcriptomes. We identified 229 genes co-regulated by all three enzymes and that co-regulated genes were involved in cell cycle processes. We identified that 53% and 48% of KDM4B-regulated genes were also regulated by KDM3A and FOXA1, with co-regulatory gene signatures being involved with estrogen response signatures and cell proliferation. We also identified that depletion of KDM3A and KDM4B together inhibits ER-target gene expression and ER-positive breast cancer cell growth more than depletion of either gene on its own.

overall_design: MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a KDM4B targeting siRNA (siKDM4B#1) using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 48 hours prior to treatment with 10 nM E2 for 4 hours before RNA extraction using TRIzol (Ambion, Life Technologies) and hybridization of duplicate samples to an Illumina HT-12 v4 BeadChip array.


title: Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of regulatory T-cell gene expression program [RNA-Seq]

status: Public on Aug 07 2019

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

type: Expression profiling by high throughput sequencing

summary: In order to acquire in depth understanding of Treg specific molecular functions of Bcl11b, we performed RNA-Seq from Bcl11b-suffcient or deficient Treg cells to determine transcriptional profile.

overall_design: Transcriptional profiles from Bcl11b-suffcient or deficient Treg cells were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2500 or MiSeq.

first: Nurul

last: Syed

first: Amit

last: Sharma

first: Ghosh

last: Sayantani

first: Sung-Wook

last: Hong

first: Sinchita

last: Roy-Chowdhuri

first: Sin-Hyeog

last: Im

first: Alexander

last: Rudensky

first: Dipayan

last: Rudra


title: Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of regulatory T-cell gene expression program [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to identify Bcl11b-bound sites in Treg cells(WT) and Tn cells and to determine Bcl11n and Foxp3 peak overlaps, we performed Bcl11b and Foxp3 ChIP-seq on respective cell populations. In order to understand whether Bcl11b recruitment to it's target sites is dependent on Foxp3 we performed Bcl111b ChIP-Seq in Tfn cells(derived from Foxp3GFPKO mice). Finally, to ask whether genome-wide occupancy of Foxp3 is affected in the absence of Bcl11b, we performed Foxp3 ChIP-seq in Bcl11b-deficient Treg cells(KO Treg).

overall_design: Genome-wide Chromatin Immunoprecipitation followed by next generation sequencing (ChIP-seq) for each conditions (3 replicates for Bcl11b ChIP in wild type Treg, 3 replicates for Bcl11b ChIP in wild type Tn, 2 replicates for Foxp3 ChIP in wild type Treg, 2 replicates for Bcl11b ChIP in Tfn and 2 replicates for Foxp3 ChIP in Bcl11b KO Treg) was done using Illumina HiSeq 2500.


title: Non-catalytic functions of Tet2 are essential to regulate hematopoietic stem and progenitor cell homeostasis

status: Public on Aug 05 2019

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

summary: To identify genes that are influenced by the catalytic and non-catalytic functions of Tet2 in hematopoietic stem and progenitor cells (HSPCs), we analyzed the gene expression profiles of Tet2 catalytic mutant (Tet2 Mut), Tet2 knockout (Tet2 KO) and wild-type HSPCs (or LSK, Lin–Sca-1+c-Kit+) and multi-potent progenitor (or MPP, Lin–) cells by RNA-seq.

overall_design: LSK and MPP cells were sorted from pooled bone marrow of two 10-week-old Tet2 Mut, Tet2 KO and wild-type mice by FACS. RNA was extracted using QIAGEN RNAeasy Kit. RNA was amplified and barcoded and used to prepare libraries of two technical replicates, with ERCC spike in controls. As such, there were two replicates for each genotype for each cell type (total of 12 samples). The libraries were subjected to 150bp paired-end sequencing (Illumina Next-seq 500 platform) at the Einstein Epigenomics core following their protocols. This generated 15~40 million read pairs per sample. The reads were trimmed using the TrimGalore (v 0.4.1, https://github.com/FelixKrueger/TrimGalore) to remove adaptors and then mapped to the mouse genome (mm10) by TopHat2 software (v 2.0.13) with default parameters. Details of RNA-seq and data analysis are described in the methods sections of the manuscript.

first: Yilin

last: Zhao

first: Deyou

last: Zheng

first: Keisuke

last: Ito


title: Rinf regulates pluripotency network and Tet enzymes in embryonic stem cells (ESCs)

summary: In this study: (1) We have mapped the genome wide binding distribution and enrichment of Rinf/CXXC5 at genes and regulatory regions in mouse ESCs by ChIP-seq using a specific antibody against Rinf. (2) We have examined the role of Rinf in regulation of ESC gene expression programs by performing transcriptomic analysis of Rinf wild type and knockout ESCs by RNA-seq to identify differentially expressed genes. (3) We have investigated the role of Rinf in differentiation and lineage specification programs of ESCs by analyzing the transcriptomic profile of wild type and Rinf–/– ESCs during differentiation to embroyoid bodies (EBs) at three time points (day 0, 3, 6).

overall_design: Rinf ChIP-seq: It was performed on two independent wild type V6.5 mESC lines and one Rinf–/– ESC line (negative control) as previously described (Johnson et al., 2007). To ensure the specificity of the antibody, we also performed ChIP-seq in a Rinf–/– ESC line as a negative control. Briefly, ESCs were cultured on gelatin, harvested, crosslinked, lysed, sonicated and subjected to ChIP using an anti-Rinf/CXXC5 antibody (Cat#84546S, CST). 100bp paired end sequencing was performed at the Einstein Epigenomics core following their established protocols using Illumina HiSeq 2500 platform. Reads were mapped to the mouse genome (mm10) using the software Bowtie2 (VN: 2.2.3) with default (Langmead and Salzberg, 2012). The Rinf binding peaks were called with the software MACS2 using the input as controls and default parameters (Yong Zhang et al., 2008), with the final peaks called from the merged reads of the two biological replicates. Details of ChIP-seq and data analysis are described in the methods sections of the manuscript. The ChIP-seq analysis identified a total of 2,342 Rinf peaks that were mapped to promoters and gene bodies as well as distal regulatory elements and intergenic regions. We examined the role of Rinf in regulation of ESC gene expression programs by performing transcriptomic analysis of Rinf wild type and knockout ESCs by RNA-seq to identify differentially expressed genes.  RNA-Seq of ESCs: Two independent ESC of each genotype (Wild type and Rinf KO) were cultured on feeders then pre-plated to remove feeders and seeded on gelatin overnight. Total RNA was extracted (Omega E.Z.N.A Total RNA kit), barcoded and used to prepare libraries. ERCC spike in controls were included. The libraries were subjected to 150 bp paired-end sequencing using Illumina Next Seq 500 platform at the Einstein Epigenomics core following their protocols. We generated ~25 million reads per sample. The reads were trimmed using trim galore (v 0.4.1, https://github.com/FelixKrueger/TrimGalore) to remove adapters and then mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters (D. Kim et al., 2013). Details of RNA-seq and data analysis are described in the methods sections of the manuscript. RNA-seq of EBs: Two independent ESC line of each genotype (Wild type and Rinf KO) were differentiated to EBs following standard hanging drop methods (described in manuscript) and total RNA was isolated (Omega E.Z.N.A Total RNA kit) at three time points (day 0, 3, 6) of differentiation (total of 12 RNA samples). Samples were barcoded and used to prepare libraries. ERCC spike in controls were included. Libraries were subjected to 75bp single-end sequencing using Illumina Next-Seq 500 platform at Einstein Epigenomics core following their protocols. We generated ~30 million reads per sample.  The reads were trimmed using trim galore (v 0.4.1, https://github.com/FelixKrueger/TrimGalore) to remove adapters and then mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters (D. Kim et al., 2013). Data analysis and identification of DEGs between the two genotypes for each time point are explained in detail in the manuscript methods section. Details of RNA-seq and data analysis are described in the methods sections of the manuscript.

first: Qin

last: Tang


title: Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of regulatory T-cell gene expression program

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

overall_design: Refer to individual Series


title: Cell Autonomous and non-cell autonomous effects of neuronal Bin1 loss in vivo

status: Public on Aug 02 2019

city: Cambridge

first: Jacob

last: Gagnon

state: Massachusetts

address: 225 Binney St

institute: Biogen

summary:
Purpose: investigate the impact of neuronal Bin1 Loss on surrounding microglia transcriptome.
Methods: mRNA profile of  microglia cells FACS-sorted from brains of mice homozygous and heterozygous conditional knock-out for Bin1 in excitatory neurons  (B6.129S6-Bin1tm2Gcp/J (Bin1flox/flox), <FVB/N-Tg(Thy1-cre)1Vln/J> (Thy1-Cre) ) and Bin1-expressing littermates at 3 month of age had been generated from 10ng of total RNA using SMARTer Ultra Low Input RNA kit v4 (Clontech).  The cDNA was amplified by 8 PCR cycles, followed by QC analysis on BioAnalyzer 2100 (Agilent).  Sequence libraries were produced from 150pg of cDNA using Nextera XT DNA library kit (Illumina), cleaned up with AMPure XP beads, and QC checked with Caliper LabChip GX.  Single-end sequencing data were generated on an Illumina Illumina HiSeq 2500, at a depth of 30 million reads per sample, with read length 50bp.The reads were aligned with the OmicSoft OSA4 to the mouse genome (mm10) and the Ensembl.R84 gene model. Gene counts were estimated using RSEM.  Two samples were removed (one sample from WT_Female cohort and one samples from Heterozygote_Male cohort) due to low fraction of uniquely mapped single reads and higher than expected duplication.  Of note, these samples with poor technical QC metrics were also clear outliers in PCA.  Normalization and differential expression analysis were carried out with the Bioconductor package DESeq2. Differentially expressed genes (DEGs) were defined as having adjpval < 0.05, and |FC| > 1.5.
Results: Microglia from homozygous Bin1-cKO mice showed 265 (|FC| > 1.5, FDR <0.05) statistically significant Differentially Expressed Genes (DEGs) in comparison to WT mice. Interestingly, microglia from heterozygous Bin1-cKO mice showed no statistically significant (FDR <0.05) DEGs in comparison to WT mice.
Conclusion: neuronal disfunction resulting from Bin1 loss alters gene expression of the surrounding microglia.

overall_design: 3 month-old mice: Bin1flox/flox X Thy1-Cre+ (Homo-cKO) male mice =5, female mice =5;  Bin1flox/wt Thy1-Cre+ (Het-cKO) male mice = 4, female mice =4; Bin1flox/wt Thy1-Cre- (WT) male mice = 4, female mice =3

first: Kathleen

last: McAvoy

first: Hameetha

last: Rajamohamend Sait

first: Galina

last: Marsh

first: Michael

last: Peterson

first: Taylor

middle: L

last: Reynolds

first: Jake

first: Sarah

last: Geisler

first: Prescott

last: Leach

first: Chris

last: Roberts

first: Ellen

last: Cahir-McFarland

first: Richard

last: Ransohoff

first: Andrea

last: Crotti


title: Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas

status: Public on Aug 01 2019

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

summary: Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene. Here, we established induced pluripotent stem cells (iPSCs) from EWS/ATF1-controllable murine CCS cells harboring sarcoma-associated genetic abnormalities. Sarcoma-iPSC mice develop secondary sarcomas immediately after EWS/ATF1 induction, but only in soft tissue. EWS/ATF1 expression induces oncogene-induced senescence in most cell types in sarcoma-iPSC mice but prevents it in sarcoma cells. We identify Tppp3-expressing cells in peripheral nerves as a cell-of-origin for these sarcomas. We show cell type-specific recruitment of EWS/ATF1 to enhancer regions in CCS cells. Finally, epigenetic silencing at these enhancers induces senescence and inhibits CCS cell growth through altered EWS/ATF1 binding. Together, we propose that distinct responses to premature senescence are the basis for the cell type-specificity of cancer development.

overall_design: ChIP-seq was performed in a murine EWS/ATF1-induced sarcoma cell line (G1297) or sarcoma iPSC-derived MEFs (sarcoma MEF). In these cells, exogeneous EWS/ATF1 which is conjugated with an HA tag is inducible by treatment with Doxycycline (Dox).

first: Shingo

last: Komura

first: Fumiaki

last: Itakura


title: Gene expression profile of human iPSC-derived nephron progenitor cells

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: During development, nephron progenitor forming one million nephrons, a functional unit in the kidney. However, nephron progenitor ceases before birth in human when they terminally differentiated to the nephron. Our lab established the method for induction of nephron progenitors from mouse Embryonic Stem (ES) cells and/or human induced Pluripotent Stem Cells (iPSCs) (Taguchi et al., Cell Stem Cell. 2014, 2017). For application of induced nephron progenitors to regenerative medicine, a large number of cells are required such as disease modeling and drug screening. To selectively propagate human iPS-derived nephron progenitors in vitro in an undifferentiated state, we developed SIX2-GFP iPS line and optimized culture condition of induced nephron progenitors by modifying our previously developed condition (Tanigawa et al., Cell Rep. 2016). To understand how whole gene expression profiles of human iPS-derived nephron progenitor cells are changed during culture, we isolated nephron progenitor cells by FACS and cultured in our defined culture condition. Purified RNAs from cultured cells at day 7 or un-cultured nephron progenitor cells were analyzed by RNA-seq.

overall_design: In order to propagate the human iPS-derived nephron progenitors, we generated iPSCs that express GFP in the SIX2 locus by TALEN-mediated homologous recombination and then purified SIX2-positive population from iPSCs-derived tissues by FACS. Isolated ITGA8+/PDGFRA-/SIX2-GFP+ cells were cultured for 7 days in our defined conditions and compared uncultured cells.

first: Ryuichi

last: Nishinakamura


title: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [chromatin-associated RNA-Seq]

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Dynamic control of the accessibility of the genomic regulatory information is at the heart of stimulus-induced gene expression changes. Whereas chromatin accessibility assays describe dynamic changes in open chromatin over time, they provide only indirect and limited information on the nucleosome remodeling events that underlie such changes. Here, we combined accessibility assays and ChIP-seq on nucleosomes generated by micrococcal nuclease digestion in resting and LPS-activated macrophages. We devised a novel quantitative framework to discriminate different types of nucleosome remodeling events and used it to analyze nucleosome organization at genomic cis-regulatory elements modulated by stimulation on a genomic scale. At typical stimulus-activated enhancers, remodeling events were commonly asymmetric, with only one of the two nucleosomes flanking the central accessible region being remodeled. A systematic analysis of nucleosome organization revealed distinct associations of individual TFs with remodeling and showed that most remodeling events tended to occur early in the response and to be maintained over time, with progressively fewer novel events occurring at later times.

overall_design: Chromatin-associated RNA profiling of murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in triplicates in untreated cells as well as in cells treated for 30', 1hrs, 2hrs or 4hrs with lipopolysaccharide (LPS).

first: I

first: F

last: Comoglio

first: M

last: Simonatto

first: S

last: Polletti

first: G

last: Natoli


title: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages


title: Modular organization of the motor space in the mouse superior colliculus

status: Public on Jul 31 2019

first: Marco

last: Tripodi

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue

department: Neurobiology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: In order to characterize the genetic diversity within the Stratum Griseum Intermediale (SGI), we screened gene expression by extracting RNA from sensory and motor layers of the Superior Colliculus (SC) at post-natal day (P)7.

overall_design: Sensory and motor domains were manually dissected from P7 mice in order to obtain four samples from each mouse: sensory anterior SC, sensory posterior SC, motor anterior SC and motor posterior SC. RNA was extracted from these samples RNeasy Mini kit (Qiagen, Venlo, Netherlands) and  cDNA libraries were generated from total RNA using a TruSeq® Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) and sequenced on an Illumina HiSeq 4000 machine (single read, 50bp read length).

first: Laura

last: Masullo

first: Paula

last: Freire-Pritchett


title: Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (CAF_vs_Norm_affy)

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: The molecular basis for heterogeneity of cancer-associated fibroblast (CAF) populations remains to be established. We report that fibroblast growth factor (FGF) and transforming growth factor-beta (TGFB) signaling are strong opposite modulators of key CAF effector genes. While FGF activation in normal human dermal fibroblasts (HDFs) induces a number of mitogenic growth factors and metalloproteases, it suppresses expression of pro-fibrotic and cancer-associated extracellular matrix proteins, with TGFB exerting reverse effects. Genetic abrogation or pharmacological inhibition of either pathway results in induction of CAF effector genes responsive to the other, with the ETV1 transcription factor mediating FGF effects and suppressing those of TGFB. This duality of FGF- and TGFB- signaling is reflected in the distinct gene expression profiles of HDFs derived from a large cohort of individuals, multiple Squamous Cell Carcinoma (SCC)-derived CAF strains and stromal fibroblasts underlying premalignant (Actinic Keratoses) and desmoplastic versus non-desmoplastic skin SCC lesions. Functionally, an altered balance between FGF or TGFB signaling, by genetic suppression of either, is sufficient to confer upon HDFs growth enhancing properties on neighboring SCC cells, in vitro and in vivo, in an orthotopic skin cancer model. Thus, activation of heterogeneous CAF populations by deregulation of distinct signaling pathways converges on cancer development with implications of translational significance.

overall_design: Gene expression profiling of 8 skin cancer-associated fibroblast (CAF) strains and normal fibroblasts from matched donors.

first: Pino

last: Bordignon

first: Giulia

last: Bottoni

first: Xiaoying

last: Xu

first: Emmanuella

last: Guenova

first: Paris

last: Jafari

first: Gian

middle: P

last: Dotto


title: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ChIP-Seq]

overall_design: Chromatin immunoprecipitations of H3 lysine 4 mono-methylated, H3 lysine 27 acetylated, H3 lysine 4 tri-methylated on MNase-digested chromatin, followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in duplicates in untreated cells as well as in cells treated for 30', 1hrs, 2hrs or 4hrs with lipopolysaccharide (LPS).


title: Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (RNA-Seq_65_HDF)

overall_design: RNA-Seq experiments on human dermal fibroblasts from 65 individuals


title: Effect of cannabinoids on microRNA regulation of neuroinflammation in EAE

status: Public on Aug 03 2019

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

summary: We used microRNA microarrays to identify dysregulated microRNAs in CD4+ T cells isolated from brains of EAE mice treated with vehicle or THC+CBD.

overall_design: CD4+ T cells were isolated from brains of EAE mice treated with vehicle or THC+CBD at the peak of disease.

first: Zinah

middle: Z

last: Al-Ghezi

first: Mitzi

middle: S


title: Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages [ATAC-Seq]

first: Iros

last: Barozzi

overall_design: ATAC-seq of murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in triplicates in untreated cells as well as in cells treated for 30', 1hrs, 2hrs or 4hrs with lipopolysaccharide (LPS).

first: I

first: F


title: Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development


title: Changes in gene expression predictably shift and switch genetic interactions

city: Barcelona

first: Xianghua

last: Li

state: Barcelona

address: carrer Dr. Aiguader 88, PRBB building

country: Spain

institute: Centre for Genomic Regulation

summary: An important goal in disease genetics and evolutionary biology is to understand how mutations combine together to alter phenotypes and fitness.  Non-additive genetic (epistatic) interactions between mutations occur extensively within and between genes, which makes accurate genetic prediction a difficult challenge.  Moreover, for unclear reasons, the interactions between mutations change quite extensively across conditions, cell types, and species, with important consequences for both evolution and precision medicine such as the exploitation of synthetic lethality in cancer. To better understand the plasticity of genetic interactions, we reduced the problem to a minimal system where we combined mutations within a single protein performing a single cellular function. The only perturbation to the system was a change in the expression level of the mutated gene itself. Even in this minimal system, the interactions between mutations were highly plastic, with interactions changing in both magnitude and sign when the expression level was altered. Mathematical modelling revealed the cause of this as the non-linear relationship between the concentration of the protein and the cellular phenotype.These non-linearities are widespread in biology and transform expression level-independent effects of mutations on protein folding and stability into mutation outcomes and interactions that shift and switch as gene expression changes. This plasticity of mutation effects and genetic interactions has important implications for human disease and evolutionary theory.

overall_design: Individual and double mutational effects were analyzed within the same gene (lambda repressor CI helix turn helix domain; GeneID: 3827059) at two protein expression levels (high and low). Mutated region: 52nd-210th nucleotide bases. The mutational effects were analysed based on their ability to repress expression of GFP from the PR promoter on plasmid constructs (based on pBADM-11 vector, lambda repressior was expressed with inducible arabinose-controled pBAD promoter, and GFP under the control of PR promoter regulated by lambda repressor). Both expression-level experiments were performed in three biological replicates. The library was sequenced before functional selection (Input as a control, also with three biological replicates). Selection was by flourescent-activated cell sorting, with each replicate matching each input replicate. Two output populations were sequenced: output1 corresponds to the cell population carrying functional genetic variants (repressing the target gene GFP expression levels to wild type protein level) and output 2 corresponds to the cell population with intermediate target gene expression levels.

first: Jasna

last: Lalic

first: Pablo

last: Baeza-Centurion

first: Riddhiman

last: Dhar

first: Ben

last: Lehner


title: Role of TLR9 signaling in GC response

status: Public on Jul 30 2019

city: San Francisco

first: Eric

middle: Joseph

last: Wigton

state: CA

address: 500 Parnassus Ave.

department: Immunology

institute: UCSF

summary: NGS analysis of transcriptomes of MyD88 sufficient vs deficient GC B cells

overall_design: Examination of MyD88 WT vs KO GC B cell transcriptomes at D14 post immunization with T-dependent antigen tightly bound to CpG DNA oligo.

first: Karl

last: Ansel

first: Anthony

last: DeFranco


title: Comparison between infant and adult primary human hepatocytes (PHHs) in terms of their responsiveness to FAC (FBS + A83-01 + CHIR99021)

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Infant PHHs (IPHHs) and adult PHHs (APHHs) were cultured in the presence of FBS only or FAC, and their transcriptomic changes throughout the 2-week culture were assessed by mRNA microarray.

overall_design: IPHHs and APHHs were cultured in FBS or FAC.

first: Takahiro

last: Ochiya


title: Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in CHO-K1 cells

city: Louisville

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in CHO-K1 cells

overall_design: Methods: CHO-K1 cells were transfected, in three separate experiments, with pre-miR-29b-1, pre-miR-29a, or anti-miR-29a (which blocks both miR-29b-1 and miR-29a).  RNA seq profiles were generated by deep sequencing, in triplicate, using Illumina Nextseq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cuffdiff.

first: Penn

last: Muluhngwi

first: Theodore

last: Kalbfleisch

middle: C

first: Carolyn

last: Klinge


title: Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (RNA-Seq_FGF2)

first: Paola

last: Ostano

overall_design: RNA-Seq experiments on human dermal fibroblasts plus/minus FGF-2 treatment

first: Pino

last: Bordignon

first: Giulia

last: Bottoni

first: Xiaoying

last: Xu

first: Emmanuella

last: Guenova

first: Paris

last: Jafari

first: Gian

last: Dotto


title: Dualism of FGF and TGFb signaling in activation of heterogeneous cancer-associated fibroblast populations converging on cancer development (DNFGFR1_affy)

overall_design: Gene expression profiling of 2 strains of human dermal fibroblasts (HDF) lentivirally transduced with either a dominant negative mutant FGFR1 receptor (DNFGFR1)- or a dominant negative mutant TGFBR2 receptor (DNTGFBR2)-expressing vector, versus empty vector control.


title: Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells [RNA-Seq IL]

status: Public on Jul 29 2019

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in pituitary secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the physiological UPR pathway prevents triggering the protein stress response. The pituitary differentiation factor Tpit activates Creb3l2 expression, the Creb3l2-dependent regulatory network as well as the physiological UPR pathway. Thus, Creb3l2 implements high basal translation levels through direct targeting of translation effector genes acting downstream of signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins.

overall_design: RNAseq in WT and loss-of-function Tg pituitary intermediate lobes (IL)

first: Konstantin

last: Khetchoumian

first: Jacques

last: Drouin


title: Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: Meiosis is the specialized cell division during which parental genomes recombine to create genotypically unique gametes. Despite its importance, mammalian meiosis cannot be studied in vitro, greatly limiting mechanistic studies. In vivo, meiocytes progress asynchronously through meiosis and therefore the study of specific stages of meiosis is a challenge. Here, we describe a simple method for isolating pure sub-populations of meiocytes that allows for detailed study of meiotic sub-stages. Interrogating the H3K4me3 landscape revealed dynamic chromatin transitions between sub-stages of meiotic prophase I, both at sites of genetic recombination and at gene promoters. We also leveraged this method to perform the first comprehensive, genome-wide survey of histone marks in meiotic prophase, revealing a heretofore unappreciated complexity of the epigenetic landscape at meiotic recombination hotspots. Ultimately, this study presents a simple, scalable framework for interrogating the complexities of mammalian meiosis.

overall_design: We devised a method to isolate specific populations of meiotic nuclei from whole testis of mice. We subsequently interrogated the dynamic histone modification landscape using ChIP-Seq.

first: Kwan-Wood

middle: G

last: Lam

first: Gang

last: Cheng

first: Florencia

last: Pratto

first: Rafael

middle: D

last: Camerini-Otero


title: Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells

overall_design: Refer to individual Series


title: Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells [ChIP-Seq]

overall_design: ChIPseq in normal AtT-20 and Creb3l2 gain-of-function Tg corticotrope AtT-20 cells


title: T cell and Monocyte Specific RNAseq Analysis in Septic and Non Septic Critically-Ill Patients and in Patients with Cancer

city: Collegeville

first: James

middle: Raymond

last: Brown

address: 1250 S. Collegeville Road

institute: GlaxoSmithKline

summary: The purpose of this study was to determine the potential differential effect of sepsis on innate versus adaptive immune effector cells by examining RNA expression in monocyte/macrophages and CD4 and CD8 T cells respectively using next generation sequencing.

overall_design: mRNA profiles of CD4, CD8 and CD14 cells were generated for sepsis, critically-ill non-septic, cancer patients and age-matched healthy controls using Illumina Hiseq 2500.

first: Zhang

last: Wang

first: Michael

last: Washburn

first: Richard

last: Hotchkiss

middle: R


title: Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells [RNA-Seq AtT-20 cells]

overall_design: RNAseq in control (Neo), Creb3l2 and/or XBP1s gain-of-function AtT-20 cells


title: miRNA expression in spatially-sorted hepatocytes

status: Public on Jul 26 2019

city: Rehovot

first: Shalev

last: Itzkovitz

state: Israel

address: 234 Herzl

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. We applied transcriptomics, miRNA array measurements and Mass spectrometry proteomics to reconstruct spatial atlases of multiple zonated hepatocyte features. We found that protein zonation largely overlapped mRNA zonation, with the periportal HNF4α as an exception. We identified zonation of miRNAs such as miR-122, and inverse zonation of miRNAs and their hepatocyte target genes, implying potential regulation through zonated mRNA degradation. These targets included the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstructing spatial atlases of multiple cellular features in the liver and other structured tissues.

overall_design: Single tetraploid hepatocytes were isolated from three mice, and FACS-sorted according to expression of the surface markers Nt5e (CD73) and Cdh1 (E-cadherin), yielding 8 subpopulations of hepatocytes originating from distinct positions in the liver lobule.

first: Shani

last: Ben-Moshe

first: Yonatan

last: Shapira

first: Andreas

middle: E

last: Moor

first: Rita

last: Manco

first: Tamar

last: Veg

first: Keren

last: Bahar-Halpern


title: Genome-wide mapping of GATA2 in human iPS

status: Public on Jul 25 2019

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

overall_design: List of ChIPseq samples of GATA2 in two time points (iPS and differentation into Embryoid bodies).

first: Sergi

last: Aranda

first: Luciano

last: DiCroce


title: The WT1-like transcription factor Klumpfuss maintains lineage commitment in the intestine

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: RNA-Seq experiment of sorted Esg+ stem-progenitors expressing either RNA (kluRNAi) against Klu or overexpression of klu (UAS-klu)

overall_design: The transcriptome of Control esg+ cells is compared with that of Esg+ cells expressing either RNA (kluRNAi) against Klu or overexpression of klu (UAS-klu)

first: Jerome

last: Korzelius

first: Marco

last: Groth


title: GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary:
 In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 in mouse hematopoiesis is well established, its involvement during early human hematopoietic development is not clear. By combining time-controlled overexpression of GATA2 with genetic knockout experiments, we found that GATA2, at the mesoderm specification stage, promotes the generation of hemogenic endothelial progenitors and their further differentiation to hematopoietic progenitor cells, and negatively regulates cardiac differentiation.

Surprisingly, genome-wide transcriptional and chromatin immunoprecipitation analysis showed that GATA2 bound preferentially to regulatory regions, and repressed the expression of cardiac development-related genes. By contrast, genes important for hematopoietic differentiation were upregulated by GATA2 in a mostly indirect manner. Collectively, our data reveal a hitherto unrecognized role of GATA2 as repressor of cardiac fates, and highlight the importance of coordinating the specification and repression of alternative cell fates.

overall_design: RNA sequencing of HEPS/CD45+ cells treated with or without Dox.

first: Julio

last: Castaño

first: Clara

last: Bueno

first: Fernando

middle: J

last: Calero-Nieto

first: Eva

last: Mejia-Ramirez

first: Jose

last: Mosquera

first: Cristina

last: Prieto

first: Lorea

last: Zabaleta

first: Elisabetta

last: Mereu

first: Meritxell

last: Rovira

first: Senda

last: Jiménez-Delgado

first: Daniel

last: Matson

first: Holger

last: Heyn

first: Emery

middle: H

last: Bresnick

first: Berthold

last: Gӧttgens

last: Di Croce

first: Pablo

last: Menendez

first: Angel

last: Raya

first: Alessandra

last: Giorgetti


title: Glucose-dependent Insulinotropic polypeptide receptor-expressing cells in the hypothalamus regulate food intake

status: Public on Jul 24 2019

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Ambiguity regarding the role of glucose-dependent insulinotropic polypeptide (GIP) in obesity arises from conflicting reports asserting that both GIP receptor (GIPR) agonism and antagonism are effective strategies for inhibiting weight gain. To enable identification and manipulation of Gipr-expressing (Gipr) cells we created GIPR-Cre knock-in mice. As GIPR-agonists have recently been reported to suppress food intake we aimed to identify central mediators of this effect. Gipr cells were identified in the arcuate, dorsomedial, and paraventricular nuclei of the hypothalamus, as confirmed by RNAscope in mouse and human. Single cell RNAseq identified clusters of hypothalamic Gipr cells exhibiting transcriptomic signatures for mural, glial and neuronal cells, the latter expressing somatostatin, but little proopiomelanocortin or agouti-related peptide. Activation of Gq-DREADDs in hypothalamic Gipr cells suppressed food intake in vivo, which was not obviously additive with concomitant GLP1R activation. These data identify hypothalamic GIPR as a target for the regulation of energy balance.

overall_design: Hypothalamic Gipr-expressing cells isolated from 4-6 week old mice were sequenced using single cell RNA-seq.

first: Alice

last: Adriaenssens

first: Joseph

last: Polex-Wolf


title: Target suppression effect by methylated miRNA

city: Suita

first: Ayumu

last: Asai

address: 2-2 Yamadaoka

institute: Osaka University

summary: To confirme the difference of target supression effect, we transfected non-methylated micro RNA or methylated microRNA in DICER knockout HCT116 cell.

overall_design: Microarray for DICER knockout HCT116 cell which were transfected non-methylated micro RNA (miR200c) or methylated microRNA (5mC containing miR200c, m6A containing miR 200c)

first: Masamitsu

last: Konno

first: Jun

last: Koseki

first: Hideshi

last: Ishii


title: Deletion of Lats 1 and 2 in mouse pancreatic acinar cells

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Mice with adult pancreatic acinar cell–specific deletion of Lats1&2 genes by using CreER/LoxP were generated. Pancreata were collected and profiled using RNA-seq. The RNA-sequencing data identified upregulation of pro-inflammatory and pro-fibrotic genes in Lats1&2 null pancreata, which may play important roles in stimulating PSC activation and promoting pancreatic fibrosis.

overall_design: 6-12 week old mice with Lats 1 & 2 double knockout (PL) were used in the study

first: Ming

last: Gao

last: Liu

first: Michael

last: Nipper

first: Pei

last: Wang


title: Molecular and immunological interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild type infection

city: Irvine

first: Arlo

middle: Zan

last: Randall

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

summary: Enterotoxigenic Escherichia coli (ETEC) infections are a common cause of diarrheal illness in low- and middle-income countries. The live-attenuated ACE527 vaccine, adjuvanted with double mutant LT (dmLT), affords clear but partial protection against ETEC challenge inhuman volunteers. Comparatively, initial wild-type ETEC challenge completely protects against severe diarrhea on homologous re-challenge...To investigate molecular determinants of protection, vaccine antigen content was compared to wild-type ETEC, and proteome microarrays were used to assess immune responses following vaccination and ETEC challenge... Although molecular interrogation of the vaccine confirmed expression of targeted canonical antigens, relative to wild-type ETEC, vaccine strains were deficient in production of flagellar antigens, immotile, and lacked production of the EtpA adhesin. Similarly, vaccination ± dmLT elicited responses to targeted canonical antigens, but relative to wild-type challenge, vaccine responses to some potentially protective non-canonical antigens including EtpA were diminished or absent...These studies highlight important differences in vaccine and wild-type ETEC antigen content and call attention to distinct immunologic signatures that could inform investigation of correlates of protection, and guide vaccine antigen selection for these pathogens of global importance.

overall_design: A total of 250 ALS samples were analyzed from 36 subjects: 10 placebo, 13 ACE527 vaccinated, and 13 ACE527+dmLT vaccinated. The vaccine was administered at days 0, 28, and 56. Thirty four of the subjects have 7 samples taken at days 0, 7, 28, 35, 56, and 63 with respect to the first vaccination and another sample taken 7 days after challenge. The remaining two subjects are missing one sample day each.

first: Subhra

last: Chakraborty

first: Tim

last: Vickers

first: Doug

last: Molina

first: Clayton

last: Harro

first: Barbara

last: DeNearing

first: Jessica

last: Brubaker

first: David

middle: A

last: Sack

first: A

last: Bourgeois

first: Philip

last: Felgner

first: Xiaowu

last: Liang

first: Sachin

last: Mani

first: Heather

last: Wenzel

first: R

last: Townsend

first: Petra

last: Gilmore

last: Darsley

last: Rasko

first: James

last: Fleckenstein


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 7]

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

summary: In this study, we generated genome-wide data sets for four histone modifications, including  H3K9ac, H3K27ac, RNA pol II, H3K9me3, which were collected from MDBK cell line before and after (24h) Butyrate treatment. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: The MDBK cell line was purchased from ATCC (ATCC CCL-22; Manassas, VA, USA) and grown in Eagle’s essential medium with 5% fetal bovine serum. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. ChIP-seq of MDBK cells were performed as reported in our earlier publication. In short, DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt single end reads, using an Illumina HiSeq 2500 platform.

first: Lingzhao

last: Fang

first: Congjun

last: Li


title: Gene expression analysis of R1 mESCs stably expressing WT ESRRB and Ser 25A (the O-GlcNAc residue mutant) ESRRB

status: Public on Jul 27 2019

city: Beijing

first: Xing

last: Chen

address: Yiheyuan Road

department: Chemical Biology

institute: Peking University

summary: Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling.  As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per O-acetylated, which, however, can induce a long-overlooked side reaction, non enzymatic S-glycosylation.  Herein, we develop 1,3-di-esterified N azidoacetylgalactosamine (GalNAz) as the next generation chemical reporters for metabolic glycan labeling.  Both 1,3-di-O-acetylated GalNAz (1,3-Ac2GalNAz) and 1,3-di-O propionylated GalNAz (1,3-Pr2GalNAz) exhibited high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation.  Applying 1,3-Pr2GalNAz in mouse embryonic stem cells (mESCs), we identified ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein.  We showed that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency.  Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase (OGT) at serine 25 (Ser 25), which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

overall_design: Three biological replicates of R1 embryonic stem cells stably expressing WT ESRRB and Ser 25A ESRRB were analysed.

first: Che

last: Zhang

first: Yi

last: Hao


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 4]

summary: In this study, we generated CTCF and four  histone modifications, including  H3K27ac, H3K27m3, H3K4m1, H3K4m3, which were collected from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing RNA polymerase II, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24 hrs.  CTCF-seq and ChIP-Seq of H3K27ac, H3K27m3, H3K4m1, H3K4m3, of rumen primary epithelial cells (RPEC) were performed at Active Motif according to proprietary methods. For ChIP-seq, CTCF-seq, the 75-nt single end reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA).


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 3]

summary: In this study, we generated four ATAC-seq data that were colloced from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA methylation and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24 hrs.  ATAC-seq of rumen primary epithelial cells (RPEC) were performed at Active Motif, Inc. (Carlsbad, CA, USA) according to proprietary methods. The paired-end 42-nt sequencing reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA).


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 6]

summary: In this study, we generated genome-wide data sets for four histone modifications, including  H3K9ac, H3K27ac, RNA pol II, H3K9me3,, which were collected from rumen tissues before and after Butyrate treatment. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen tissues were collected before and after 24-h butyrate treatment. DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt single end reads, using an Illumina HiSeq 2500 platform.


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation  [dataset 2]

type: Methylation profiling by high throughput sequencing

summary: In this study, we generated six whole-genome bisufite sequencing (WGBS) data that were colloced from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. Briefly, DNA from REPC culture was isolated by phenol/chloroform extraction. DNA (100 ng) was bisulfite-converted and subjected to library preparation using the Pico Methyl-Seq™ Library Prep Kit (Zymo) following the instructions of the supplier. High-Sensitivity DNA chips were used to assess libraries for quality on the Agilent Bioanalyzer and quantified with Qubit fluorometer. Libraries were sequenced on an Illumina HiSeq2500 (150-bp paired-end sequencing).


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation

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

overall_design: Refer to individual Series


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 1]

summary: In this study, we generated six RNA-seq data that were collected from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and DNA methylation, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24 hrs.RNA extraction was following the procedure reported previously 54. Total RNA from 6 rumen epithelial cell samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).


title: Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 5]

summary: In this study, we generated genome-wide data sets for four histone modifications, including H3K9ac, H3K27ac, RNA pol II, H3K9me3, which were collected from rumen tissues before and after weaning. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

overall_design: Rumen tissues were collected from Holstein calves before and after weaning. DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt single end reads, using an Illumina HiSeq 2500 platform.


title: Estrogen receptor-depended gene signatures in the mouse mammary gland after acute estradiol treatment (RNA-Seq)

status: Public on Jul 23 2019

city: Houston

first: MURUGESAN

last: PALANIAPPAN

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Estrogen receptor α (ERα) is the major driving transcription factor in normal mammary gland development as well as breast cancer initiation and progression.However,the fundamental mechanisms,including global cistromic and genomic transcriptional responses that are required to elicit mammary epithelial cell proliferation in response to estradiol, have not been elucidated.
We used RNA-seq analysis to identify global gene expression signatures that are acutely regulated by estroegn receptors in the mouse mammary gland after acute estradiol treatment.

overall_design: Mammary gland gene expression data from 6-week-old ovariectomized wildtype mice treated subcutaneously with 17β-Estradiol for 2 hours . Two replicate pools were tested with five mice per pool.

first: Murugesan

last: Palaniappan

first: Sandra

middle: L

last: Grimm

first: Cristian

last: Coarfa

first: Orla

middle: M

last: Conneely


title: Estrogen receptor-depended gene signatures and ER  binding sites in the mouse mammary gland after acute estradiol treatment


title: Transcriptomic analysis of CD44+CD62L- CD8+ T cells purified from tumors and lymph nodes (LN) of whole-body irradiated or unirradiated MC38 tumor-bearing mice, by microarray

city: Chicago

first: Ainhoa

last: Arina

state: Illinois

department: Radiation and Cellular Oncology

institute: The University of Chicago

summary: In the present manuscript we show that T cells within tumors are highly radio-resistant compared to T cells in lymphoid organs. To better understand this different response to ionizing radiation (IR), gene expression is compared for T cells from lymph nodes and those from transplantable MC38 tumors, in mice treated or not with whole body irradiation. We find that T cells from tumors and lymph nodes respond similarly to IR in terms of gene expression, and this response is dominated by p53 signaling. In contrast, gene expression at baseline (i.e. in the absence of radiation) shows profound differences between T cells from tumors and T cells from lymph nodes, and suggests transcriptomic reprogramming of the intratumoral T cells in the tumor microenvironment .

overall_design: CD44+CD62L- CD8+ T cells were FACS-sorted from tumors and lymph nodes of four whole-body irradiated (5 Gy) MC38-bearing C57BL/6 mice 5h after IR, and four non-irradiated mice. Cells from the different mice were pooled, for a total of four samples per experiment (Tumor-Nor IR, Tumor-IR, LN-No IR, LN-IR).  Two independent experiments were performed. Gene expression was analyzed using Affymetrix Mouse 430 2.0 microarray.

first: Michael

last: Beckett

first: Christian

last: Fernandez

first: Wenxin

last: Zheng

first: Sean

last: Pitroda

first: Steven

last: Chmura

first: Jason

last: Luke

first: Martin

last: Forde

first: Yuzhu

last: Hou

first: Byron

last: Burnette

first: Helena

last: Mauceri

first: Israel

last: Lowy

first: Tasha

last: Sims

first: Nikolai

last: Khodarev

first: Yang-Xin

last: Fu

first: Ralph

last: Weichselbaum


title: Transcriptome-wide expression analyses of HCT116 cell line under 5 conditions

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Selective regulation of target genes by transcription factors is fundamental to cell-fate determination. The tumour suppressor p53, encoded by the most frequently mutated gene in human cancer, selectively regulates subsets of target genes in response to different cues. It remains poorly understood at the genomic level and structurally how p53 target selectivity is determined by cellular factors. Here we combine transcriptomic, chromatin binding and crystallographic studies to show that p53’s genome-wide discrimination between different sets of targets is influenced by its partner iASPP.

overall_design: Construct transcriptome-wide expression profiles of HCT116 cell line under 5 conditions

first: Yunhao

last: Wang

first: Jiale

last: Wu

first: Yuntong

last: Li

first: Shuo

last: Chen

first: Min

last: Lu

first: Kin

middle: F


title: hCINAP regulates the DNA damage response and mediates the resistance of acute myelocytic leukemia cells to therapy

status: Public on Jul 22 2019

first: Ruidan

last: Xu

address: Haidian district

summary: Through RNA-seq of wildtype and hCINAP-deleted U2OS cells and whole genome bisulfite sequencing of the two U2OS cells, we show here that hCINAP is responsible for genomic stability and DNA damage response. Deletion of hCINAP directly decreased genomic stability and caused drug sensitivity. Also, when hCINAP is deleted, many genes are upregulated. These genes are involved in aging, DNA damage response and leukemia. In our wet lab experiment results, knockdown of hCINAP sensitizes a patient-derived xenograft (PDX) mouse model to chemotherapy. In clinical AML samples, low hCINAP expression is associated with a higher overall survival rate in patients. These results provide mechanistic insight into the function of hCINAP during the DNA damage response and its role in AML resistance to therapy. RNA-seq analysis was performed by ANNOROAD. Briefly, the total RNA from wild-type and knockout hCINAP U2OS cells was extracted, and sequences were performed with Illumina Solexa Ultrasequencing.

first: Shuyu

last: Yu


title: Expression data from IL-25 treated hepatocytes isolated from wild-type(WT) or Tpl2-deficient(KO) mice

first: Tao

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of Science

summary: We conducted gene expression profile analysis by using WT and Tpl2-deficient hepatocytes with IL-25 treatment.

overall_design: Genome-wide expression profiling of wild-type and Tpl2-deficient hepatocytes stimulated for 8 h with IL-25 were generated by RNA-sequencing analysis

first: Yichuan

last: Xiao

first: Xu

last: Jing


title: Finding new proteins encoded by long non-coding RNAs in human cells

status: Public on Jul 20 2019

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: We performed ribosome profiling to assess the translation elongation on translating RNA in HBE, A549, and H1299. We detected the new proteins in the cells.

overall_design: HBE, A549 and H1299 cells were cultured in the complete DMEM medium. We detected and analyzed the new proteins with ribosome profiling.

first: Xinlei

last: Lian


title: The Genomic Landscape of Estrogen Receptor α Binding Sites in Mouse Mammary Gland

first: MURUGESAN

last: PALANIAPPAN

summary:
Estrogen receptor α (ERα) is the major driving transcription factor in normal mammary gland development as well as breast cancer initiation and progression.However,the fundamental mechanisms,including global cistromic and genomic transcriptional
responses that are required to elicit mammary epithelial cell proliferation in response to ERα, have not been elucidated.
We used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to identify estrogen regulated genes that directly recruit ERα in the WT mouse mammary gland

overall_design: Two replicate ERα ChIP samples and one input DNA samples from 6weeks old WTmouse mammary glands after mice are treated subcutaneously with 17β Estradiol for 2 hours.

first: Murugesan

last: Palaniappan

first: Sandra

last: Grimm

first: Cristian

last: Coarfa

first: Orla

last: Conneely


title: Genome-wide gene-expression profile of mouse intestinal stem cells/progenitors/Paneth cells

status: Public on Jul 19 2019

city: Cambridge

first: Chia-Wei

last: Cheng

state: MA

address: 500 Main St

institute: Koch Institute at MIT

summary: The goal of this project is to generate transcriptome profiling of Lgr5-GFP high intestinal stem cells (High)/Lgr5-GFP low progenitors (Low) and CD24+C-kit+ Paneth (PA) cells for a systemic analysis of cellular pathways involved in responses to fasting and aging.

overall_design:
Intestinal crypt cells were isolated from mice fed ad libitum or fasted for 24 hours, at young and old ages. The goal is to compare the differential responses of three cell types to fed/fasiting states under the effects of aging.
Please note that the original RNA-Seq libraries were sequenced three times,  the first run was submitted as mm9-mapped bam files  and the other two runs are provided as fastq files.  All analytical steps were performed against mm10.

first: O

last: Yilmaz

first: D

last: Sabatini


title: GREB1, a novel target of Wnt signaling, promotes development of hepatoblastoma by suppressing TGFβ signaling

status: Public on Jul 18 2019

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The β-catenin mutation is frequently observed in hepatoblastoma (HB), but the underlying mechanism by which Wnt/β-catenin signaling induces HB tumor formation is unknown. We found that expression of growth regulation by estrogen in breast cancer 1 (GREB1) depends on Wnt/β-catenin signaling in HB patients. GREB1 was localized to the nucleus where it bound Smad2/3 in a competitive manner with p300 and inhibited TGFβ signaling, thereby promoting HepG2 HB cell proliferation. Forced expression of β-catenin, YAP, and c-Met induced HB-like mouse liver tumor (BYM mice), with an increase in GREB1 expression and HB markers. Depletion of GREB1 strongly suppressed marker gene expression and HB-like liver tumorigenesis, and instead enhanced TGFβ signaling in BYM mice. Furthermore, antisense oligonucleotides for GREB1 suppressed the formation of HepG2 cell-induced tumors and HB-like tumors in vivo. We propose that GREB1 is a novel target molecule of Wnt/β-catenin signaling and required for HB progression.

overall_design: RNA-sequencing analyses were performed in HepG2 cells transfected with control or β-catenin siRNA in triplicates.

first: Shinji

last: Matsumoto

first: Akira

last: Kikuchi


title: Transcriptomic characterization of CRISPR/Cas9-edited THP1 cells to test the effect of disrupting the 3q23 genomic region containing TB-risk associated variants marking a putative  monocyte-specific enhancer

city: Boston

first: Yang

last: Luo

state: Massachusetts

address: 77 avenue louis pasteur, room 255

institute: Harvard Medical School

summary: We applied CRISPR/Cas9 technology to introduce insertions/deletions around the top associated variant rs73226617. Among 23 single-cell sorted and expanded clones that had unchanged 3q23 genomic region with the risk locus (i.e. wildtype), or harbored unique edits and deletions around rs73226617.

overall_design: Low input RNA-seq was performed on all 23 sorted and grown THP1 clonal cell lines that had unchanged 3q23 genomic region with the TB-risk variants or harbored unique edits and deletions

first: Sara

last: Suliman

middle: B

last: Moody

first: Soumya

last: Raychaudhuri


title: Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3

status: Public on Jul 17 2019

first: Armand

last: Bankhead

address: 1415 Washington Heights

department: Biostatistics

summary: Inhibiting STAT3 signaling reduces tumor progression, metastases and chemoresistance, however the precise molecular mechanism has not been fully delineated in ovarian cancer.  Methods: In this study, we generated STAT3 knockout (KO) ovarian cancer cell lines. Effect of STAT3 KO on cell proliferation, migration and spheroid formation was assessed in vitro and effect on in vivo tumor growth was tested using several tumor xenograft models. We used multi-omic genome-wide profiling to identify multi-level (Bru-Seq, RNA-Seq, and MS Proteomic) expression signatures of STAT3 KO ovarian cancer cells.

overall_design:
Cells were lysed with TRIzol® Reagent (ThermoFisher Scientific) at room temperature. RNA was further purified with DirectZol kit (Zymo Research, Irvine, CA). RNA quality was assessed using the TapeStation (Agilent Technologies, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared with TruSeq Stranded mRNA Library Prep (Illumina) per the supplier’s protocol with 1g of RNA and 12 cycles of PCR amplification. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (Illumina). The libraries were barcoded, pooled and sequenced on the HiSeq 4000 at the University of Michigan DNA Sequencing Core using 50bp single-end 50bp (OVCAR3 and OVCAR8) and paired-end 50bp (SKOV3) sequencing. Reads were mapped to GRCh38 using STAR v2.5.2 [69] and gene quantifications were calculated using Cufflinks v2.2.1 [70] to quantify refGene annotations. Gene read counts calculated using featureCounts [71] v1.6.1 were used to evaluate differential expression using DESeq2 v1.18.1 [72]. For OVCAR3 and OVCAR8, genes were considered significantly differentially expressed with a mean FPKM > 0.5 and absolute fold change > 1.5 and FDR adjusted p-value < 0.05. For SKOV3, genes were considered significantly differentially expressed with mean FPKM > 0.5 and absolute log2 fold change > 1.5 and FDR adjusted p-value < 0.05. All gene readouts where required to be mappable to both an HGNC and Entrez identifier to be considered for gene set enrichment analyses.
Please note: Majority of paper figures are based on OVCAR3=OV3,OVCAR8=OV8, and SKOV3 with CAS9 control.

first: Nouri

last: Neamati

first: Tiangong

last: Lu


title: siRNA in cer7, rst1 and ripr mutants

city: Strasbourg

first: Heike

last: Lange

address: 12 Rue de général Zimmer

department: IBMP

country: France

institute: CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: identify and compare siRNAs in wildtype and mutants of the RNA exosome

overall_design: small RNA libraries prepared from wildtype + six mutants, three biological replicates each

first: Dominique

last: Gagliardi


title: Expression profiles of mouse skeletal muscle tissues, mouse skeletal muscle from Aged animals with high fat diet and chemical treatment

status: Public on Jul 16 2019

first: Youqiong

last: Ye

address: 280 Chongqing south road

overall_design: Expression profiles were generated from mouse skeletal muscle tissues, which isolated from 24-26 month old male C57BL/6 mice. Mice were purchased from NIA at the age of 21-22 month old and treated with high fat diet with or without 0.1 % Nobiletin compound.

first: Kazunari

last: Nohara


title: Natural killer cells suppress T cell tumor immune evasion [B16-F10 CRISPR/Cas9 NK cell screen]

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

summary: Investigation of tumor genes which limit sensitivity to killing by NK cells through a genome-wide in vitro CRISPR/Cas9 screen

overall_design: B16-F10 Cas9 expressing cells transduced with a genome-wide CRISPR library were successively co-cultured overnight with activated NK cells at an equal ratio. Experiment was performed in technical duplicate. An untreated control cultured alongside was used for comparison

first: Andrew

last: Freeman

first: Conor

last: Kearney

first: Jane

last: Oliaro


title: Natural killer cells suppress T cell tumor immune evasion [Supernatant treated control or Jak1 sgRNA B16-F10 RNA Seq]

summary: Investigation of the transcriptional response in Jak1 depleted tumor cells upon NK-derived cytokine presence using 3’ RNA sequencing

overall_design: Control or Jak1 sgRNA B16-F10 tumor cells were treated for 7 hours with supernatant derived from a separate WT B16-F10/NK co-culture. Experiment was performed in technical triplicate. Cells treated with IFN-γ were used as a positive control and cells treated with TNF were used as a negative control


title: Natural killer cells suppress T cell tumor immune evasion [B16-F10 CRISPR/Cas9 MHC I low]

summary: Investigation of tumor genes which are involved in the upregulation of MHC I expression through a genome-wide in vitro CRISPR/Cas9 screen

overall_design: B16-F10 Cas9 expressing cells transduced with a genome-wide CRISPR library were successively treated overnight with IFN-γ and FACS sorted for cells that failed to upregulate MHC I expression. An untreated population of transduced cells frozen after puromycin selection were used for comparison


title: Long-term persistent infection with equine arteritis virus is associated with the upregulation of specific CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis in the ampullae of the stallion reproductive tract

city: Lexington

first: Udeni

middle: B. R.

last: Balasuriya

state: KY

address: 108 Maxwell H. Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary: We performed whole transcriptome analysis of the ampullae, the primary site of EAV persistence, derived from long-term carrier stallions to understand the molecular signature of persistent infection. We demonstrated that long-term persistence is characterized by a local CD8+ T lymphocyte response predominantly driven by the transcription factors EOMES and NFATC2.We showed that EAV persistence is associated with an enhanced expression of CXCL16/CXCR6 in infiltrating lymphocytes. Furthermore, we established a link between the CXCL16 genotype and the gene expression profile at the site of persistence following EAV infection. Co-expression network analysis identified CXCL16 as a “hub” gene, likely driving a specific transcriptional network.

overall_design: We have perfomed whole transcriptome sequencing (RNAseq) on 12 ampulla samples derived from naïve stallions (n=3), short-term equine arteritis virus carrier (n=6) and long-term equine arteritis virus carrier stallions (n=3). Findings were further confirmed by RT-qPCR and other experiments were performed to characterize the inflammatory response and the involvement of the chemokine CXCL16 and its receptor CXCR6. Gene expression was also analyzed based on the CXCL16 genotype (CXCL16S or CXCL16R).

first: Mariano

last: Carossino

first: Pouya

last: Dini

first: Theodore

middle: S

last: Kalbfleisch

first: Alan

middle: T

last: Loynachan

first: Igor

last: Canisso

first: R

last: Cook

first: Ernest

last: Bailey

first: Peter

last: Timoney


title: Natural killer cells suppress T cell tumor immune evasion [NK treated B16-F10 RNA Seq]

summary: Investigation of the tumor transcriptional response upon NK cell attack using 3’ RNA sequencing

overall_design: B16-F10 cells were left untreated or co-cultured with activated murine NK cells for 7 hours. Experiment was performed in technical triplicate


title: The Developmental Heterogeneity of Human Natural Killer Cells Defined by Single-cell Transcriptome

status: Public on Jul 15 2019

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

summary: The heterogeneity of human NK cells has not been fully-defined. Using single-cell RNA-sequencing technology, we find more human NK subsets than previously defined by cell surface markers. The transcriptome-based pseudotime analysis support that CD56bright NK cells are precursors of CD56dim NK cells with identification of a transitional stage. Our data significantly expand our understanding of the heterogeneity and development of human NK cells.

overall_design: Single-cell RNA-sequencing analysis of NK cells from bone marrow of six healthy donors, blood of two healthy donors and a blood sample from a donor with GATA2T354M mutation

first: Chao

last: Yang

first: Jason

last: Siebert

first: Robert

last: Burns

first: Zachary

last: Gerbec

first: Benedetta

last: Bonacci

first: Amy

last: Rymaszewski

first: Mary

last: Rau

first: Matthew

last: Riese

first: Sridhar

last: Rao

first: Karen-Sue

last: Carlson

first: John

last: Routes

first: James

middle: W

last: Verbsky

first: Monica

last: Thakar


title: Natural killer cells suppress T cell tumor immune evasion

first: Madison

last: Kelly

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

overall_design: Refer to individual Series


title: EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (ChIP-Seq)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: We identified a novel cofactor of PRC2, expresesd predominantly in the gonad, that lmits PRC2 enzymatic activity by impeding the interaction between the core complex and its accessory subunits.

overall_design: We profiled the H3K27 histone mark in EED or CXORF67 mutants and WT in ipNF05.5 cells.

first: R

last: Raggazini

last: Pérez-Palacios

first: HI

last: Baymaz

first: D

last: Zielinski

first: A

last: Michaud

first: M

last: Givelet

last: Borsos

first: P

middle: C

last: Jansen

first: N

last: Torres-Padilla

last: Bourc'his

last: Fouchet

last: Vermeulen

first: Raphaël

last: Margueron


title: EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (RNA-Seq)

summary: We identified a novel cofactor of PRC2, expressed predominantly in the gonad, that limits PRC2 enzymatic activity by impeding the interaction between the core complex and the accessory subunits.

overall_design: We characterized gene expression changes upon CXORF67 deletion in murine spermatogonia and oocytes.


title: The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

summary: N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5-TRMT112, supporting that its RNA binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5-TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.

overall_design: Single-nucleotide resolution m6A mapping (miCLIP) was performed on wild-type, ZCCHC4, and METTL5 knockout HCT116 cells to identify any ZCCHC4- or METTL5-dependent methylation events.

middle: V

last: Tran

first: F

last: Ernst

first: Ben

middle: R

last: Hawley

first: C

last: Zorbas

last: Ulryck

last: Hackert

first: K

last: Bohnsack

last: Graille

first: Denis

last: LaFontaine


title: SOX11 and SOX4 drive the reactivation of an embryonic gene program during wound repair

status: Public on Jul 13 2019

first: Matthew

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Tissue injury induces changes in cellular identity, but the underlying molecular mechanisms remain obscure. Here, we show that upon damage, epidermal cells at the wound edge convert to an embryonic-like state, altering particularly the cytoskeletal/extracellular matrix (ECM) components and differentiation program. We show that SOX11 and its closest relative SOX4 dictate embryonic epidermal state, regulating genes involved in epidermal development as well as cytoskeletal/ECM organization. Correspondingly, postnatal induction of Sox11 represses epidermal terminal differentiation while deficiency of Sox11 and Sox4 accelerates differentiation and dramatically impairs cell motility and re-epithelialization. Amongst the embryonic genes reactivated at the wound edge, we identify fascin actin-bundling protein 1 (FSCN1) as a critical direct target of SOX11 and SOX4 regulating cell migration. Our study identifies the reactivated embryonic gene program during wound repair and demonstrates that SOX11 and SOX4 play a key part in this process

overall_design:
ChIP-seq analysis of Sox11 and Sox4 in primary murine keratinocytes

Please note that each processed data was generated from both rep1 and rep2 samples, and linked to the corresponding rep1 sample.

first: Qi

last: Miao

first: Hoang

last: Nguyen


title: Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer’s disease model

status: Public on Jul 12 2019

first: Kim

last: Green

state: CA

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: This dataset allows for the exploration of microglial function on gene expression in wild-type and the 5xFAD mouse model of Alzheimer's disease, across multiple brain regions. Mice were treated with the selective CSF1R inhibitor PLX5622, which eliminates >95% of microglia in less than 5 days, from 1.5 to 7 months of age. Thus, these data  allow the exploration of the effects, and specificity, of 6 months microglial depletion, in both wild-type and 5xFAD mice.

overall_design: 5xFAD and Wild-type mice treated with vehicle or PLX5622 (1200 ppm in chow), to deplete all microglia, from 1.5 to 7 months of age. Brains microdissected into cortex, hippocampus, and thalamus+striatum. 4 mice/group

first: Paul

last: Severson


title: PPM1D Mutations Silence NAPRT Gene Expression and Confer NAMPT Inhibitor Sensitivity in Glioma

city: New Haven

first: Ranjit

last: Bindra

state: CT

address: 15 York Street Hunter Building (HRT) 313C

department: Therapeutic Radiology

institute: Yale University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of wild type and PPM1D mutant astrocytes and patient-derived DIPG cell lines. The Illumina Human EPIC Bead Array (850k) platform was used to obtain methylation beta values of over 850k CpG sites throughout the genome across a panel of DIPG cell lines.

overall_design: 50-500ng of genomic DNA was bisulfite-converted and analyzed for genome-wide methylation patterns using the Illumina Human EPIC Bead Array (850k) platform at the Yale Center for Genome Analysis (Astrocyte and SU-DIPG lines) or University College London Genomics Centre (HSJD DIPG lines), according the manufacturer’s instructions.

first: Nathan

last: Fons


title: MicroRNA profiling during neural differentiation of induced pluripotent stem cells

status: Public on Jul 11 2019

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: MicroRNAs (miRNA) play an essential role in the regulation of gene expression, influence signaling networks responsible for several cellular processes like differentiation of pluripotent stem cells. Despite several studies on the neurogenesis process, no global analysis of microRNA expression during differentiation of induced pluripotent stem cells (iPSC) to neuronal stem cells (NSC) has been done. Therefore we compared the profile of microRNA expression in iPSC lines and in NSC lines derived from them, using microarray-based analysis. Two different protocols for NSC formation were used: direct and two-step via neural rosette formation. We confirmed the new associations of previously described miRNAs in regulation of NSC differentiation from iPSC. We discovered upregulation of miR-10 family, miR-30 family and miR-9 family  and downregulation of miR-302 and miR-515 family. Moreover we showed that miR-10 family play a crucial role in the negative regulation of genes expression belonging to signaling pathways involved in neural differentiation: WNT signaling pathway, focal adhesion, signaling pathways regulating pluripotency of stem cells.

overall_design: We conducted differentiation of human induced pluripotent stem cells into neural stem cells. Then we carried out global miRNA expression analysis using the Affymetrix platform. We profiled the miRNAs which are crucial regulators of neural differentiation. We not only confirmed the involvement of previously described miRNAs characteristic for transition from ES to NSC: mir-302 family, hsa-miR-125b, hsa-miR-9, let-7, but we also pointed out others, which may be characteristic for iPSC to NSC transition.

first: Katarzyna

last: Kulcenty

first: Joanna

middle: P

last: Wroblewska

first: Emilia

last: Kozlowska

first: Karol

last: Jopek

first: Wiktoria

last: Suchorska


title: Circadian regulation of lung inflammation

city: Philadelphia

first: Shaon

last: Sengupta

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Endogenous circadian rhythms regulate the hosts response to influenza infection, more through the host tolerance pathways rater than direct effects on anti-viral resistance.

overall_design: comparing control vs influenza infected animals (lung) at ZT23 (am) and ZT11 (pm) (two time points of the day 12hrs apart)

first: Soon

middle: Y

last: Tang

first: Jill

last: Devine

first: Soumyashant

last: Nayak

first: Shirley

last: Zhang

first: Emmanuelle

last: Genoyer

first: Alex

last: Valenzuela

first: Carolina

last: Lopez

first: Gregory

last: Grant

first: Garret

last: FitzGerald


title: Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance

city: South San Francisco

first: Linda

last: Fong

state: California

address: 1170 Veterans Blvd

department: Oncology

institute: Calico Labs

summary: RNA-seq analysis of the transcriptome of K562 cells in which PTPN2 or DCAF15 had been disrupted by CRISPR/cas9 gene editing.

overall_design: K562 cells expressing cas9 were infected with lentiviruses expressing sgRNAs against a control gene, PTPN2 or DCAF15. Two weeks after sgRNA infection cells were plated at 0.33M cells/ml and either left alone or treated with 10ng/ml IFNg for 24hrs

first: Matthew

last: Pech

first: Jeff

last: Settleman


title: Dual RNAseq of pneumococcal infection

city: Glasgow

first: Tom

middle: John

last: Evans

state: Glasgow

address: 120 University Avenue

department: Infection, Immunity and Inflammation

institute: University of Glasgow

summary: Streptococcus pneumoniae is the dominant cause of community-acquired pneumonia world-wide. Invasion of the pleural space is common and results in increased mortality. We set out to determine the bacterial and host factors that influence invasion of the pleural space. In a murine model of pneumococcal infection, we isolated neutrophil-dominated samples of bronchoalveolar and pleural fluid containing bacteria 48 hours after infection. Using dual RNA-seq, we characterised bacterial and host transcripts that were differentially regulated between these compartments and bacteria in broth and resting neutrophils respectively. Pleural and lung samples showed upregulation of genes involved in positive regulation of neutrophil extravasation but down-regulation of genes mediating bacterial killing. Compared to the lung samples, cells within the pleural space showed marked upregulation of many genes induced by type I interferons, cytokines implicated in preventing bacterial transmigration across epithelial barriers. Differences in the bacterial transcripts between the infected samples and bacteria grown in broth showed upregulation of genes in the bacteriocin locus, the pneumococcal surface adhesin PsaA, and the glycopeptide resistance gene, vanZ; the gene encoding the ClpP protease was downregulated in infection. 169 intergenic putative small bacterial RNAs were also identified, of which 43 (25.4%) had been previously described. 42 of the small RNAs were upregulated in pleura compared to broth,  including many previously identified as important in virulence. Our results  have identified key host and bacterial responses to invasion of the pleural space that can be potentially exploited to develop alternative antimicrobial strategies for prevention and treatment of pneumococcal pleural disease.

sample_organism:
Streptococcus pneumoniae
Mus musculus

platform_organism:
Streptococcus pneumoniae
Mus musculus

overall_design: Comparison of trasncripts from broth, BALF and pleura, 3 replicates each

first: T

middle: J

first: N

last: Ritchie


title: Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

summary: Resistant tumours are thought to arise from the action of Darwinian selection on intratumoral genetic heterogeneity. However, clonal selection is incompatible with the late recurrence often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare sub-population of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. PA cells show reduced oestrogen receptor α activity but increased features of quiescence and migration. We find evidence for sub-clonal expression of this PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.

overall_design: Single-cell RNA-seq libraries from cell lines or FACS-sorted subpopulations, generated using 10x Chromium and subjected to high-throughput sequencing.

first: I

first: S

last: Hong

first: L

last: Magnani


title: Binding of SU(VAR)3-9 partially depends on SETDB1 in the chromosomes of Drosophila melanogaster

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: Histone modifications are a class of epigenetic marks with prominent roles in gene regulation in eukaryotes. One such mark, predominantly inactivation-related, is methylation of histone H3 lysine 9 (H3K9). In the present study, we decipher the interplay between two evolutionary conserved Drosophila H3K9-specific histone methyltransferases, SU(VAR)3-9 and SETDB1. We asked whether SETDB1 is required for targeting of SU(VAR)3-9. Using DamID-seq, we obtained SU(VAR)3-9 binding profiles for the chromosomes from larval salivary glands and germline cells from adult females, and compared profiles between the wild type and SETDB1-mutant backgrounds. Our analyses indicate that the vast majority of single-copy genes in euchromatin are targeted by SU(VAR)3-9 only in the presence of SETDB1, whereas repeated sequences in heterochromatin is largely SETDB1-independent. Interestingly, piRNA clusters 42AB and 38C behave differently in terms of SU(VAR)3-9 binding in somatic and germline cells. Namely, SU(VAR)3-9 binding to these piRNA clusters is independent of SETDB1 in somatic cells, whereas it is SETDB1-dependent in the germline. In addition, we compared SU(VAR)3-9 profiles in female germline cells at different developmental stages (whole juvenile ovaries and mature nurse cells). It turned out that SU(VAR)3-9 binding is influenced both by the presence of SETDB1, as well as by the differentiation stage.

overall_design: Examination of Su(var)3-9 protein binding on chromosomes of juvenile ovaries in presence or absence of SET-DB1 mutation using DamID technique.

middle: A

first: Dmitry

middle: E

last: Koryakov


title: H3K36me3 ChIP-seq of 2 rice lines D248 and SH881

status: Public on Jul 10 2019

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: A major maturity duration-regulatory gene, Early flowering-completely dominant (Ef-cd) was cloning in this study. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition.

overall_design: Fresh leaf blades of 40 d seedlings of early-maturing NIL D248 (BC5F11) and its recurrent parent SH881 (Shuhui881) were harvested for fixation and immunoprecipitation.

first: Jun

last: Fang

first: Fantao

first: Fei

last: Zhao

first: Zijuan

last: Li

first: Xiaojian

last: Deng

first: Chengcai

last: Chu


title: Accurate detection of m6A RNA modifications in native RNA sequences [Curlcake constructs]

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

institute: Center for Genomic Regulation

summary: The field of epitranscriptomics has experienced a major revolution in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using the platform offered by Oxford Nanopore Technologies, we can detect N6-methyladenosine (m6A) RNA modifications with high accuracy. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide, single molecule resolution.

overall_design: For synthesis purposes, a total of 4 sequences were designed by splitting the 10kb sequence into smaller sequences of slightly different size (2329bp, 2543bp, 2678bp and 2795bp, which we named ‘Curlcake 1’, ‘Curlcake 2’, ‘Curlcake 3’ and ‘Curlcake 4’, respectively). These constructs were in-vitro transcribed either in the presence of ATP or N6-Methyladenosine-5'-Triphosphate  (m6ATP). Sequencing was performed with two replicates of two libraries containing non-modified RNAs in one flowcell and m6ATP-modified RNAs in the second flowcell, giving a total of 4 samples. The FASTA file for the sequences is provided as a supplementary file.

first: Eva

first: Huanle

last: Liu

first: Oguzhan

last: Begik


title: Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development

city: Missouri

first: Qiuming

last: Yao

address: Life Science Center

institute: University of Missouri

summary: Transcriptome profiling is performed to reveal how Brassinosteroids (BRs) play a crucial role for plant vegetative growth and reproductive development.

first: Li

last: Song


title: SETD5 is a H3K36 methyltransferase which preserves transcriptional fidelity during brain development and neuronal wiring [RNA-seq]

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento

summary: We assess the role of Setd5 on trancription elongation, by profiling nascent chromatin bound RNAs after DRB treatment an release, in wild type and Setd5 heterozygous mouse neural stem cells (NSCs).

overall_design: Chromatin-bound RNA sequencing in DRB treated and at 5, 10 and 20 minutes after DRB release in wild type and Setd5+/- NSCs.

first: Luca

last: Fagnocchi

first: Alessio


title: WBGS of WS, rdm1-3 and RDM1-FLAG-2 and RDM1-FLAG-16 transgenic lines

city: Haining

first: Wanlu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: We performed WGBS of two independent transgenic lines expressing RDM1-FLAG in rdm1 mutant background, as well as WS and rdm1-3 controls.

overall_design: 4 WGBS samples

first: Javier

last: Gallego-Bartolome


title: ChIP-seq of DRD1, DMS3 and RDM1 in Arabidopsis

status: Public on Jul 09 2019

city: Los Angeles

first: Steven E.

last: Jacobsen

address: 405 Hilgard Avenue

institute: UCLA

summary: We performed FLAG ChIP-seq of transgenic lines expressing FLAG-tagged DRD1, DMS3 and RDM1, as well as Col0 as negative control.

overall_design: Get ChIP-seq signal for each sample and compare to previously published Pol V ChIP-seq signal (Liu et al, 2018. Nature plants, Series GSE100010,Samples GSM2667837 and GSM2667838)

last: Gallego-Bartolomé


title: Priming mobilization of hair follicle stem cells triggers permanent loss of regeneration after alkylating chemotherapy

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

institute: Seoul National University College of Medicine

summary: The maintenance of genetic integrity is critical for stem cells to ensure homeostasis and regeneration. Little is known about how adult stem cells respond to irreversible DNA damage, resulting in loss of regeneration in humans. Here, we establish a permanent regeneration loss model using cycling human hair follicles treated with alkylating agents: busulfan followed by cyclophosphamide. We unravel the underlying mechanisms by which hair follicle stem cells (HFSCs) lose their pool. Contrary to immediate destructive changes in rapidly proliferating hair matrix cells, quiescent HFSCs show unexpected massive proliferation after busulfan and then undergo large-scale apoptosis following cyclophosphamide. HFSC proliferation is activated through PI3K/Akt pathway, and depletion is driven by p53/p38-induced cell death. RNA-seq analysis shows that HFSCs experience mitotic catastrophe with G2/M checkpoint activation. Our findings indicate that priming mobilization causes stem cells to lose their resistance to DNA damage, resulting in permanent loss of regeneration after alkylating chemotherapy.

overall_design: Global gene expression profiles of human hair follicle stem cells after alkylating chemotherapy were generated by paired-end sequencing with 100-base pair length on an Illumina HiSeq 2500 sequencer .

first: Jungyoon

last: Ohn

first: Sookyung

first: Woochan

last: Lee

first: Jong-Il

first: Ohsang

last: Kwon