title: Identifying salt stress-responsive miRNAs and their targets in soybean (microRNA)

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

summary: MicroRNAs (miRNAs) play an important role as regulators of gene expression. In plants they affect a wide variety of biological process like growth, development and response to biotic and abiotic stress. Glycine max is one of the most important crop worldwide due to its rich protein and oil content. Drought and salt stress are the main abiotic stresses that affect soybean. Salt stress impacts the fisiology of the plants due to the damage in the photosynthetic rate, growth and development. This work aim to identify salt-stress responsive miRNAs and their respective targets in Glycine max using high-throughput RNA sequencing technology.

overall_design: Soybean smallRNAs profiles in 8 different libraries from two tissues (root and leaves). Each library consist in a pool of three different plants treated with 200mM of NaCl or control. The libraries were contructed in duplicates.

last: da Fonseca

first: Luiz

middle: V

last: de Oliveira

middle: L

last: de Morais

first: Ricardo

last: Abdelnor

first: Alexandre

last: Nepomuceno

first: Rogério

middle: R

last: Margis


title: Identifying salt stress-responsive miRNAs and their targets in soybean

status: Public on Jul 11 2017

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and abi5 Transcriptomes

city: Beijing

first: chao

last: bi

address: Tsinghua University, Beijing

country: China

institute: Tsinghua University

summary: It has been known that ABA INSENSITIVE 5 (ABI5) plays a vital role in regulating seed germination. In the present experiment, we showed that 3-amino-1,2,4-triazole (3-AT) inhibits seed germination of the loss-of-function mutant abi5-1, but promotes seed germination of the ABI5-overexpression transgenic line, and that ABI5 affects reactive oxygen species (ROS) homeostasis. RNA-sequencing analysis indicates that the transcription of the genes involved in ROS metabolic process or genes responsive to ROS stress is impaired in abi5-1 seeds. Together, all the findings suggest that ABI5 regulates seed germination at least partly by affecting ROS homeostasis.

overall_design: For RNA sequencing (RNA-Seq) analysis, total RNA was isolated from imbibed seeds of wild type and abi5-1 plants. The control sample is the wild type. For each sample, at least three biological replicates were sequenced.

first: Xiaofang

last: Wang

first: Bi

last: Chao


title: A phospho-mimicking Atf1 mutant bypasses the transcription activating function of the MAP kinase Sty1

status: Public on Jul 10 2017

city: Barcelona

first: Elena

last: Hidalgo

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

summary: The MAP kinase Sty1 of fission yeast accumulates in the nucleus upon stress, and stimulates expression of hundreds of genes, including atf1, via the constitutively nuclear transcription factor Atf1. The role on transcription of the signal-dependent phosphorylation of Atf1 by Sty1 is unclear. We have expressed the transcription factor and mutant derivatives from a constitutive promoter, to unchain Atf1 activity from its protein levels. Expression of a non-phosphorylatable Atf1 renders cells sensitive to oxidative stress, due to the impaired transcription of a subset of genes, those dependent on another transcription factor, Pap1. Cells expressing a phospho-mimicking mutant display enhanced resistance to stress, and while expression of the Pap1-dependent genes is still stress-dependent, a second subset of genes is constitutively expressed. Our study demonstrates that phosphorylation of Atf1 by Sty1 does not stimulate binding of the transcription factor to DNA but rather establishes a platform of interaction with the transcriptional machinery.

overall_design: We report the differences in gene expression of cells expressing either phosphorylated or unphosphorylatable form of Atf1 in basal and after hydrogen peroxide stress.

first: Clàudia

last: Salat-Canela


title: Identifying salt stress-responsive miRNAs and their targets in soybean (mRNA)

overall_design: Four mRNAseq libraries from soybean leaves. Each library consist in a pool of three different plants treated with 200mM of NaCl or control. The libraries were contructed in duplicates.

middle: C


title: The single-base resolution DNA methylation profiles for four developmental stages of Tribolium castaneum

city: Nanjing

first: Bin

last: Li

address: Wenyuan road NO.1

department: School of Life Science

institute: Nanjing Normal university

type: Methylation profiling by high throughput sequencing

summary: Cytosine DNA methylation in the Tribolium castaneum has been controversial, its distribution pattern and functions have not been established yet. Here, using BS-Seq, we confirmed the existence of DNA methylation and described the methylation profiles for four life stages of T.castaneum. Interestingly, two types of DNA methylation had been discovered in T.castaneum genome. One was the symmetrical CpG methylation which was typically existed among eukaryotes methylomes, but occupied small part in methylome of T. castaneum. Another type was the non-CpG methylation which was uniquely and predominated in methylome of T. castaneum. While, the symmetrical CpG methylation which was catalyzed by the conserved DNA methyltransferase DNMT1 in T.castaneum mainly enriched in gene bodies and was positively correlated with the gene expression level. The asymmetrical nonCpG (most mCpA) methylation strongly concentrated in intergenic regions and introns while absent from the exons. Gene body methylation was negatively correlated with the gene expression level. The distribution pattern and functions of this type methylation only showed similarity with the methylome of Drosophila melanogaster, which further support that there existed a novel methyltransferase in these two specieces responsible for this methylation. The DNA methylome of T. castaneum possess two differential types and unique characterizations, which will contribute to our further understanding of the variety, origin and functions of DNA methylation in eukaryotes.

overall_design: Genomic DNA was extracted from a pool of 50 individuals for the four life stages of Tribolium castaneum: 3d embryo, late larva( ~20d larva ), 3d pupa and 3d adult, respectively, using the DNeasy Blood & Tissue Kit. The extracted DNA was then bisulfite converted and Illumina sequenced to obtain direct evidence for the presence of methylation in Tribolium castaneum. To reveal the relationship between the DNA methylation and gene expression, Total RNA was extracted from each sample by using the Invitrogen TRIzol® Reagent. RNA-seq technology was used to generate the gene expression files for the four sages fo Tribolium castaneum.

first: Xiaowen

last: Song

first: Fei

last: Huang


title: Comparison of small RNA profiling in sperm susceptible or not susceptible to epigenetic silencing of the LoxP site

city: Cambridge

first: Ilaria

last: Falciatori

address: Robinson Way

department: GH Lab

country: United Kingdom

institute: CRUK-CI

summary: During our attempt to engineer a conditional Kdm1a knockout using germline expressed Vasa-Cre transgene, we observed that the efficiency of LoxP recombination is dramatically reduced after the first recombination event occurs. This is due to a transvection event in which the recombination of one allele in one generation, blocks the recombination of the other allele in the following generation. Interestingly, this inhibition can be relieved by introducing an additional cross to a wildtype mouse between the first and the second Kdm1a recombination event. The recombination inhibition is therefore the result of epigenetic silencing that is erased once spermatogenesis is allowed to happen in the absence of Vasa-Cre. After excluding other possibilities,  we considered the hyphotesis that a diffusible molecule targeting the LoxP site that could be deposited in sperm following the first Cre recombination event (original cross). This molecule should not be present anymore when the sperm is collected after the additional cross to wildtype (extra cross). To test whether this diffusible molecule could be a small RNA, we produced and compared small RNA libraries prepared from sperm derived from the original cross and from the extra cross. These samples are genetically identical but differ in their parental history as well as in the ability to recombine the second floxed Kdm1a allele in the following generation. The comparison aimed at finding potential small RNAs mapping to or close to the loxP site present only, or more abundantly, in the original cross. Unfortunately, we were not able to identify such small RNAs and we also could not find any consistent difference in small RNA profiles among the different samples. We therefore concluded that the transvection event is not connected to a diffusible small RNA accumulated in sperm.

overall_design: Sperm was isolated from the cauda epidydimis and washed with PBS. Trizol was used to extract RNA from the sperm samples with slight modificatiosn retain small RNAs. Sperm from each mouse was processed separately and treated as a replicate. Two biological replicates per condition were produced. For each sample, 250-1500ng of RNA were used for size-selection on a polyacrylamide gel. After elution from the gel we proceeded to library preparation.

first: Gregory

middle: J

last: Hannon

first: David

last: Katz


title: PHF6 regulates B-cell identity in acute lymphoblastic leukemia [RNA-Seq]

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

country: USA

institute: Massachusetts Institute of Technology

summary: Inactivating mutations in the zinc finger gene PHF6 are seen in approximately 40% of adult T-cell acute lymphoblastic leukemias (T-ALLs) and 3% of adult acute myeloid leukemias (AMLs). The absence of PHF6 mutations in B-cell lineage malignancies has led to the hypothesis that PHF6 may act as a lineage-specific tumor suppressor gene. Here, we demonstrate that PHF6 plays a critical role in regulating B-cell identity in the context of B-cell precursor acute lymphoblastic leukemia (preB-ALL). Transplantation of Phf6 knockout preB-ALL cells (hereafter referred to as Phf6KO cells) into immunocompetent syngeneic recipients resulted in the development of a fully penetrant lymphoma-like disease. Strikingly, the resulting lymphomas showed robust up-regulation of the canonical T-cell marker CD4, suggesting that Phf6KO cells adopt a T-cell program in the context of leukemogenesis. RNA sequencing analysis revealed numerous differentially expressed (DE) genes in Phf6WT and Phf6KO cells, including a significant down-regulation of genes and gene sets involved in pathways important for B-cell development. Chromatin immunoprecipitation followed by high-throughput sequencing analysis revealed that PHF6 co-localizes with H3K27ac signals close to the transcription start sites (TSSs) and enhancer regions of a significant proportion of DE genes. Notably, regions flanking the TSS of DE genes showed significant enrichment for binding sites of several well-described master regulators of B-cell development, including PU.1, EGR-1, EBF-1, NF-kB, TCF3 and TCF12. We found that PHF6 and TCF12 physically interact in preB-ALL cells, suggesting that these factors act synergistically in the establishment and maintenance of B-cell identity. In addition, we found that a human PHF6 mutant T-ALL cell line has an incompletely rearranged IGH locus, strongly suggesting that T-ALL can have a B-cell origin. These findings reveal an essential role for PHF6 in the establishment and maintenance of B-cell identity in preB-ALL by directly activating genes that are crucial for B-cell lineage commitment and maintenance. Collectively, these results indicate that loss of function of PHF6 in preB-ALL leads to an unstable cellular state in which cells acquire alternate developmental programs (such as the T-lineage program) to survive, potentially explaining the apparent absence of PHF6 mutations in human B cell-lineage malignancies.

overall_design: Gene expression profiles by RNA-Seq of 3 Phf6 wild-type preB-ALL cells, 3 shPhf6 preB-ALL cells, 6 Phf6 knockout (2 different sgRNAs) preB-ALL cells

first: Yadira

middle: M

last: Soto-Feliciano

middle: T


title: PAR-TERRA RNA directs homologous sex chromosome pairing

city: Boston

first: Hsueh-Ping

last: Chu

state: MA

address: 185 Cambridge St

department: molecular biology

institute: MGH, Harvard Medical School

summary: In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a ‘tetrad’ of pairwise homologous interactions (Xic–Xic, PAR–PAR, and Xic–PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a ‘constrained diffusion model’ in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.

overall_design:
Identify genome-wide binding sites for TERRA RNA by CHIRT-seq in ES cells and MEFs. TERRA capture RNA-seq to discover TERRA sequence.
Investigation of PAR-interacting domains using 4C-Seq.

Please note that GSM2429690-93 are duplicated sample records of GSM1711915-18, respectively, for the convenient retrieval of the complete raw data from SRA.

first: Hsueh

middle: P

first: John

middle: E

last: Froberg

first: Barry

last: Kesner

first: Hyun

last: Oh

first: Stefan

middle: F

last: Pinter

last: Ji

first: Ruslan

last: Sadreyev

first: Jeannie

last: Lee


title: Transcriptomic profiling of hemp bast fibres at different developmental stages

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

summary: Cellulosic phloem fibres, also known as bast fibres, find a wide array of applications in industry, for example as eco-friendly substitutes of glass fibres in the manufacture of biocomposites. Bast fibres are cells characterized by a noteworthy length and by a tertiary cell wall (gelatinous or G-layer) mainly composed of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, then they cease elongation and start to thicken. In the light of their importance in fostering a bio-economy, it is desirable to widen our knowledge on the molecular mechanisms underlying the differentiation and maturation of bast fibres. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development. The stages going from rapid elongation to cell wall thickening are here studied in textile hemp (Cannabis sativa L.), a fibre crop of great economic importance.

overall_design: Analysis of the fibre transcriptome of hemp plants age 6 weeks. Samples were taken at the TOP, MID (with the snap point) and BOT. Bast fibres were separated using EtOH 80%, a morar and a pestle. The number of biological replicates is four with 13 plants in each replicates.

first: Marc

last: Behr

first: Sylvain

last: Legay

first: Lauralie

last: Mangeot-Peter

first: Simone

last: Zorzan

first: Mohammad

last: Ghoniem

first: Jean-Francois

last: Hausman


title: Multipotent Peripheral Glial Cells Generate Neuroendocrine Cells of the Adrenal Medulla

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary:
Cells producing adrenalin are largely derived from nerve-associated Schwann cell precursors via an intermediate progenitor “bridge” cell.
We demonstrate that large numbers of chromaffin cells arise from peripheral glial stem cells, termed Schwann cell precursors (SCPs)

overall_design: SCPs migrate along the visceral motor nerve to the vicinity of the forming adrenal gland where they detach from the nerve and form post-synaptic neuroendocrine chromaffin cells. An intricate molecular logic drives two sequential phases of gene expression, one unique for a distinct transient cellular state and another for cell-type specification. Subsequently, these programs downregulate SCP- and upregulate chromaffin-cell-gene networks. The adrenal medulla forms through limited cell expansion and requires the recruitment of numerous SCPs. Thus, peripheral nerves serve as a stem cell niche for neuroendocrine system development.

first: Alessandro

last: Furlan

first: Vyacheslav

last: Dyachuk

first: Maria

last: Kastriti

first: Laura

last: Calvo-Enrique

first: Hind

last: Abdo

first: Saida

last: Hadjab-Lallemend

first: Tatiana

last: Chontorotzea

first: Natalia

last: Akkuratova

first: Dimitry

last: Usoskin

last: Kamenev

first: Julian

last: Petersen

first: Kazunori

last: Sunadome

first: Fatima

last: Memic

first: Ulrika

last: Marklund

first: Kaj

last: Fried

first: Piotr

last: Topilko

first: Francois

last: Lallemend

first: Patrik

last: Ernfors

first: Igor

last: Adameyko


title: DNA methylation drift as a marker of lifespan in mammals [human]

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: We analyzed levels of 5-methyl cytosine CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of human whole blood genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.

first: Shinji

last: Maegawa

first: Jean-Pierre

last: Issa


title: RNA sequencing to identify common targets for GSK3

city: Miami

first: Eleonore

last: Beurel

state: FL

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

summary: common targets with different GSK3 inhibition approaches

overall_design: mice were treated with siRNA forGSK3b or GSK3 inhibitors, and sacrificed, RNA were extracted from hippocampus and sequenced

first: Richard

last: Jope


title: Experimental validation of candidate regulators of KRAS transcriptional components.

first: Jong Wook

last: Kim

address: 45 Main Street

department: Cancer Program

institute: Broad Institute

summary: We sequenced mRNA from HCC44 and YAPC cell lines stably expressing Cas9, and infecting with indicated gRNAs against regulators of KRAS transcriptional components.

overall_design: KRAS mutant cell lines HCC44 and YAPC stably expressing with Cas9 were infected with three independent gRNAs targeting indicated genes or controls (GFP, RFP, random gRNAs) and harvested 8 days after infection.

first: Jong

middle: W

first: Jill

last: Mesirov

first: William

last: Hahn

first: Pablo

last: Tamayo


title: DNA methylation drift as a marker of lifespan in mammals

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus


title: RNA-Seq Analysis of the Transcriptomes of Tomato+ and Tomato- HNSCC cells

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

summary: The role of this study is to compare the global gene expression profiles between Bmi1+ Cancer stem cells and Bmi1- cancer cells

overall_design: Oral cancer from Bmi1CreER;tdTomato mouse treated with 4NQO for 26 weeks were havested 24 hr after tamoxifen injection. Tumor tissues were dissociated into single cell suspension and FACS-sorted based on the tomato expression. mRNA were isolated from sorted cells and RNAseq were performed.


title: Unraveling multifaceted contributions of small regulatory RNAs to the photomorphogenic development in Arabidopsis

city: Taipei

first: Meng-Chun

last: Lin

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology

summary: Small RNA-mediated post-transcriptional control of gene expression is critical for the growth and development of plants. Previous investigations on Arabidopsis suggest that photomorphogenesis may be regulated by the action of sRNAs. However, current information on sRNAs and their regulation of target genes during photomorphogenesis remain mostly unknown. We aim to provide a more systemic view on sRNA-controlled gene expression in this developmental process. We have found that, in addition to microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs), other siRNAs may also act as regulators of the de-etiolating process. In addition, we have discovered several miRNA-target pairs that act as new players of photomorphogenesis.

overall_design: Examine the expression patterns of Arabidopsis small RNAs under 6 time points of light exposure.

first: Huang-Lung

last: Tsai

first: Shu-Hsing

last: Wu


title: DNA methylation drift as a marker of lifespan in mammals [monkey]

summary: We analyzed levels of 5-methyl cytosine at CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of monkey whole blood genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the rheMac2 reference genome.


title: Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

status: Public on Jul 09 2017

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Efforts to manipulate locus-specific histone acetylation to assess their causal role in gene expression and cellular and behavioural phenotypes have been impeded by a lack of experimental tools. The Cas9 nuclease has been adapted to target epigenomic modifications, but a detailed description of the parameters of such synthetic epigenome remodellers is still lacking. Here we describe a Cas9-based histone deacetylase (HDAC) and the design principles required to achieve locus-specific histone deacetylation. We assess its range of activity and specificity, and analyse target gene expression in two different cell types to investigate cellular context-dependent effects. Our findings demonstrate that the chromatin environment is an important element to consider when utilizing this synthetic HDAC.

overall_design: ChIP-seq, GRO-seq, and RNA-seq in Neuro 2a cells.

first: Deborah

middle: Y

last: Kwon

first: Janine

last: Lamonica

first: Zhaolan

last: Zhou


title: DNA methylation drift as a marker of lifespan in mammals [mouse]

first: Jaroslav

last: Jelinek

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of mouse whole blood genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the mouse genome.

first: Shinji


title: The Staphylococcus aureus nitric oxide synthase (saNOS) modulates respiratory metabolism and cell physiology

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Nitric oxide synthase (NOS) enzymes produce nitric oxide (NO), a highly reactive free radical capable of interacting with multiple cellular targets. Although saNOS contributes to Staphylococcus aureus virulence, as well as protection against exogenous oxidative stress and antimicrobials, the current mechanism behind these phenotypes is unknown. Here we report a previously-undescribed role for saNOS in modulating S. aureus physiology. When grown aerobically, endogenous reactive oxygen species (ROS) and superoxide levels were elevated in a S. aureus nos mutant. NO has been shown to slow respiration in other organisms, and likewise, comparison of respiratory dehydrogenase activity and membrane potential in wild-type, nos mutant, and complement strains suggested that saNOS-derived NO limits S. aureus aerobic respiration. Multiple transcriptional and metabolic changes were also observed in a S. aureus nos mutant, as assessed by RNAseq and targeted metabolomics analyses, respectively. Specifically, expression of genes associated with oxidative and nitrosative stress responses, anaerobic and lactate metabolism, and cytochrome biosynthesis and assembly were increased in the nos mutant relative to wild-type. Metabolites utilized to produce reducing equivalents by the right arm of the TCA cycle were depleted in a nos mutant (citrate and α-ketoglutarate), whereas fumarate and malate levels were increased relative to wild-type and complement strains. A significant reduction in lactate levels was also observed in the nos mutant. Collectively, these results support a model in which the absence of saNOS results in increased respiration and ROS accumulation, which may signal the cells to switch to an alternative lactate-based respiratory metabolism.

overall_design: Three RNAseq data sets in total.  Each sample was generated by pooling three independent biological replicate RNA preps

first: Austin

middle: B

last: Mogen

middle: K

first: Kimberly

last: James

first: Genevy

last: Lima

first: Dona

last: Silva

first: Jeffrey

middle: A

last: Culver

first: Christopher

last: Petucci

first: Lindsey

middle: N

last: Shaw

first: Kelly

last: Rice


title: miRNAs in flowers of Viburnum macrocephalum f. keteleeri

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: High-throughput small RNA sequencing were performed to identify a large number of miRNAs and their targets in fertile and sterile flowers of V. macrocephalum f. keteleeri for the first time. We ascertained that the regulatory networks of the miRNAs are involved in many different primary biological processes based on potential target designations. Our study is the first to provide useful information for uncovering the regulatory networks of miRNAs in  V. macrocephalum f. keteleeri flowers.

overall_design: small RNA sequencing in  fertile and sterile  flowers of V. macrocephalum f. keteleeri

first: Li

last: Zhang


title: RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation.

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

summary: The stepwise and sequential expression of viral genes underlies progression of the infectious life cycle. The Epstein-Barr virus (EBV) is both a tractable model for elucidating principles of transcription as well as a global health threat. We describe an experimental protocol and bioinformatics pipeline for functional identification of EBV true late genes, the last step of transcription prior to virion packaging and egress. All data have been uploaded to the Gene Expression Omnibus under accession code GSE96689. The key improvement over previous approaches is leveraging the sensitivity of RNA-seq to detect gene expression changes during spontaneous reactivation.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design:
Examination of late gene expression in 2 cell types after acyclovir treatment.

Please note that the wig files are a slightly modified format in that they display a viral genome not available as a chromosome on the UCSC genome browser. The wig files are readable by the IGV browser (as described in the associated publication).

first: Delsy

last: Martinez


title: Mouse ES Timecourse

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary:
High temporal resolution RNAseq timecourse of mouse ES differentiation
Investigations of transcriptional responses during developmental transitions typically use time courses with intervals that are not commensurate with the timescales of known biological processes. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report the effects of increased temporal resolution on the characterization of the underlying molecular processes.

overall_design:
Biological duplicate 120 hours of undirected mouse ES cell differentiation sampled 6 hourly
Biological duplicate, low passage number (P18) W9.5 ESCs were cultured and differentiated as described previously [PMID:18562676; 17286599]. Cultures were harvested every six hours from the induction of differentiation to 120 hours post differentiation induction. Total RNA from cultures was purified using Trizol (Life Technologies) and DNase treatment was performed by RQ1 DNase (Promega) according to the manufacturer’s instructions. RNA integrity was measured on a Bioanalyzer RNA Nano chip (Agilent). RNA-Seq library preparation and sequencing of Poly-A-NGS libraries generated from 500 ng total RNA using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s instructions. Paired-end libraries were sequenced to the first 100 bp on a HiSeq 2500 (Illumina) on High Output Mode. Library sequencing quality was determined using FastQC (Babraham Bioinformatics) and FastQ Screen (Babraham Bioinformatics). Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore! (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/). Tophat2 [PMID:23618408] was used to align reads to the December 2011 release of the mouse reference genome (mm10) as outlined by Anders et al.[PMID:23975260]. Read counts data corresponding to GENCODE vM2 transcript annotations were generated using HTSeq[PMID:25260700]. All analyses were performed in the R Statistical Environment [PMID:18000755]. Briefly, counts data were background corrected and normalized for library size using edgeR [PMID:19910308],  then transformed using voom[PMID:24485249] for differential expression analysis using LIMMA[PMID: 16646809].

first: Marcel

last: Dinger


title: Generation of KRAS signatures using immortalized isogenic lung cells.

first: Jong Wook

last: Kim

summary: We generated RNAseq profiles from Small Airway Epithelial Cells (SALE) expressing either KRAS G12V or GFP control.

overall_design: SALE stably expressing with KRAS G12V or GFP were harvested two weeks after infection.

first: Jong

first: Jesse

last: Boehm

first: Jill

last: Mesirov

first: William

last: Hahn

first: Pablo

last: Tamayo


title: DNA Methylation Targets Influenced by Bisphenol A and/or Genistein Are Associated with Survival Outcomes in Breast Cancer Patients

city: San Antonio

first: Rohit

middle: Ramakant

last: Jadhav

state: TX

address: Rm. 261 South Texas Research Facility, MC 8257 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Early postnatal exposures to Bisphenol A (BPA) and genistein (GEN) have been reported to predispose for and against mammary cancer, respectively, in adult rats. Since the changes in cancer susceptibility occurs in the absence of the original chemical exposure, we have investigated the potential of epigenetics to account for these changes. DNA methylation studies reveal that prepubertal BPA exposure alters signaling pathways that contribute to carcinogenesis. Prepubertal exposure to GEN and to BPA + GEN suggests pathways involved in maintenance of cellular function, indicating that the presence of GEN either reduces or counters some of the alterations caused by the carcinogenic properties of BPA. We subsequently evaluated the potential of epigenetic changes in the rat mammary tissues to predict survival in breast cancer patients via The Cancer Genomic Atlas (TCGA). We identified 12 genes that showed strong predictive values for long-term survival in estrogen receptor positive patients. Importantly, two genes associated with improved long term survival, HPSE and RPS9, were identified to be hypomethylated in mammary glands of rats exposed prepuberally to GEN or to GEN + BPA respectively, reinforcing the suggested cancer suppressive properties of GEN.

overall_design: We conducted MBDCap-seq on mammary glands procured from 100 day-old rats exposed prepubertally to vehicle control, BPA, GEN, or BPA + GEN (n = 5/ group)

first: Tim

last: Huang

first: Victor

middle: X

first: Coral

last: Lamartiniere


title: Trancriptional profiling of Bacillus subtilis BsB1 and NCIB3610 rho-deletion mutant

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

summary: With these experiments we investigate the impact of the deletion of the gene encoding transcription termination Rho on the transcriptomes of two different Bacillus subtilis strains, BsB1 and NCIB3610. The results confirm massive increase of antisense transcription initially observed with tiling arrays in B. subtilis strain 1012 (Nicolas et al. 2012; PMID:22383849; GSE27303).

overall_design: The rho-deletion associated with a phelomycin resistance cassette  from Bacillus subtilis 1012 rho :phleo (described in Nicolas et al. 2012) was introduced into Bacillus subtilis BsB1 and NCIB3610 backgrounds by natural competence and SPP1-mediated transduction, respectively.  Mutant and parental backgrounds of these two strains were subjected to stranded RNA-Seq profiling. A total of 6 biological samples were examined (biological duplicates for NCIB3610).

first: Elena

last: Bidnenko

first: Cyprien

last: Guérin


title: Understanding the role of microRNAs in the interaction of Aedes aegypti mosquitoes with an insect-specific flavivirus

status: Public on Jul 08 2017

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

summary: The Flavivirus genus contains some of the most prevalent vector-borne viruses such as dengue, Zika and yellow fever viruses that cause devastating diseases in humans. However, the insect-specific clade of flaviviruses is restricted to mosquito hosts; albeit they have retained the general features of the genus such as genome structure and replication. The interaction between insect-specific flaviviruses (ISFs) and their mosquito hosts are largely unknown. Pathogenic flaviviruses are known to modulate host-derived microRNAs (miRNAs), a class of non-coding RNAs that are important in controlling gene expression. Alteration in miRNAs may represent changes in host gene expression and provide understanding of virus-host interactions. The role of miRNAs in ISF-mosquito interactions is largely unknown. A recently discovered Australian ISF, Palm Creek virus (PCV), has the ability to suppress medically relevant flaviviruses. Here, we investigated the potential involvement of miRNAs in PCV infection using the model mosquito Aedes aegypti. By combining small RNA sequencing and bioinformatics analysis, differentially expressed miRNAs were determined. Our results indicated that PCV infection hardly affects host miRNAs. Out of 101 reported miRNAs of Ae. aegypti, only aae-miR-2940-5p had significant altered expression over the course of infection. However, further analysis of aae-miR-2940-5p revealed that this miRNA does not have any direct impact on PCV replication in vitro. Thus, the results overall suggest that PCV infection has a limited effect on the mosquito miRNA profile and therefore, they may not play a significant role the PCV- Ae. aegypti interaction.

overall_design: To obtain RNA samples from PCV infections, 4 day old Ae. aegypti mosquitoes (Townsville, Australia strain) were injected with 102.3 virus/ml (106 TCID50/ml) in 200 nl of stock PCV diluted in Opti-MEM medium (Gibco, Invitrogen Corporation, Grand Island, NY) with 3% FBS without antibiotics or antimycotics. Control group mosquitoes were injected with the same growth medium without PCV. Mosquitoes were collected and stored at -80°C on days 2, 6 and 12 post-inoculation. For each day and treatment, 15 mosquitoes were collected and divided into three groups of five mosquitoes, which were pooled to create three biological replicates.

first: Sassan

last: Asgari


title: Comprehensive Assessment of Concordance Between Fresh-frozen and Formalin-fixed Paraffin Embedded Tumour DNA Methylation using a Targeted Sequencing Approach

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

summary: DNA methylation controls gene expression and is altered in many types of disease, including metastatic colorectal cancer. Studying this phenomenon in archival material such as formalin-fixed paraffin embedded (FFPE) tumour biopsies would represent a significant step in unlocking a previously unavailable source of data. Methylation at base-pair resolution has not been fully described in FFPE samples in the context of matched fresh frozen (FF) tumour material using a targeted next-generation sequencing approach. Here, we used three pairs of matched FFPE and FF samples, along with two cell lines in duplicate, to determine the extent of their similarity. We identified a “bowing” pattern in FFPE samples showing lower CpG proportion at the start of sequence reads, but found no evidence that this significantly affected methylation calls. We also found no significant increase in deamination, measured by C > T transitions, previously considered a result of cross-linking DNA by formalin fixation and a barrier to FFPE use in methylation studies. Finally, our method has shown sensitivity of between 60-70% based on positions also methylated in cell lines. This level is not affected by coverage, and we believe that FFPE material is useful as a tissue source for similar methylation studies.

overall_design: Three matched pairs of FFPE and FF from the same patient  tumour biopsy were used, along with 2 cell lines (SW480, SW620) in duplicate as controls

first: Sudipto

last: Das

first: Dominiek

last: Smeets

first: Gillian

last: Peutman

first: Rut

last: Klinger

first: Bozena

last: Fender

first: Kate

last: Connor

first: Matthias

last: Ebert

first: Timo

last: Gaiser

first: Jochen

last: Prehn

first: Orna

last: Bacon

first: Elaine

last: Kay

first: Bryan

last: Hennessy

first: Verena

last: Murphy

first: Bauke

last: Ylstra

first: Diether

last: Lambrechts

first: Annette

last: Byrne

last: Gallagher

first: Darran

last: O'Connor


title: PHF6 regulates B-cell identity in acute lymphoblastic leukemia

first: Michael

last: Hemann

address: 500 Main St, Building 76 Room 301

institute: Massachusetts Institute of Technology

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

overall_design: Refer to individual Series


title: RNA-seq based transcriptinal profiling of intracellular Brucella abortus and Brucella abortus-infected murine macrophages

city: Seongnam-si

first: Jee Soo

last: Son

state: Gyeonggi-do

address: Room 903, JungAng Induspia V, 137, Sagimakgol-ro, Jungwon-gu

country: South Korea

institute: iNtRON Biotechnology

summary: We describe the isolation of sufficient Brucella abortus RNA from primary host cell environment using modified reported methods for RNA-seq analysis, and simultaneously characterize the transcriptional profiles of intracellular B. abortus and bone marrow-derived macrophages (BMM) from BALB/c mice at 24 h (replicative phase) post-infection.

sample_organism:
Mus musculus
Brucella abortus 544

platform_organism:
Mus musculus
Brucella abortus 544

overall_design: Each infection and control time point was performed in triplicates using different preparations of BMMs, and processed independently to give three biological replicates. The intracellular B. abortus and infected BMM gene expression were compared to the gene expression of the inoculum and uninfected BMMs, respectively. qRT–PCR validation was performed using SYBR Green assays

first: Suk

last: Kim

first: Jee-Soo


title: Transcriptome Analysis of piRNAs during testicular development and spermatogenesis of Mongolian horse

status: Public on Jul 07 2017

city: Huhhot

first: Bei

last: Li

address: Zhaowuda Rd.306

institute: Inner Mongolia Agriculture University

summary: PIWI-interacting RNAs (piRNAs), have been identifed in mammalian testes, and were essential for development of testis and spermatogenesis.

overall_design: In order to study those physiological processes, the 3 immature and 3 mature testis of Mongolian horse were collected and 6 libraries were established, using Small RNA sequencing technology, the related piRNAs of Mongolian horse development of testis and spermatogenesis were detected.

first: Xiaolong

last: He


title: Cell type-specific alternative splicing during mammalian neuronal differentiation

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Alternative precursor-mRNA splicing (AS) is a key regulation of gene expression and protein diversity. AS is highly happened in the nervous system and misregulation of AS caused neurological diseases. In current research, we identified and validated the differential AS events from purified neural progenitor cells (NPCs) and neurons. Our data demonstrated a systematic characterization of AS events between endogenous NPCs and neurons, which may serve as a useful resource for further investigations.

overall_design: Differential alternative splicings of neural progenitor cells (NPCs) and neurons were analyzed

first: Jiancheng

last: Liu

first: Qiang

last: Lu


title: Gene expression profiles of brain endothelial cells during embryonic development at bulk and single-cell levels

status: Public on Jul 12 2017

city: Würzburg

first: Mike

last: Hupe

address: Biocenter Am Hubland

department: Department of Developmental Biochemistry

country: Germany

institute: University of Würzburg

summary:
Purpose: Exploring mechanisms defining the unique nature of vascular development and differentiation in the brain .
Methods: High-resolution gene expression profiles of embryonic endothelial cells (EC) using translating ribosome affinity purification (TRAP) and single cell RNA-sequencing. RNA-sequenzing of transcription factor infected HUVEC.
Results: Comparisons of different organ-, temporal- or Ctnnb1 knock out-specific vascular translatomes revealed extensive molecular changes during the unique development of the brain endothelium. We identified brain endothelial-specific transcription factors – Foxf2, Foxl2, Foxq1, Lef1, Ppard, Zfp551 and Zic3 – that are associated with the temporal maturation of the blood-brain barrier and act downstream of the Wnt/Ctnnb1 signaling pathway. Profiling individual EC revealed a remarkable heterogeneity. Nevertheless, high levels of Foxf2, Foxq1, Ppard and Zic3 were correlated with elevated expression of differentiation markers. This could be recapitulated in vitro, where expression of Foxf2 and Zic3 in HUVEC led to an induction of blood-brain barrier differentiation markers.
Conclusions: Our study provides further insights into the temporal and cellular complexity of the developing embryonic brain endothelium. Our data raises many questions and provides a basis for further studies aiming to unravel cellular and molecular mechanisms that underlie vascular development and differentiation in the CNS. We anticipate that additional investigation of the identified transcription factors is likely to be a fruitful approach in understanding and manipulating the development of BBB and to engineer more advanced blood brain barrier in vitro models.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: TRAP-seq profiles for E11.5 till E17.5 wild type (WT) brain EC; E14.5 and E17.5 endothelial Ctnnb1 -/- brain EC; E14.5 head, heart, kidney, limb, liver and lung WT EC in triplicate, using Illumina HiSeq 2000. Single cell RNA-sequencing of E14.5 brain EC. RNA-sequenzing of HUVEC infected with either control, Foxf2, Foxq1, ZIC3 or three transcription factors combined in triplicate.

first: Minerva

first: Susanne

last: Kneitz

first: Daria

last: Davydova

first: Chika

last: Yokota

first: Julianna

last: Kele-Olovsson

first: Belma

last: Hot

first: Manfred

last: Gessler

first: Jan

last: Stenman


title: Zika virus directly infects human peripheral neurons and induces cell death

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

summary: Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes mosquitoes, has spread to 59 countries and territories throughout the world. ZIKV-infected patients can have several symptoms and there is scientific consensus that ZIKV is a cause of microcephaly. Most studies are focusing on the central nervous system (CNS), and it is largely unknown whether ZIKV also affects the developing peripheral nervous system. Here, using a human pluripotent stem cell-based model, we demonstrated that Puerto Rican ZIKV strain, PRVABC59, efficiently infects human neural crest cells (hNCCs). In contrast to little infection of CNS neurons, ZIKV readily infects human peripheral neurons (hPNs), leading to cell death. Global gene expression analyses of infected hNCCs and hPNs reveal transcriptional dysregulation, notably of cell-death- and cell-cycle-related pathways. Our results identify hNCCs and hPNs as a direct ZIKV target and provide a framework to investigate the ZIKV pathology on the peripheral neurons.

overall_design: Gene expression analyses of the cells in peripheral nervous system infected with the PRVABC59 strain of Zika virus


title: Activation of LINE-1 after fertilisation regulates global chromatin accessibility

city: Princeton

last: Levine

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Upon fertilisation, the highly differentiated gametes reprogram to a totipotent state to initiate a new developmental programme. Approximately half of the mammalian genome is composed of repetitive elements, including retrotransposons, some of which are transcriptionally activated after fertilisation. It is generally assumed that retrotransposons become activated as a side-effect of the large chromatin remodelling underlying the epigenetic reprogramming of the gametes. Here, we have used a targeted epigenomic approach to address whether specific families of retrotransposons play a direct role in chromatin organisation and developmental progression after fertilisation. Using this approach, we demonstrate that precocious silencing of LINE-1 reduces chromatin accessibility, while their prolonged activation prevents gradual chromatin compaction, natural to developmental progression. Preventing LINE-1 activation and interfering with their silencing results in a reduced developmental rate independently of the coding nature of the LINE-1 transcript, suggesting that LINE-1 functions primarily at the chromatin level. Our data suggest that activation of LINE-1 regulates global chromatin accessibility at the beginning of development and indicate that activation of retrotransposons is an integral part of the developmental programme.

overall_design: RNAseq was done on pooled injected embryos(4-5) as indicated in methods.

first: Xinyang

last: Bing

first: Ana

last: Boskovic

first: Oliver

last: Rando

first: Maria-Elena

last: Torres-Padilla


title: Smelling the difference: Transcriptome, proteome and volatilome changes after mating

city: Jena

first: Katrin

last: Krause

address: Neugasse 25

department: Institute of Microbiology

institute: Friedrich Schiller university of Jena

summary: Mushrooms, such as Schizophyllum commune, have a specific odor. Whether this is linked to mating, prerequisite for mushroom formation, or also found in monokaryotic, unmated strains, was investigated with a comprehensive study on the transcriptome and proteome of this model organism. Mating interactions were investigated using a complete, cytosolic proteome map for unmated, monokaryotic, as well as for mated, dikaryotic mycelia. The regulations of the proteome were compared to transcriptional changes upon mating and to changes in smell by volatilome studies. We could show a good overlap between proteome and transcriptome data, but extensive posttranslational regulation was identified for more than 80 % of transcripts. This suggests down-stream regulation upon interaction of mating partners and formation of the dikaryon that is competent to form fruiting bodies. The volatilome was shown to respond to mating by a broader spectrum of volatiles and increased emission of the mushroom smell molecules 3-octanone and 1-octen-3-ol, as well as ethanol and ß-bisabolol in the dikaryon. Putatively involved biosynthetic proteins like alcohol dehydrogenases, Ppo-like oxygenases, or sesquiterpene synthases showed correlating transcriptional regulation depending on either mono- or dikaryotic stages.

overall_design: With RNA sequencing RNA expression was investigated in two different wild type strains (12-43, E6) and mutant Δdhc2, a knock-out of dynein heavy chain gene 2. Two replicates samples were analyzed  for each condition.

first: Melanie

last: Brunsch

first: Daniela

last: Freihorst

first: Sophia

last: Wirth

first: Olaf

last: Kniemeyer

first: Maritta

last: Kunert

first: Wilhelm

last: Boland

first: Jörg

last: Linde

first: Erika

last: Kothe


title: PHF6 regulates B-cell identity in acute lymphoblastic leukemia [ChIP-Seq]

city: Cambridge

first: Michael

last: Hemann

department: Koch Institute

summary: Inactivating mutations in the zinc finger gene PHF6 are seen in approximately 40% of adult T-cell acute lymphoblastic leukemias (T-ALLs) and 3% of adult acute myeloid leukemias (AMLs). The absence of PHF6 mutations in B-cell lineage malignancies has led to the hypothesis that PHF6 may act as a lineage-specific tumor suppressor gene. Here, we demonstrate that PHF6 plays a critical role in regulating B-cell identity in the context of B-cell precursor acute lymphoblastic leukemia (preB-ALL). Transplantation of Phf6 knockout preB-ALL cells (hereafter referred to as Phf6KO cells) into immunocompetent syngeneic recipients resulted in the development of a fully penetrant lymphoma-like disease. Strikingly, the resulting lymphomas showed robust up-regulation of the canonical T-cell marker CD4, suggesting that Phf6KO cells adopt a T-cell program in the context of leukemogenesis. RNA sequencing analysis revealed numerous differentially expressed (DE) genes in Phf6WT and Phf6KO cells, including a significant down-regulation of genes and gene sets involved in pathways important for B-cell development. Chromatin immunoprecipitation followed by high-throughput sequencing analysis revealed that PHF6 co-localizes with H3K27ac signals close to the transcription start sites (TSSs) and enhancer regions of a significant proportion of DE genes. Notably, regions flanking the TSS of DE genes showed significant enrichment for binding sites of several well-described master regulators of B-cell development, including PU.1, EGR-1, EBF-1, NF-kB, TCF3 and TCF12. We found that PHF6 and TCF12 physically interact in preB-ALL cells, suggesting that these factors act synergistically in the establishment and maintenance of B-cell identity. In addition, we found that a human PHF6 mutant T-ALL cell line has an incompletely rearranged IGH locus, strongly suggesting that T-ALL can have a B-cell origin. These findings reveal an essential role for PHF6 in the establishment and maintenance of B-cell identity in preB-ALL by directly activating genes that are crucial for B-cell lineage commitment and maintenance. Collectively, these results indicate that loss of function of PHF6 in preB-ALL leads to an unstable cellular state in which cells acquire alternate developmental programs (such as the T-lineage program) to survive, potentially explaining the apparent absence of PHF6 mutations in human B cell-lineage malignancies.

overall_design: Examination of PHF6 localization and H3K27 acetylation and trimethylation in mouse preB-cell leukemia cells by ChIP-Seq analysis.

first: Yadira

last: Soto-Feliciano


title: Identification of downstream genes regulated by YAP1 through knockdown and overexpression of YAP1 in U251 cell with a stably expression of mutant APP

status: Public on Jul 06 2017

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

summary: Upstream regulator genes are central hub nodes in a network and their expression may response to  upstream trigger factors of a disease and influence expression of hundreds of downstream genes, and further facilitate disease development. Therefore, the identification of upstream regulator genes are vital for understanding the pathophysiology of the disease and seek for potential therapeutic targets for the treatment of the disease. YAP1 was identified as a candidate upstream regulator for Alzheimer's disease (AD) in our study. To test whether expression alterations of YAP1 can lead to AD expression network disturbance and thus promoting AD progression, we knockdown and overexpressed YAP1 in U251 cell line with a stably expression of mutant APP (K670N/M671L) (U251-APP cells). RNA-seq (by IlluminaHiseq 4000) and following analyses were then performed to detect genes whose expression were influenced by YAP1 expression changes. The results indicated that expression alterations of YAP1 can significantly disturbe the whole AD expression network.

overall_design: YAP1 inteference and overexpression were performed in U251 cell with a stably expression of mutant APP (K670N/M671L) (U251-APP cells) with three biological triplicates for each condition (siNC, si-YAP1, vector, and YAP1, one outlier for YAP1 overexpression was removed).  Differential expression genes were obtained by comparing gene expression levels in YAP1 knockdown (si-YAP1) or overexpression (YAP1) cells with control cells (siNC or vector).

first: Min

last: Xu

first: Deng-Feng

last: Zhang

first: Rongcan

last: Luo

first: Yong

last: Wu

first: Hejiang

last: Zhou

first: Li-Li

last: Kong

first: Rui

last: Bi


title: Genome-wide transcriptional analysis of Drosophila ring gland

city: Edmonton

first: Kirst

last: King-Jones

state: AB

address: 77 University Campus

country: Canada

institute: University of Alberta

summary:
Samples 1-8: Tissue-specific RNA sequencing (Illumina) using dissected ring glands isolated from TWO different time points of control (phm>w1118) third instar larvae. Time points are: light phase zt0-4 (which corresponde to 2-4 hours from second to third instar larvae molt);  and dark phase zt18-22 (which corresponde to 16-20 hours from second to third instar larvae molt)
Samples 9-32: Tissue-specific gene expression (RNA seq Illumina) using dissected ring glands isolated from TWO different time points of third instar larvae. Genotypes were Timeless-RNAi (phm>tim-RNAi), Period-RNAi (phm>per-RNAi), UAS-TimcDNA (phm>UAS-Tim) and UAS-TimcDNA;UAS-PercDNA (phm>UAS-TimcDNA;UAS-PercDNA). Goal was to identify circadin pathway dependent gene sets in the ring gland. Time points were 2-4 hours and 18-20 hours after L2-L3 molt.

overall_design: This study comprises two parts: First, Next generation sequencing was used to determine transcriptional profiles from Drosophila ring glands at ZT0-4 versus ZT18-22 in control larvae. Encore Complete RNA-Seq IL Multiplex System 1-8 (Nugen Part No. 0312) and Encore Complete RNA-Seq IL Multiplex System 9-16 (Nugen Part No. 0313) was used for barcoding and multiplex sequencing. Library prep was based on total RNA isolated from dissected ring glands  at two different time points during the third instar (the last larval stage of Drosophila development). Libraries were sequenced on a High-Seq Illumina platform. The second part examined gene expression changes in ring glands where we altered circadian signaling by genetic means. Encore Complete RNA-Seq IL Multiplex System was used to prep the cDNA library from total RNA isolated from ring glands of controls, ring gland-specific Timeless-RNAi (phm>tim-RNAi), Period-RNAi (phm>per-RNAi), UAS-Tim-cDNA (phm>UAS-Tim) and UAS-Tim-cDNA; UAS-Per-cDNA (phm>UAS-Tim-cDNA;UAS-Per-cDNA) larvae at two different time points in the day (ZT0-4 and ZT18-22) for the first three genotypes and exclusively at ZT18-22 for the last two genotypes. Each condition was measured by using two biological samples.

first: Francesca

last: Di Cara


title: Comparative dose-response analysis of liver and kidney transcriptomic effects of trichloroethylene and tetrachloroethylene in B6C3F1 mouse

city: College Station

first: Ivan

last: Rusyn

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

summary:
Purpose: Trichloroethylene (TCE) and tetrachloroethylene (PCE) are ubiquitous environmental contaminants and occupational health hazards. The goals of this study were to establish the common and differing transcriptional effects of TCE and PCE. This study examined liver and kidney effects of TCE and PCE in a dose-response study design.
Methods: Equi-molar doses of TCE (24, 80, 240, 800 mg/kg) or PE (30, 100, 300, 1,000 mg/kg) were administered by gavage in aqueous vehicle to male B6C3F1/J mice.  Tissues were collected 24 hrs after exposure. Trichloroacetic acid (TCA), a major oxidative metabolite of both compounds, was measured and RNA sequencing was performed on liver and kidney samples, with ~30 samples for each organ (29 after QC).
Results: Most dose-responsive pathways were common among chemicals/tissues, with the strongest effect on peroxisomal beta-oxidation. Effects on liver and kidney mitochondria-related pathways were notably unique to PCE. Tissue-specific acute transcriptional effects of TCE and PCE occurred at human equivalent doses comparable to those for apical effects.
Conclusions: Our study is the first RNA-Seq transcriptional study of TCE vs. PCE in both liver and kidney, enabling a detailed comparison of the chemicals and effects on different organs. Our results show strong commonalities of effects, although PCE shows stronger transcriptional responses than TCE for the same equimolar doses.

overall_design: Male B6C3F1/J mice were subjected to equi-molar doses of TCE or PCE by gavage in aqueous vehicle, with liver and kidney samples sequenced in triplicate using Illumina HiSeq-2000 for each dose and with a larger number of sequenced reads for control and the highest concentration in liver, to maximize discoveries of differential exon usage.

first: Yi-Hui


title: A UTX–MLL4–p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription (RNA-Seq)

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Enhancer activation is a critical step for gene activation. Here we report a novel epigenetic crosstalk at enhancers between the UTX (H3K27 demethylase)-MLL4 (H3K4 methyltransferase) complex and the histone acetyltransferase p300. We demonstrate that UTX, in a demethylase activity-independent manner, facilitates conversion of naïve (unmarked) enhancers in embryonic stem cells to an active (H3K4me1+/H3K27ac+) state by recruiting and coupling the enzymatic functions of MLL4 and p300. Loss of UTX leads to attenuated enhancer activity, characterized by reduced levels of H3K4me1 and H3K27ac as well as impaired transcription. The UTX-MLL4 complex enhances p300-dependent H3K27 acetylation through UTX-dependent stimulation of p300 recruitment while MLL4-mediated H3K4 monomethylation, reciprocally, requires p300 function. Importantly, MLL4-generated H3K4me1 further enhances p300-dependent transcription. This work reveals a previously unrecognized cooperativity among enhancer-associated chromatin modulators, including a unique function for UTX, in establishing an “active enhancer landscape” and defines a mechanism for the joint deposition of H3K4me1 and H3K27ac.

overall_design: RNA-sequencing of mouse ES cells.

first: Shu-Ping

last: Wang

first: Robert

middle: G

last: Roeder


title: Effects of ATRA and ATO on expression profiles of APL cells in vivo

city: shanghai

first: XiangZhen

last: Liu

address: 197, rui-jin 2nd Road

institute: Shanghai institute of hematology

summary: To characterize the genes that are responsive or refractory to ATRA or ATO treatment in mouse APL cells

overall_design: Using FACS, we isolated GFP+ mouse APL cells and treated with or without ATRA or ATO in vivo. Each sample had 3 biological replicates.

first: Jiang

last: Zhu

first: Xiangzhen

first: Juan

last: Chen


title: Ebola virus (EBOV) infection of ARPE-19 cells

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

institute: Flinders University

summary: We inoculated ARPE-19 human retinal pigment epithelial cells with EBOV, and followed course of infection by immunocytochemistry and measurement of titer in culture supernatant. To interrogate transcriptional responses of infected cells, we combined RNA sequencing with in silico pathway, gene ontology, transcription factor binding site and network analyses. Human retinal pigment epithelial cells were permissive to infection with EBOV, and supported viral replication and release of virus in high titer. Unexpectedly, 28% of 560 up-regulated transcripts in EBOV-infected cells were type I IFN responsive, indicating a robust type I IFN response.

overall_design: Transcriptomic profiles of ARPE-19 cells 24 hours following infection with EBOV or mock-infection

first: Michael

last: Michael


title: miRNAs affected by antagomiR-17 treatment

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: To understand the the effect of antagomir-17 treatment on human endothelial cells derived from human umbilical cord blood (UCB) CD34+ hematopoietic stem cells, we have employed mRNA sequencing. The antagomiR-17 used in this study was purchased from Dharmacon and cell transfection was performed using Lipofectamine RNAiMAx from Life Technologies. Scramble antagomiR from Ambion was used as control. Cells were transfected with antagomiR-17 or scrambled antagomiR for 48 hours.  After 48 h, the cells were collected, RNA was isolated and RNA samples were shipped to Exiqon Services, Denmark for mRNA sequencing. All sequencing experiments (RNA integrity measurements, library preparation and next generation sequencing) were conducted at Exiqon Services, Denmark.

overall_design: CD34+ endothelial cells differentiated from umbilical cord blood hematopoietic stem cells (CD34+) were treated with 50 nM antagomiR-17 (Dharmacon) or scrambled antagomiR (Ambion) using Lipofectamine RNAiMAx (Life Technologies) for 48 h.  Three replicates were used for each condition (i.e. antagomiR-17 and scramble antagomiR conditions).


title: A UTX–MLL4–p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription (ChIP-Seq)

overall_design: ChIP-sequencing of mouse ES cells.


title: A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease

first: Eric

last: Schadt

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue.  Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department.  Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine.

overall_design: Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine. The samples were collected fresh and the tissue was further processed for isolation. A representative 0.5 cm tissue fragment was isolated from the collected surgical specimen samples, flash frozen and stored at -80C. Tissue was homogenized in Trizol following the manufacturer's protocol (Life Technologies) and RNA extraction was performed. RIN scores >7 were used for Poly A RNA-seq.


title: A UTX–MLL4–p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription

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

overall_design: Refer to individual Series


title: MHC Transcriptomic landscape at haplotype-specific resolution

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

summary: To explore the effect of human MHC haplotype on gene expression phenotype across the MHC, we examine the MHC transcriptomic landscape at the haplotype-specific resolution for three prominent MHC haplotypes (A2-B46-DR9, A33-B58-DR3 and A1-B8-DR3) derived from the RNA-sequencing of MHC-homozygous B-LCLs. We demonstrate that MHC-wide gene expression pattern is dictated by the underlying MHC haplotype and identify 37 differentially expressed genes among the haplotypes.

overall_design: Comparing gene expression patterns between multiple MHC haplotypes in B-LCLs. A total of 16 libraries were prepared with two libraries generated per cell line.

first: Ee

middle: C

last: Ren

first: Tze

middle: H


title: Discovery of Drug Candidates that Inhibit and Eliminate Zika Virus Infection in Fetal and Adult Brain

first: Shuibing

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Zika virus (ZIKV) infects fetal and adult human brains, and is associated with serious neurological complications including microcephaly and Guillain-Barré Syndrome (GBS). To date, no prophylactic or therapeutic treatment is available to prevent or treat ZIKV infection. Here, we performed a high content chemical screen using a library containing FDA-approved drugs or drug candidates. Two compounds, hippeastrine hydrobromide (HH) and amodiaquine dihydrochloride dihydrate (AQ), were discovered to inhibit ZIKV infection in human cortical neuron progenitor cells (hNPCs). HH was further validated to inhibit ZIKV infection and to rescue ZIKV-induced growth and differentiation defects in hNPCs and human fetal-like forebrain organoids. Finally, HH and AQ suppressed ZIKV infection in adult mouse brain in vivo. Strikingly, HH and AQ fully rescued the severe limb paralysis syndrome developed in ZIKV infected adult mice. This study identifies drug candidates for treatment of ZIKV infection and ZIKV-related neurological complications in fetal and adult patients.

overall_design: 6 samples were included as following design: 1) neural progenitor cells (NPCs) with MOCK infection and DMSO treatment, 2) NPCs with MOCK infection and treated with AQ, 2) NPCs with MOCK infection and treated with HH, 4) NPCs infected with ZIKA (MR766 strain) and treated with DMSO, 5) NPCs infected with ZIKA and treated with AQ, 6) NPCs infected with ZIKA and treated with HH. All treatment above was lasted for 3 days.

first: Ting

last: Zhou

first: Lei

last: Tan

first: Gustav

last: Cederquist

first: Lorenz

last: Studer


title: Spatiotemporal- and sex-specific Dynamics of lncRNA expression links to brain development and aging in Rhesus Macaque (CAGE-seq)

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Dynamic remodeling in architecture and function of mammalian brain, especially in primate, rely on a precisely orchestrated molecular and cellular regulation at distinct levels. Here, we applied comprehensive RNA-seq and CAGE-Seq analysis to characterize dynamics of lncRNA expression in Rhesus macaque brain across postnatal development and aging. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities respectively. Highly spatiotemporal- and sex-specific dynamic changes in lncRNA but mRNA expression and the negative correlation between lncRNAs and mRNAs, functionally associate with brain development and aging, especially in the neocortex. Together with in situ hybridization (ISH) and quantitative real time-PCR (qRT-PCR) data, our findings provide an initial insight into spatial-, age- and sex-related dynamics of lncRNA expression during postnatal brain development and aging in macaque, implying that high dynamics of lncRNA expression might represent a previously unappreciated regulatory system in shaping brain architecture and function.

overall_design: Examination of 8 different brain regions in Rhsesu Macaque across the four ages (1-, 4-, 10- and 20-year old )

first: Jiali

last: li

first: Yi

last: Zhang


title: EWS-FLI1 represses Rho-actin signaling via MRTFB/YAP-1/TEAD perturbation in Ewing Sarcoma [RNA-Seq]

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary: Ewing Sarcoma (EwS) is a EWS-FLI1- fusion driven pediatric bone cancer with high metastatic potential. Cellular plasticity, typically regulated via the Rho-pathway, is a prerequisite for metastasis initiation. Here we interrogated the role of the Rho transcriptional effectors MRTFA/B in EwS. We find MRTFB transcriptional function strongly repressed by EWS-FLI1. Under EWS-FLI1-low (knock-down) conditions, MRTFB is activated and antagonizes global EWS-FLI1-dependent transcription. Furthermore, ChIP-Seq revealed strong overlaps in MRTFB and EWS-FLI1 chromatin occupation, especially for EWS-FLI1 suppressed-(anticorrelated) genes. Enrichment of TEAD binding motifs in these shared genomic binding regions, and overlapping transcriptional footprints of MRTFB and TEAD1-4 perturbation led us to propose synergy between MRTFB and TEAD in the regulation of EWS-FLI1 suppressed-anticorrelated genes. Finally, we find F-actin assembly to be already perturbed in our EwS model, F-actin polymerization is perturbed by EWS-FLI1 in our model cell line, however,but pharmacological inhibition of actin polymerization still reduced expression serum-induced expression of MRTFB/YAP-1/TEAD target genes. In summary our data support a model of indirect and direct EWS-FLI1-driven perturbation of MRTFB/YAP-1/TEAD target gene regulation .

overall_design: 1. Transient si-RNA mediated knockdown of MRTFA (MKL-1), MRTFB (MKL-2) and doxycyline-induced EWS-FLI1 knockdown in A673/TR/shEF EwS cells (8 samples/replicate: 2 replicates total); 2. Combined transient knockdown of MRTFA, MRTFB and EWS-FLI1 in SK-N-MC EwS cells (4 samples/replicate: 2 replicates total); 3. Combined knockdown of TEAD1-4 by pooling si-RNA against TEAD1, TEAD2, TEAD3 and TEAD 4 combined with doxycycline-inducible EWS-FLI1 knockdown (4 samples/replicate: 8 samples total)

first: Anna

middle: M

last: Katschnig

middle: O

first: Raphaela

last: Schwentner

first: Eleni

last: Tomazou

first: Cornelia

last: Mutz

first: Markus

last: Linder

first: Maria

last: Sibilia

first: Javier

last: Alonso

first: Dave

last: Aryee

first: Heinrich

last: Kovar


title: EWS-FLI1 represses Rho-actin signaling via MRTFB/YAP-1/TEAD perturbation in Ewing Sarcoma [Chip-Seq]

overall_design: Chromatin Immunoprecipitation  coupled with Next-generation sequencing (ChIP-seq) of MRTFA, MRTFB, SRF and EWS-FLI1 (2 replicates each) under serum-induced conditions.


title: PGE2 mediated gene expression changes in human cervical stromal cells

city: Dallas

first: Kishore

last: Annavarapu

address: 5323 Harry Hines Blvd

department: Department of Obstetrics & Gynecology

institute: UT Southwestern Medical Center

summary: The cervix represents a formidable structural barrier for successful induction of labor. Approximately 10% of pregnancies undergo induction of cervical ripening and labor with prostaglandin (PG) E2 or PGE analogs, often requiring many hours of hospitalization and monitoring. On the other, preterm cervical ripening in the second trimester predicts preterm birth. The regulatory mechanisms of this paradoxical function of the cervix are unknown. Here, we show that PGE2 utilizes cell-specific EP2 receptor-mediated increases in Ca2+ to dephosphorylate and translocate HDAC4 to the nucleus for repression of 15-hydroxy prostaglandin dehydrogenase (15-PGDH). The crucial role of 15-PGDH in cervical ripening was confirmed in vivo. Although PGE2 or PGDH inhibitor alone did not alter gestational length, treatment with PGDH inhibitor+PGE2 or metabolism-resistant dimethyl-PGE2 resulted in preterm cervical ripening and delivery in mice. The ability of PGE2 to selectively auto-amplify its own concentrations in stromal cells by signaling transcriptional repression of 15-PGDH elucidates long-sought-after molecular mechanisms that govern prostaglandin action in the cervix. This is the first report detailing unique mechanisms of action in the cervix and serves as a catalyst for (i) the use of PGDH inhibitors to initiate, or amplify low-dose PGE2-mediated cervical ripening, or (ii) EP2 receptor antagonists, HDAC4 inhibitors, and 15-PGDH activators to prevent preterm cervical ripening and preterm birth.

overall_design: human cervical stromal cells were treated with DMSO (vehicle) or PGE2 (100 nM) for 1 h or 24 h followed by RNA sequencing

first: Ann

last: Word

first: Annavarapu

last: Kishore

first: Hanquan

last: Liang

first: Mohammed

last: Kanchwala

first: Chao

last: Xing


title: The functional enhancer repertoire of human embryonic stem cells [ChIP-seq]

status: Public on Jul 05 2017

first: Florian

last: Halbritter

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: We combined Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) with an enrichment step using chromatin immunoprecipitation in a massively parallel reporter assay. We applied this assay, termed ChIP-STARR-seq, to normal (primed) and naive human embryonic stem cells, building up a comprehensive catalogue of functional enhancers. This database record describes the ChIP-seq and BAC component.

overall_design: ChIP-seq for OCT4 (POU5F1), NANOG, H3K27ac, H3K4me1 + Input control in naive and primed hESCs = 14 datasets total + 1 BAC library

first: Tahsin

last: Barakat

first: Andre

last: Rendeiro

first: Man

last: Zhang

first: Christoph

last: Bock

first: Ian

last: Chambers


title: A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Ribo-zero RNAseq mouse distal colon DSS Colitis model of genetically engineered mice

first: Eric

last: Schadt

summary: Ribo-zero RNAseq experiments were carried out with mouse distal colon DSS Colitis model of genetically engineered mice. For each mouse line for: Gpsm3 (3% DSS), Aif1 (3% DSS), Nckap1l (Hem1), Dock2 (3% DSS), Dok3 (3.5% DSS) DSS treatment for five days followed by water for 5 days, (7 days for Nckap1l).  Tissue was collected at Day 10 (Day 12 for Nckap1l (HEM1)).

middle: E


title: RNAseq comparison of WT vs Progranulin KO brain

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
RNA was extracted from cortex of 1 year old wildtype, heterozygous or homozygous PGRN knockout mice.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007808

first: Michael

last: Chang

first: Morgan

last: Sheng


title: EWS-FLI1 represses Rho-actin signaling via MRTFB/YAP-1/TEAD perturbation in Ewing Sarcoma

first: Maximilian

last: Kauer


title: RNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488 FK506 biosynthesis is encoded by a gene cluster that spans 83.5 kilobases. A whole transcriptome differential shotgun sequencing of S. tsukubaensis was performed to analyze transcription at two different time points; before and during active FK506 production. In total 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5'-UTR length of the corresponding transcripts as well as the identification of two consensus sequence motifs in the promoter regions. The transcription start sites of all gene operons within the FK506 cluster were identified, including three examples of leaderless RNA transcripts. These data provide detailed insight into the transcription of the FK506 biosynthetic gene cluster and supports future regulatory studies and genetic manipulations.

overall_design: Differential whole transcriptome shotgun sequencing of Streptomyces tsukubaensis NRRL18488 was performed in duplicates at two time points of growth.

first: Judith

last: Bauer

first: Sven

last: Fillinger

first: Alexander

last: Herbig

first: Adam

last: Jones

first: Katrin

last: Flinspach

first: Cynthia

last: Sharma

first: Harald

last: Gross

first: Kay

last: Nieselt

last: Apel


title: IL-6/Stat3-Dependent Induction of Distinct, Obesity-Associated Natural Killer Cells Deteriorates Energy and Glucose Homeostasis

city: Köln (Cologne)

first: Sebastian

last: Theurich

address: Gleueler Str. 50

institute: Max-Planck-Institute for Metabolism Research and University Hospital of Cologne

summary: Natural killer (NK) cells contribute to the development of obesity-associated insulin resistance. We demonstrate that in mice obesity promotes the expansion of interleukin-6 receptor (IL6Ra)-expressing NK cells, which also express a number of other myeloid lineage genes such as the colony-stimulating-factor 1 receptor (Csf1r). Selective ablation of Csf1r- expressing NK cells prevents obesity and insulin resistance. Moreover, conditional inactivation of IL6Ra or Stat3 in NK cells limits obesity-associated formation of myeloid signature NK cells, protects from obesity, insulin resistance and obesity-associated inflammation. Also in humans IL6Ra+ NK cells increase in obesity, correlate with markers of systemic low-grade inflammation and their gene expression profile overlaps with characteristic gene sets of NK cells in obese mice. Collectively, we demonstrate that obesity-associated inflammation and metabolic disturbances depend on IL-6/Stat3-dependent formation of distinct NK cells, which may provide a novel target for the treatment of obesity, metaflammation-associated pathologies and diabetes.

overall_design: RNA sequencing of two types of NK cells from mouse and human (IL6Ra negative NK cells vs. IL6Ra positive NK cells) and mouse organs (IL6Ra_NKdel vs. IL6Ra_NKflox)

first: Eva

last: Tsaousidou

first: Ruth

last: Hanssen

first: Adelheid

last: Lempradl

first: Jan

last: Mauer

first: Katharina

last: Timper

last: Schilbach

first: Kat

last: Folz-Donahue

first: Christian

last: Heilinger

first: Veronika

last: Sexl

first: John

last: Pospisilik

first: F

middle: T

last: Wunderlich

first: Jens

last: Brüning


title: Characterization of mammalian NEF-sp as a testis-specific nuclear 3′→5′ exoribonuclease

status: Public on Jul 04 2017

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Ribonucleases catalyse maturation of functional RNAs or mediate degradation of cellular transcripts, activities that are critical for gene expression control. Here we identify a previously uncharacterized mammalian nuclease family member NEF-sp (LOC81691) as a testis-specific factor. Recombinant human NEF-sp demonstrates a divalent metal ion-dependent 3′→5′ exoribonuclease activity. This activity is specific to single-stranded RNA substrates and is independent of their length. Presence of a 2′-O-methyl modification at the 3′ end of the RNA substrate is inhibitory. Ectopically-expressed NEF-sp localizes to the nucleolar/nuclear compartment in human cell cultures and this is dependent on an N-terminal nuclear localization signal. Finally, mice lacking NEF-sp are viable and display normal fertility, likely indicating overlapping functions with other nucleases. Taken together, our study provides the first biochemical and genetic exploration of the role of the NEF-sp exoribonuclease in the mammalian genome.

overall_design: Testicular transcriptome of Nef-sp-/- and Nef-sp+/- mice was analyzed using RNA-Seq.

first: Sara

last: Silva

first: David

last: Homolka

first: Ravi

last: Sachidanandam


title: H3K9me2 and BRCA1 cooperate to prevent satellite repeat transcription, R-loop formation and germline sterility [RNA-seq]

city: Mainz

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Repetitive sequences, transposable elements and silent tissue-specific genes in C. elegans are differentially enriched for di- and tri-methyl H3 lysine 9 (H3K9). SET-25 (SUV39h1/h2) catalyzes H3K9me3, while MET-2 (SetDB1) deposits only H3K9me1/me2. RNA-seq and genome-wide H3K9 methylation mapping in met-2 and set-25 single mutants showed that H3K9me2-mediated repression of satellite repeats by MET-2 correlates with germline integrity. Aberrant transcription of repeats and DNA transposons generates R-loops, loss of fertility and hydroxyurea hypersensitivity. In a genome-wide synthetic lethal screen, we identified the BRCA1 complex and factors implicated in the degradation of nuclear RNA as essential for germline integrity in met-2 mutants. Highly additive with met-2, the loss of the BRCA1 complex triggers satellite repeat transcription, generating R-loops on transcribed repeats. Supporting direct causality between satellite repeat transcription and BRCA1-mediated genome integrity, the targeted induction of MSAT1 transcripts at endogenous sites leads to damage-induced loss of fertility in wild-type C. elegans.

overall_design: Total RNAseq of RNA isolated from early C. elegans embryos (~1-300 cell stage) in N2 (Bristol), met-2(n4256) III, set-25(n5021) III and met-2(n4256) III; set-25(n5021) III mutants. Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.

first: Peter

last: Zeller

first: Benjamin

last: Towbin

first: Iskra

last: Katic

first: Veronique

last: Kalck

first: Micol

last: Guidi

first: Susan

last: Gasser


title: GRN knockout, sorted brain cells

first: Brad

last: Friedman

summary:
1 year old mice were perfused and brains were dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The "SAMID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007717

overall_design: Astrocytes, microglia and neurons were sorted from PGRN heterozygous or knockout mice.

first: Michael

last: Chang

first: Morgan

last: Sheng


title: H3K9me2 and BRCA1 cooperate to prevent satellite repeat transcription, R-loop formation and germline sterility [ChIP-seq]

first: Jan

overall_design: Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturers recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).


title: DOC1-dependent recruitment of NURD reveals antagonism with SWI/SNF during epithelial-mesenchymal transition in oral cancer cells.

city: Rotterdam

first: C. Peter

last: Verrijzer

address: Dr Molewaterplein 50

department: Department of Biochemistry

country: Netherlands

institute: Erasmus MC

summary: The Nucleosome Remodeling and Deacetylase (NURD) complex is a key regulator of cell differentiation that has also been implicated in tumorigenesis. Loss of the NURD subunit DOC1 is associated with human oral squamous cell carcinomas (OSCC). Here, we show that restoration of DOC1 expression in OSCC cells leads to a reversal of epithelial-mesenchymal transition (EMT). This is caused by the DOC1-dependent recruitment of NURD to repress the Twist master regulators of EMT. NURD recruitment drives extensive epigenetic reprogramming, including eviction of the SWI/SNF remodeler, formation of inaccessible chromatin, H3K27 deacetylation, recruitment of PRC2 and KDM1A, followed by H3K27 methylation and H3K4 demethylation. Strikingly, depletion of SWI/SNF mimics the effects of DOC1 re-expression. Our results suggest that SWI/SNF and NURD function antagonistically to control chromatin state. We propose that disturbance of this dynamic equilibrium may lead to defects in gene expression that drive human cancer.

overall_design: Examination of NURD binding with loss of NURD subunit DOC1.

first: Adone

last: Mohd-Sarip

first: Miriam

last: Teeuwssen

first: Alice

last: Bot

first: Maria

middle: J

last: De Herdt

first: Stefan

last: Willems

first: Robert

last: Baatenburg de Jong

first: Job

last: van Riet

first: Harmen

last: van de Werken

first: Edwin

last: Oole

first: Wilfred

middle: F

last: van Ijcken

first: Leendert

last: Looijenga

first: Diana

last: Zatreanu

first: Karel

last: Bezstarosti

first: Jeroen

last: Demmers

first: Riccardo

last: Fodde


title: Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a

city: Berlin

first: Jinhua

last: Liu

address: Ihnestra§e 73

institute: Max Planck Institute for Molecular Genetics

summary: The mouse t haplotype, a variant 20 cM genomic region on Chromosome 17, harbors sixteen embryonic control genes identified by recessive lethal mutations isolated from wild mouse populations. Due to technical constraints so far only one of these, the tw5 lethal has been cloned and molecularly characterized. Here we report the molecular isolation of the tw18 lethal. Embryos carrying the tw18 lethal die from major gastrulation defects commencing with primitive streak formation at E6.5. We have used transcriptome and marker gene analyses to describe the molecular etiology of the tw18 phenotype. We show that both WNT and Nodal signal transduction are impaired in the mutant epiblast causing embryonic patterning defects and failure of primitive streak and  mesoderm formation. We have used a candidate gene approach, gene knockout by homologous recombination and genetic rescue to identify the gene causing the tw18 phenotype as Ppp2r1a, encoding the PP2A scaffolding subunit PR65. Our work highlights the importance of phosphatase 2A in embryonic patterning, primitive streak formation, gastrulation, and mesoderm formation downstream of WNT and Nodal signaling.

overall_design: The transcriptomes of E6.5 epiblast cells from WT, tw18/+ and tw18/tw18 embryos, obtained via matings, were analyzed by strand-specific RNA-Seq of ribosomal RNA-depleted total RNA.

first: Lisette

last: Lange

first: Matthias

last: Marks

first: Hermann

last: Bauer

first: Lars

last: Wittler

first: Sandra

last: Piehl

first: Bernd

last: Timmermann

first: Bernhard

last: Herrmann


title: H3K9me2 and BRCA1 cooperate to prevent satellite repeat transcription, R-loop formation and germline sterility

first: Jan

last: Padeken


title: A multipartite enhancer ensemble coordinates pleiotropic developmental functions of Indian hedgehog

first: Darío

last: Lupiáñez

address: Ihnestrasse 73

summary: Copy number variations (CNVs) including enhancers frequently appear associated with disease, induced by pathomechanisms that are poorly understood. Here we show through transgenic reporter and genome editing studies in mice that Indian hedgehog (Ihh) is regulated by a constellation of enhancers of unusual complexity and we uncover how duplications within this enhancer architecture cause phenotypes reminiscent of those observed in human patients. At least nine enhancers with distinct combinations of activities orchestrate the expression of Ihh in the digit anlagen, growth plates, skull sutures, and digit tips. Consecutive deletions show that they function in an additive manner resulting in growth defects. Duplications, in contrast, cause not only dose-dependent upregulation of Ihh, but also misexpression, leading to phenotypes influenced by the copy number and relative positioning of individual elements. Taken together, our results uncover a complex regulatory landscape at the Ihh locus and exemplify the intricate and precise control of gene expression during morphogenetic processes.

overall_design: Circular Chromosome Conformation Capture (4C-seq) at the Ihh locus in mouse forelimb tissues (digit 2-5) of mutants and WT animals at E14.5.

first: Anja

last: Will

first: Verena

last: Heinrich

first: Stefan

last: Mundlos


title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide

city: RENNES

first: Yoann

last: AUGAGNEUR

address: 2 Avenue du Pr Leon Bernard

department: Pharmaceutical Biochemistry

institute: University Rennes 1

summary: We report the use of Next Generation RNA Sequencing to identifiy novel sRNAs in the human pathogen Staphylococcus aureus

overall_design: Extraction of RNAs in exponential phase of growth in Newman

first: Julie

last: Bronsard

first: Gaetan

last: Pascreau

first: Mohamed

last: Sassi

first: Tony

last: Mauro

last: Augagneur

first: Brice

last: Felden


title: Genome-wide chromatin accessibility profiling in maize using DNase-seq on two different tissues: inner stem tissue of V2 seedlings and husk

status: Public on Jul 03 2017

first: Johan

last: Zicola

address: Carl-von-Linné

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary:
Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism.  This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers.  Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches.
Importantly, enhancers carry characteristic chromatin signatures such as low DNA methylation, high chromatin accessibility and histone modifications such as H3K9ac and H3K27ac.  Computational enhancer identification approaches often use machine learning methods in combination with a number of experimental genome-wide datasets to identify key enhancers features and scans the whole genome.
Limited knowledge on plant enhancers restricts us in available approaches we can use to perform genome-wide enhancer prediction in plant species.  In this work, we have integrated genome-wide low DNA methylation (Regulski et al., 2013, GSE39232), chromatin accessibility and H3K9ac data from two tissues, inner stem tissue in seedlings and husk tissue, in a crop plant Zea mays.  This study identified approximately 1,400 candidate enhancers.

overall_design:
Examination of DNase I hypersensitivity in 2 tissue types (GSE94291)
Examination of H3K9ac in 2 tissue types (GSE94251)
Examination of gene expression in 2 tissue types (GSE94252)

first: Rurika

last: Oka


title: Comparing single cell sequences between WT vs. Spp1-/- BM multi-potent progenitor cells (MPP) cells

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

summary: WT vs. Spp1-/- MPPs showed distict patterns in tgene transcription profiles when analyzed with single cell sequencing

overall_design: MPPs from mice treated with thioglycollate were FACS-sorted, and gene expression profiles were compared between WT vs. Spp1-/- cells.

first: Masashi

last: Kanayama

first: Jason

last: Gibson

first: Simon

last: Gregory