title: Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis

first: Andrew

last: Cox

state: MA

address: 77 Avenue Louis Pasteur

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary: Selenium, one of a class of selenocysteine-containing proteins (selenoproteins), is an essential micronutrient known for its cancer prevention properties. Selenoprotein H (SepH) is a recently identified nucleolar oxidoreductase whose function is not well understood. Here we report that seph is an essential gene regulating organ development in zebrafish. Metabolite profiling by targeted LCMS/ MS demonstrated that SepH deficiency impairs redox balance by reducing the levels of ascorbate and methionine, while increasing methionine sulfoxide. Transcriptome analysis revealed that SepH deficiency induces an inflammatory response and activates the p53 pathway. Consequently, loss of seph renders larvae susceptible to oxidative stress and DNA damage. Finally, we demonstrate that seph interacts with p53 deficiency in adulthood to accelerate gastrointestinal tumor development. Overall, our findings establish that seph regulates redox homeostasis and suppresses DNA damage. We hypothesize that SepH deficiency may contribute to the increased cancer risk observed in cohorts with low selenium levels.

overall_design: 4 WT zebrafish samples and 4 SepH mutant samples

first: Wolfram

last: Goessling


title: microRNA expression profiling of the normal and regenerating liver of Chiloscyllium plagiosum

status: Public on Aug 30 2016

city: Hangzhou

first: conger

last: lu

address: No.2 Street

country: China

institute: zhejiang sci-tech university

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to improve our understanding of the mechanisms of liver regeneration in sharks and to identify the microRNAs that participate in liver regeneration and other liver-related diseases. To this end, normal and regenerating liver tissues from C. plagiosum were harvested 0, 3, 6, 12 and 24 h after partial hepatectomy (PH) and were sequenced using the Illumina/Solexa platform. In total, 309 known microRNAs and 590 novel microRNAs were identified in C. plagiosum. There were 368 microRNAs differentially expressed between the normal and regenerating livers. Using target prediction and GO analysis, most of the differentially expressed microRNAs were assigned to functional categories that may be involved in regulating liver regeneration, such as cell proliferation, differentiation and apoptosis.  Additionally, this study adds several novel microRNAs to the database, which will help identify microRNAs in other genetically related species and provides a starting point for future studies aimed at understanding the roles of microRNAs in liver regeneration and other liver diseases.

overall_design: Sample 1 is  the normal C. plagiosum liver, sample 2,  sample 3, sample 4 and sample 5 is the regenerating liver obtained 3, 6, 12 and 24 h after PH, respectively.

first: Conger

last: Lu

first: Zhengbing

last: Lv


title: Follicular Helper T Cells Progressively Differentiate to Regulate the Germinal Center Response

status: Public on Aug 29 2016

city: New Haven

first: Edward

middle: Isaac

last: Herman

state: Connecticut

address: 300 Cedar St, 541D TAC, PO Box 208031

department: School of Medicine

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Purpose: To compare the transcriptomes of IL-21-expressing, IL-21 and IL-4-expressing, and IL-4 expressing follicular helper T (Tfh) cells and Th2 cells in the spleen at 8 days following helminth infection Methods: Cell sorting of the populations was done for CD4+B220-CD44hiCXCR5hiPD-1hi cells of the various types, followed by mRNA purification.

overall_design: CD4+Splenic T cell mRNA profiles 8 days post-infection of IL-21/IL-4 dual reporter mice with Nippostrongylus brasiliensis were generated by mRNA sequencing using Illumina HiSeq 2000.

first: Jason

middle: S

last: Weinstein

middle: I

first: Begoña

last: Lainez

first: Paula

last: Licona-Limón

first: Enric

last: Esplugues

first: Richard

last: Flavell

first: Joe

last: Craft


title: A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report [Seq]

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

type: Genome variation profiling by high throughput sequencing

summary:
Purpose: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8% cases). A 2-month-old female patient presented with a mass arising in the fibula which was excised at our surgical center. This is only the eighth case of MNTI affecting an extremity, and the first reported in the fibula. To understand better the etiology of this MNTI, we used high-throughput sequencing technology to carry out an exhaustive genomic, transcriptomic and epigenetic characterization on the excised primary tumor and a derived cell line.
Methods: RNA was extracted from the flash frozen tumor and paired-end RNA-Seq was performed to identify potential oncogenic fusion genes and to quantify gene expression in the MNTI transcriptome. Genomic DNA was extracted from the tumor and from a sample of the patient's blood and whole-exome sequencing was done to detect somatic and germline variants. Copy number variation in the MNTI was determined by comparative genomic hybridization (CGH) of DNA from the tumor and blood to a SNP array. A cell line was derived from the tumor and was tested for sensitivity to a panel of compounds targeting epigenetic regulators.
Results: Whole-exome analysis indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A).  SNP-array CGH revealed the tumor to be euploid, with no detectable gene copy number variants.  Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells (GEO acession: GSE28875) and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed.  Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. The derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators.
Conclusions: In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case.

overall_design:
An mRNA profile was generated from an MNTI excised from the fibula of a 2-month-old female patient. The paired-end RNA-Seq reads were also used to detect putative fusion genes. Genomic DNA was extracted from the tumor and whole-exome and copy number comparative analyses were performed relative to a reference sample of genomic DNA from the patient’s blood (germline DNA).
This dataset represents RNA-Seq and Exome-seq samples.
Submitter has indicated there are no patient privacy concerns regarding the Exome-Seq samples.

first: David

middle: J

last: Barnes

last: Hookway

first: Nick

last: Athanasou

first: Takeshi

last: Kashima

first: Udo

last: Oppermann

first: Simon

last: Hughes

first: Daniel

last: Swan

first: Dietrich

last: Lueerssen

first: John

last: Anson

first: A

middle: B


title: Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription [RNA-Seq]

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

summary: gene expression data from 3 pairs of cancer associated fibroblasts and normal fibroblasts from the same individual

overall_design: mRNA seq data from 3 normal and 3 cancer associated fibroblast cell lines

first: Riina

last: Kaukonen


title: Genome-wide analysis of mitosis, early G1, late G1 and G2 in mouse pluripotent cells

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We provide the genome-wide map of Esrrb binding in mitotic and asynchronous ES cells together with the Esrrb-induced transcriptomic changes in early G1, late G1 and G2.

overall_design: Mitotic cells were obtained by mitotic shake-off and used for Esrrb ChIP-Seq studies. Cell-cycle RNA-Seq was performed on FACS-purified populations using a Ccna2-Gfp reporter


title: RIP-seq of RNA associated in vivo with the ProQ, Hfq or CsrA proteins, performed in Salmonella Typhimurium SL1344 or Escherichia coli W3110

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset includes representative RIP experiments carried out to characterize the in vivo interactome of the bacterial global RNA-binding protein ProQ. They include a series of RIPs performed on a Salmonella Typhimurium SL1344 ProQ-3xFLAG strain grown to the exponential (OD600=0.5), transition (OD600=2.0) or stationary (6 hours after cells reached OD600=2.0) phases; a RIP perfomed on an Escherichia coli W3110 ProQ-3xFLAG strain grown to the transition phase; a control series of RIPs performed on Salmonella Typhimurium SL1344 ProQ-3xFLAG and PhoP-3xFLAG strains grown to the transition phase. The first series shows how the ProQ RNA interactome evolves over growth in Salmonella, the second reveals ProQ targets in Escherichia, the third illustrates the lack of RNA-binding activity in a negative control, DNA-binding transcription regulator PhoP.

overall_design: This set includes 4 samples from Escherichia ProQ experiments

first: Alexander

last: Smirnov

last: Reinhardt

first: Regina

last: Günster

middle: U

first: Dörte

last: Becher

first: Jörg

last: Vogel


title: The TfoX regulon of Vibrio cholerae

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

summary: In this study, we determined the TfoX regulon of V. cholerae WT strain A1552 compared to a ΔhapR and ΔqstR strain using RNA-seq to better understand the protein's function.

overall_design: mRNA profiles of a V. cholerae strain A1552-TntfoX without (-ara) and with arabinose (+ara) induction and of strains A1552ΔhapR-TntfoX (+ara) and A1552ΔqstR-TntfoX (+ara). 3 independent biological replicates are provided for each bacterial strain. The bacteria were grown to high cell density and in the absence or presence of arabinose (to induce TfoX).


title: Novel apple miRNAs and their possible involvement in Fire Blight defense

status: Public on Aug 28 2016

city: Poznan

first: Elzbieta

last: Kaja

address: Umultowska 89

department: Bioinformatics

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: Fire blight (FB) is a bacterial disease affecting plants from Rosaceae family, including apple and pear. FB develops after the infection of Erwinia amylovora, gram-negative enterobacterium, and results in burnt-like damages and wilting, which can affect all organs of the plant. Although the mechanisms underlying disease response in apples are not elucidated yet, it has been well described that FB resistance depends on the rootstock type. The main objective of this work was to identify miRNAs involved in response to bacterial infection in order to better explain apple defense mechanisms against fire blight disease. We performed deep sequencing of eighteen small RNA libraries obtained from inoculated and non-inoculated Gala apple leaves.  233 novel plant mature miRNAs were identified together with their targets and potential role in response to bacterial infection. We identify three apple miRNAs responding to inoculation (mdm-miR168a,b, mdm-miR194C and mdm-miR1392C) as well as miRNAs reacting to bacterial infection in a rootstock-specific manner (miR395 family). Our results provide insights into the mechanisms of fire blight resistance in apple.

overall_design: Actively-growing leaf tissue samples were collected from eighteen apple trees, which includes three biological replicates of inoculated and non-inoculated Gala scions grown on G.30 or M.27 rootstock.

first: Michal

middle: W

last: Szczesniak

first: Michael

last: Axtell

first: Timothy

last: McNellis

first: Izabela

last: Makalowska


title: H3K4me2 profiling in C3H-10T1/2 preadipocytes [ChIP-seq]

city: Shanghai

first: Wei

last: Qi

address: Jinke Road

department: Biology

institute: China Novartis Institutes for BioMedical Research

summary: By screening a collection of epigenetic compounds, we find that Lysine-Specific Demethylase 1 (LSD1) inhibitors repress brown adipocyte differentiation. RNAi-mediated Lsd1 knockdown shows similar effect, which can be rescued by expression of wild-type, but not catalytically inactive, LSD1. Furthermore, adenoviral Cre-mediated Lsd1 deletion in mice leads to inhibition of brown adipogenesis, validating the pivotal role of LSD1 in brown fat development in vivo. LSD1 represses gene expression by demethylating H3K4. To identify the target genes of LSD1 during BAT differentiation, we analyzed the H3K4me2 enrichment in preadipocyte.

overall_design: Using ChIP-seq, we examined the H3K4me2 genomic enrichment locations in C3H-10T1/2 preadipocytes.

first: Yan

last: Chen


title: Transformation of mature adipocytes to liposarcoma in Ad/NICD mice

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Analysis of inguinal white adipose tissue (WAT) and liposarcoma (LPS) isolated from Notch1 overexpression mice (Ad/NICD). Results provide insight into molecular mechanisms underlying tumorigenic transformation of Ad/NICD mature adipocytes

overall_design: Two-condition experiment, Ad/N1ICD WAT vs. Ad/N1ICD LPS. Biological replicates: 4 Ad/N1ICD WAT and 8 Ad/N1ICD LPS

first: Pengpeng

last: Bi

first: Christopher

middle: A

last: Bidwell


title: Fraction-wise RNA-seq of the Salmonella Typhimurium SL1344 cell lysate resolved on a 10-40% glycerol gradient

last: Förstner

summary: While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset is a representative experiment carried out to characterize sedimentation properties of bacterial transcripts genome-wide. Downstream analysis of their sedimentation profiles enables their biochemical classification and is a prerequisite for identification of global RNA-binding proteins.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The set includes 20 samples corresponding to gradient fractions numbered from the top to the bottom of the gradient. Each fraction is spiked-in with an artificial RNA to enable normalization.

first: Richard


title: RNA-seq of dexamethasone-treated mouse primary hepatocytes infected with shControl or shSETDB2 adenovirus

city: Orlando

first: Manuel

last: Roqueta-Rivera

state: FL

address: 6400 Sanger Rd

institute: Sanford Burnham Preby Medical Research Institute

summary:
Purpose:  The goal of this study is to identify differentially expressed genes in SETDB2 deficient mouse primary hepatocytes (MPH) treated with dexamethasone when compared to control MPH
Methods: Total RNA from MPH treated with either shControl or shSETDB2 adenovirus (pool of 3 mice per group) was isolated by the TRIzol method (Life Technologies) according to manufacturer’s instructions. Total RNA was DNase-treated and RNA integrity was evaluated by Biolanalyzer (Agilent). RNA sequencing was performed by the SBP Genomics Core Facility in Lake Nona (Orlando, FL) using the Illumina HiSeq platform and the following parameters: paired-end read length: 100 BP; number of output reads: 300m reads. The Tophat+Cufflinks pipeline was used for the RNA-seq analysis as described previously (Haas et al., 2013; Trapnell et al., 2012). Differentially expressed genes in shSETDB2 vs. shControl MPH were determined using a 2-fold cutoff, p-value of less than 0.05, and FPKM (fragments per kilobase of transcript per million mapped reads) cutoff of 1. The shSETDB2 and shControl RNA-seq reads were mapped to the mm10 genome using Tophat (Trapnell et al., 2009). The mapping results were further analyzed by Cufflinks, which outputs the final differential gene list.

overall_design: mRNA profiles of shControl and shSETDB2 adenoviral infected mouse primary hepatocyte (n=3 mice) were generated by deep sequencing using Illumina HiSeq platform.

first: Jun

last: Ding

first: Xiaoman

last: Li


title: Transcriptome-wide analysis of gene expression regulated by LSD1 during brown adipocyte differentiation [RNA-seq]

summary: By screening a collection of epigenetic compounds, we find that Lysine-Specific Demethylase 1 (LSD1) inhibitors repress brown adipocyte differentiation. RNAi-mediated Lsd1 knockdown shows similar effect, which can be rescued by expression of wild-type, but not catalytically inactive, LSD1. Furthermore, adenoviral Cre-mediated LSD1 deletion in mice leads to inhibition of brown adipogenesis, validating the pivotal role of LSD1 in brown fat development in vivo. LSD1 is a histone H3 demethylase, which selectively removes methyl groups from mono- and di-methylated lysine 4 (H3K4me1 and H3K4me2) under most circumstances, and only from lysine 9 (H3K9me1/2) when bound with androgen receptor (AR) or estrogen receptor (ER). K4 demethylation causes transcription repression, while K9 demethylation may lead to activation of gene transcription. To investigate the target genes of LSD1 during BAT differentiaiton, we performed RNA-seq to profile the gene expression in brown adipocytes treated with DMSO or LSD1 inhibitor 611 (Cpd A) for 6 days, and gene set enrichment analysis (GSEA) was then employed to identify Gene Ontology (GO) terms that were significantly enriched.

overall_design: RNA-Seq data for brown adipocytes treated with DMSO or LSD1 inhibitor 611 (Cpd A). Biological triplicates were performed for each group.


title: Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: We were interested in how the complex mammalian transcriptomes were established. Using spermatogenesis as a model system, we address this question first by profiling the mRNAs, lncRNAs and circRNAs and examining their relative abundances in 4 types of SPCs (priSG-A, plpSC, pacSC, rST).

overall_design: F1 pups of DBA/2 and C57BL6 mice were used for cell isolation and SSC culture. priSG-A, plpSC and pacSC were isolated from prepubertal mice undergoing the first wave of spermatogenesis while rST were from 60 dpp adult mice.

first: Xiwen

last: Lin

first: Miao

first: Ting

last: Shen

last: Ni


title: Transcriptional profiling of zen homozygous and zen heterozygous Drosophila melanogaster embryos

status: Public on Aug 27 2016

city: Santiago

first: Christian

middle: E

last: Hodar

state: Santiago

address: Av. El Libano 5524

department: INTA

country: Chile

institute: Universidad de Chile

summary:
In D. melanogaster, the subdivision of dorsal ectoderm into amnioserosa (AS) and dorsal epidermis is controlled by the combined actions of two morphogens of the TGF-β family, Decapentaplegic (Dpp) and Screw (Scw). They form an extracellular gradient with peak levels of Dpp/Scw signalling in the dorsal-most region of the embryo. Dpp/Scw signalling is transduced to the nucleus by a complex containing the phosphorylated Smad transcription factor, pMad and the co-Smad, Medea, which are responsible for the transcriptional activation of a number of targets in specific dorsal territories, including zerknullt (zen) gen. zen encodes a homeobox transcription factor, which is expressed for a brief period of time in the early developing embryo and is required for all aspects of AS formation, including the initial cell shape changes that drive the morphogenesis of the AS epithelium. However, the number and nature of Zen-target genes involved in AS differentiation subsequent to its specification are currently unknown. The only known target genes of Zen are the so called u-shaped genes; they encode transcription factors that control the maintenance of AS after Zen activity has faded away, so they are not informative for elucidating the specification of morphological properties on a cellular level. In this project, we attempted to identify Zen-target genes required for AS differentiation and/or maintenance.
Methods: D. melanogaster flies were grown at 22 ºC on standard cornmeal, molasses, agar, yeast medium. Staged embryos were obtained as described in Zuñiga et al. (2009). Fly strain was zen7, a null allele balanced over TM3, ftz-lacZ (Rushlow et al., 1987). zen7 homozygous embryos were selected using a genotyping procedure described by Ghanim and White (2006). In our case, both the absence of lacZ specific band together with the presence of a control band (non-coding region of gene Dtg) were indicators of homozygous lethal embryos. For RNA extractions, extracts of homozygous (zen7) and heterozygous (zen7/TM3, ftz-lacZ) embryos at stage 5 or stage 6-7 of embryogenesis , previously preserved in RNAWIZ reagent (N = 100) were pooled, then samples were carefully homogenized in a 1.5 mL Eppendorf tube on ice with the aid of RNAse-free polypropylene pellet pestle. After homogenization, RNA extraction was performed using standard protocols. RNA was quantified using Qubit® RNA HS Assay Kit (Thermo Fisher) and the integrity was assayed in a Tape station 2200 (Agilent Technologies). Samples were treated with Turbo DNA-free DNase (Ambion) to remove contaminating DNA.  Two biological replicates of RNA from of homozygous and heterozygous embryos were sequenced using XXX and the sequence reads that passed quality filters were analyzed using XXX

overall_design: Two biological replicates of RNA from  zen7 homozygous embryos and zen7/TM3, ftz-lacZ heterozygous embryos (reference) at stage 5 or stage 6-7 of embryonic development were sequenced using Illumina HiSeq 2000.

first: Verónica

last: Cambiazo


title: RNA-seq study of directed sclerotome, Lon non-coding RNA PEAT, and the embryonic Dll1 lineage form E9.0-9.5

city: Berkeley

last: Harland

state: CA

address: 571 Life Sciences Addition #3200

department: Department of Molecular and Cell Biology

institute: UC Berkeley

summary: We sequenced RNA from embryonic mouse tissue directed to form sclerotome in culture.  Using Crispr/Cas9, we generated a mouse line bearing a complete deletion of the PEAT, a LncRNA adjacent tp Pax1 and highly enriched in sclerotome. We perform RNA-seq on samples from 4 stages of maturation of the Dll1 lineage.

overall_design: Examination of sclerotome using RNA-seq

first: David

last: Stafford

middle: M


title: Identifying RBBP4-regulated transcriptome in T98G glioblastoma cells using RNA sequencing (RNA-seq)

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

summary: Retinoblastoma-binding protein 4 (RBBP4) is a chromatin modifying protein regulating multiple cellular functions. We have identified RBBP4 as a critical modulator of therapy response in glioblastoma (GBM). The purpose of this study was to identify genes through which RBBP4 regulates this important role with expectation of identifying candidates for therapy sensitizing strategy in GBM, and perhaps in other human malignancies.

overall_design: RNA was extracted from T98G cells expressing either a control shRNA (shNT) or RBBP4 shRNA (shRBBP4), and RNA-seq was used to evaluate the patterns of gene expression comparing T98G-shNT with the T98G-shRNA.

first: Gaspar

last: Kitange

first: Jann

middle: N

last: Sarkaria


title: Epigenome screening for genes regulated by retinoblastoma-binding protein 4 (RBBP4) in glioblastoma (GBM) cells

summary: We report that RBBP4 has dual effect on gene regulation, whereby some genes are downregulated (~60%) while others are activated (~40%).

overall_design: Examination of chromatin landscape of H3K9Ac in T98G cells expressing control NTshRNA compared with RBBP4 shRNA.


title: Mesenchymal tumors can derive from pericytes.

city: Toronto

first: Benjamin

last: Alman

state: Ontario

address: PGCRL 16th Floor, 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

summary: We demonstrated that deletion of the p53 tumor suppressor gene in NG2 expressing cells resulted in the development of bone and soft tissue sarcomas that closely resemble human tumors. To determine gene expression differences between NG2 expressing pericytes lacking p53 and sarcomas that arose from deletion of p53 in NG2 expressing cells, RNA sequencing analysis was implemented.

overall_design: We isolated total RNA from NG2 expressing pericytes (2 samples), which were sorted from skeletal muscle tissues of NG2-Cre;p53flox/flox mice using an NG2 antibody. We also isolated total RNA from osteosarcomas (2 samples) and soft tissue sarcomas (2 samples), which were developed in NG2-Cre;p53flox/flox mice. Differentially expressed genes were analyzed using Illumina HiSeq 2000.

first: Shingo

last: Sato


title: Identifying RBBP4-regulated transcriptome in T98G glioblastoma (GBM) cells using RNA sequencing, and epigenome screening for genes regulated by RBBP4 in GBM cells

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

overall_design: Refer to individual Series


title: Partitioning of a RNA interactome by gradient profiling (Grad-seq)

first: Konrad

last: Förstner

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: LIN-28 balances longevity and germline stem cell number in C. elegans through let-7/AKT/DAF-16 axis

status: Public on Aug 26 2016

first: Jing-Dong

middle: Jackie

address: Yueyang Road 320

department: CAS-MPG Partner Institute for Computational Biology

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

summary: Transcriptomic effects of lin-28 RNAi on N2 and glp-1 worms were compared.

overall_design: RNA samples of N2 and glp-1 worms on adult day 4 under empty vector (EV) or lin-28 RNAi from L1 were sequenced.

first: Jing

middle: D


title: Tissue-specific Emergence of Regulatory and Intraepithelial T Cells from a Clonal T-cell Precursor

city: New York

first: Luka

last: Mesin

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: We used RNA sequencing to characterize gene expression of CD4+ CD8α+ double positive (DP), Foxp3+ Treg (TR) and CD4+ single positive (SP) cells in the lamina propria (LP) and intraepithelial compartment (IEL) that had differentiante from the same clonal transnuclear (TN) precursor.

overall_design: We adoptively transferred CD4+ CD8α- Foxp3-GFP- isolated from pTregTN/RKO/Foxp3-GFP mice into TCRαβKO hosts. After 6 weeks, we sorted transferred CD4+ CD8α+, Foxp3+ pTreg as well as unconverted CD4+ CD8α- Foxp3-GFP- from the small intestine LP and IEL compartments for whole transcriptome analysis by mRNA sequencing.

first: Angelina

last: Bilate

first: Gabriel

last: Victora

first: Hidde

middle: L

last: Ploegh


title: Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

type: Methylation profiling by high throughput sequencing

summary: Gene silencing is a powerful approach for interrogating gene function and holds promise for therapeutic applications. Here we repurpose the ERV silencing machinery of embryonic stem cells to stably silence genes in somatic cells by epigenetics. This was achieved by transiently expressing combinations of artificial transcriptional repressors that bind to and synergize at the target locus to instruct de novo DNA methylation, thus ensuing long-term memory of the repressive epigenetic state. Silencing was highly specific and sharply confined to the targeted gene, was resistant to activation induced by cytokine stimulation and could be relieved only by targeted DNA demethylation. We demonstrate the portability of this technology by silencing three highly transcribed genes, B2M, IFNAR1, and VEGFA, using multiple DNA binding platforms and interrogating thousands of genomic loci after reporter insertion in different cell types, including primary T-lymphocytes. Finally, we expanded the breadth of targeted epigenome editing by multiplex gene silencing, setting the stage for its application in research and medicine.

overall_design: MeDIP-seq and RNA-seq profiling of K562 cells expressing B2M:tdTomato transgene and silenced by dCas9 or TALE directed DNA methylation targeting B2M promoter

first: Angelo

last: Amabile

first: Alessandro

last: Migliara

first: Paola

last: Capasso

first: Mauro

last: Biffi

first: Luigi

last: Naldini

last: Lombardo


title: The Genetic Networks that Orchestrate Development of Specific Waves of Fetal and Adult B-1 and B-2 Development are Distinct

city: Los Angeles

first: Kenneth

last: Dorshkind

state: California

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

summary: B lymphocyte development is often depicted as a linear process that initiates in the fetus and continues in the bone marrow after birth. Based on the dissection of B lymphopoiesis in a PU.1 hypomorphic strain of mice, generated by deletion of a 14kb upstream regulatory element of the Sfpi1 gene, and the transcriptional profiling of fetal and adult B cell progenitors, we establish the existence of three waves of B-1 and two waves of B-2 development and show that each of these waves has distinct transcriptional requirements. In addition to revealing an unappreciated complexity in the development of the humoral immune system, the results provide genetic evidence that the B-1 and B-2 lineages are distinct and a molecular basis for the layering of immune system development.

overall_design: The experiments compare gene expression in B-1 and B-2 progenitors from E15.5 fetal liver, day 2 neonatal liver, and week 9-11 adult bone marrow.

first: Encarnacion

last: Montecino-Rodriguez

first: Michael

last: Fice

first: David

last: Casero

first: Beata

last: Berent-Maoz

first: Chad

last: Barber


title: Single cell transcriptome analysis of mouse thoracic sympathetic ganglia

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: We explore the heterogeneity of mouse thoracic ganglia demonstrating the presence of an unexpected variety of cell-types and identify specialized populations of nipple- and pilo-erector muscle neurons. These neurons extend axonal projections and are born amongst other neurons during embryogenesis, but remain unspecialized until target organogenesis occurs postnatally. Target innervation and cell-type specification is coordinated by an intricate acquisition of unique combinations of growth factor receptors and the initiation of expression of concomitant ligands by the nascent erector muscles.

overall_design: RNA-seq analysis of 298 single sympathetic neuronal cells from the mouse thoracic ganglion

last: Furlan

first: Gioele

last: La Manno

first: Patrik

last: Ernfors


title: Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

summary:
BACKGROUND:
Streptococcus pneumoniae, the pneumococcus, is the main etiological agent of pneumonia. Pneumococcal infection is initiated by bacterial adherence to lung epithelial cells. The exact transcriptional changes occurring in both host and microbe during infection are unknown. Here, we developed a time-resolved infection model of human lung alveolar epithelial cells by S. pneumoniae and assess the resulting transcriptome changes in both organisms simultaneously by using dual RNA-seq.

RESULTS:
Functional analysis of the time-resolved dual RNA-seq data identifies several features of pneumococcal infection. For instance, we show that the glutathione-dependent reactive oxygen detoxification pathway in epithelial cells is activated by reactive oxygen species produced by S. pneumoniae. Addition of the antioxidant resveratrol during infection abates this response. At the same time, pneumococci activate the competence regulon during co-incubation with lung epithelial cells. By comparing transcriptional changes between wild-type encapsulated and mutant unencapsulated pneumococci, we demonstrate that adherent pneumococci, but not free-floating bacteria, repress innate immune responses in epithelial cells including expression of the chemokine IL-8 and the production of antimicrobial peptides. We also show that pneumococci activate several sugar transporters in response to adherence to epithelial cells and demonstrate that this activation depends on host-derived mucins.

CONCLUSIONS:
We provide a dual-transcriptomics overview of early pneumococcal infection in a time-resolved manner, providing new insights into host-microbe interactions. To allow easy access to the data by the community, a web-based platform was developed ( http://dualrnaseq.molgenrug.nl ). Further database exploration may expand our understanding of epithelial-pneumococcal interaction, leading to novel antimicrobial strategies.

sample_organism:
Homo sapiens
Streptococcus pneumoniae D39

overall_design:
5 time points are analysed (0, 30, 60, 120 and 240 minutes after infection). Each time point has two biological replicates except for the 240 mpi. Furthermore, each time point has two pneumococcal strains used to infect A549 cells, encapsulated and unencapsulated pneumococci. In total there are 18 samples.
cellular infection model, contains rRNA-depleted total RNA from A549 epithelial cells and D39 S. pneumoniae

first: Jelle

last: Slager

first: Siger

last: Holsappel

first: Jan-Willem

last: Veening


title: Single-base resolution methylome of Xenopus laevis embryos

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: Here we describe a base-resolution DNA methylation map of Xenopus laevis gastrula (st.10.5) embryos generated by whole genome bisulfite sequencing

overall_design: WGBS profiling of Xenopus laevis st.10.5 embryos

first: Ryan

last: Lister


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-/- Irf8-/- GMP)

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

overall_design: Single cell RNA seq of different hematopoietic populations integrated with Chip seq involving multiple markers

first: Andre

last: Olsson

first: Nathan

last: Salomonis

first: Viren

last: Chaudri

first: Bruce

last: Aronow

first: Harinder

last: Singh

first: H


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of bone marrow lineage-negative Sca1+ CD117+ cells)


title: Single cell RNA-seq analysis of sensory neurons reveal diverse injury responses after sciatic nerve transection

first: Ganlu

last: Hu

address: 695 Charles E Young Dr. South

department: human genetics

institute: University of California, Los Angeles

summary: We  reported the gene expression analysis of different types of sensory neuron with peripheral nerve transection treatment on single cell level. We found substantial variation between myelinated large diameter neurons and small diameter nonpeptidergic nociceptors, in both terms of regeneration response genes regulation as well as fraction of cells respond to nerve injury.

overall_design: Two month old adult CAST/Eij ♂ cross C57BL/6♀F1 and C57BL/6 mice were performed sciatic nerve transection on the right side. Single DRG soma from L3-5 on both side were manually picked in the lowest possible volume and then performed single cell RNA-seq using smart-seq2 protocol.  A total of 106 dissociated DRG neurons for each side with almost equal number of small, medium and large diameter neurons were lysed and split into three parts in order to constructed bulk cell control.


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of GMP)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Irf8 KO GMP)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of bone marrow lineage-negative CD117+ CD34+ cells)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-GFP GMP)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-/- GMP)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq from CMP)


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Irf8-GFP GMP)


title: ZNF750 is a lineage-specific tumor suppressor in squamous cell carcinoma [UMSCC1]

status: Public on Aug 25 2016

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: ZNF750 controls epithelial homeostasis by regulating epidermal-differentiation genes, a role underscored by its pathogenic mutations in esophageal squamous cell cancers (SCCs). However, the precise role of ZNF750 in SCC cell biology remains unclear. In this study, we report that ZNF750 is exclusively deleted, mutated and underexpressed in human SCCs, and low ZNF750 expression is associated with poor survival. Restoration of wildtype, but not mutant ZNF750 protein uniquely inhibited the malignant phenotype of SCC cells both in vitro and in vivo. Notably, ZNF750 promoted the expression of a LncRNA (TINCR) which mediated both cancer-inhibition and differentiation-induction effects of ZNF750. In addition, ZNF750 potently suppressed cell migration by directly inhibiting the transactivation of LAMC2. Together, our findings characterize ZNF750 as a crucial SCC-specific suppressor and uncover its novel anticancer-associated functions.

overall_design: RNA expression profile in UMSCC1 following ZNF750 wildtype overexpressing was analyzed by RNA-Seq.

first: Masaharu

last: Hazawa

first: De-Chen

last: Lin

first: Harish

last: Handral

first: Liang

last: Xu

first: Ye

last: Chen

first: Yan-Yi

last: Jiang

first: Anand

last: Mayakonda

first: Ling-Wen

last: Ding

first: Xuan

last: Meng

first: Arjun

last: Sharma

first: Sharon

last: Samuel

first: Mohammad

last: Movahednia

first: Richard

last: Wong

first: Henry

last: Yang

first: Cao

last: Tong

middle: P


title: Next Generation Sequencing Facilitates Comparison of Long-Term Cultured Nephron Progenitor Cells with Their Cognate Primary Cells

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary:
Purpose: Nephron progenitor cells generate nephrons, the basic units of kidney. We developed methods to culture mouse and human NPCs in their self-renewal state in vitro with full nephrogenic potentials. The RNA-seq here is used to compare the global gene expression of long-term cultured mouse NPCs and their cognate freshly isolated primary NPCs
Methods: mRNA profiles were generated by deep sequencing in duplicate from E11.5, E12.5, E13.5, E16.5 and P1 primary NPCs, and from long-term cultured NPCs derived from E11.5, E13.5, E16.5 and P1 (Passage 20 and Passage 80 for each cell line). To generate rpkm values from raw data, single-end 50bp reads were mapped to the UCSC mouse transcriptome (mm9) by STAR9, allowing for up to 10 mismatches (which is the default by STAR). Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. And expression levels of all genes were estimated by Cufflink10 using only the reads with exact matches.
Results: The gene expression levels of the "NPC-signature genes" were firstly transformed as logarithm scales. And then the program “prcomp”, a built-in program for principal component analysis in R packages, was employed with default parameters. We evaluated the variance percentage of each principal component, and found the top 3 components accounted for 84.1% of the total variance, where PC1 accounted for 46.42%, PC2 23.87% and PC3 13.81%. Those three PCs are therefore selected as candidate principal components in the further analysis. Another program “scatterplot3d” in the R packages was used to plot the 3D view of PCA, and “ggplot2” was used in 2D view of PCA. The PCA results indicate that cultured NPCs cluster together in PCA analysis while primary NPCs segregate into early (E11.5 to E13.5) and later (E16.5, P1) NPC groups. Interestingly, cultured NPCs are close to early NPCs in both PC1 and PC2 axes, suggesting that cultured NPCs are maintained in state close to early NPCs. The close cluster of P20 and P80 NPCs show the robustness of our culture condition in maintaining stable self-renewal state of NPCs.
Conclusions: Our study represents the first analysis comparing the long-term cultured NPC lines we geneated with primary NPCs, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Juan

middle: C

last: Izpisua Belmonte

first: Zhongwei

last: Li


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (ChIP-seq)

first: H. Leighton

last: Grimes

summary: Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematopoietic development

overall_design: Single cell RNA seq of 4 different hematopoietic populations integrated with ChIP-Seq involving 4 different markers

first: Andre

last: Olsson

first: Nathan

last: Salomonis

first: Viren

last: Chaudri

first: Bruce

last: Aronow

first: Harinder

last: Singh

first: H


title: iPSC-Derived Cholangiocytes

first: Asha

last: Nair

address: 200 1ST ST SW

summary: Human iPS cells were differentiated to cholangiocyte-like cells thorugh five phases of endodermal differentiation.

overall_design: Human iPSC were generated by forced expression of the Yamanaka pluripotency factors. We then pursued a stepwise differentiation strategy toward iDCs, using precise temporal exposure to key biliary morphogens, and we characterized the cells,  using a variety of morphologic, molecular, cell biologic, functional, and in vivo approaches.

first: Robert

last: Huebert

first: Thiago

last: De Assuncao


title: Next-generation sequencing and quantitative analysis of wild type and p110gamma -/- tumors and tumor-associated macrophages

first: Judith

last: Varner

address: 3855 Health Sciences Drive #0819

institute: Univeristy of California San Diego

summary:
Purpose: The goals of this study were to identify quantitative gene expression differences between whole tumor and tumor-associated macrophages (TAMs) derived from Lewis lung carcinoma (LLC) tumors grown in wild type and PI3Kinase-gamma-null mice.

Methods: mRNA profiles of whole tumor or tumor-associated macrophages (CD11b+Gr1- cells) from wild type (WT) or PI3Kinase-gamma-knockout (p110g-/-) mice were generated by single deep read sequencing, in triplicate or quadruplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were aligned to mouse transcriptome using the bowtie2 aligner. Gene-level summaries were normalized and analyzed for differential expression using DESeq.

overall_design: mRNA profiles of whole tumor and tumor-associated macrophages from WT and p110g-/- mice were generated by deep sequencing in triplicate or quadruplicate using Illumina HiSeq 2000.

first: Megan

last: Kaneda


title: Next Generation Sequencing of Control and Pbx Mutant Spinal Motor Neuron Transcriptomes

first: Jeremy

middle: S.

last: Dasen

address: 550 First Ave

department: NYU Neuroscience Institute

institute: New York University Medical Center

summary:
Purpose: Conducted expression profiling by RNA-seq as unbiased screen to identify genes that are altered in motor neurons of PbxMNΔ mice at e12.5 at brachial and thoracic levels of the spinal cord. Because loss of Pbx genes affects MN organization at all rostrocaudal levels, we focused on genes whose profiles were altered at both brachial and thoracic levels.
Methods: We compared gene expression profiles in MNs isolated from control Hb9::GFP and PbxMNΔ; Hb9::GFP embryos at e12.5. MNs were purified by FACS, and RNA was extracted from 9 PbxMNΔ; Hb9::GFP and 9 control Hb9::GFP embryos at brachial and thoracic levels using the Arcturus Picopure RNA isolation kit. 10ng of RNA was pooled from 3 RNA samples of each genotype, and used to amplify 100ng of cDNA using Nugene's Ovation RNA-Seq System V2 kit, 100ng of cDNA for each sample was used as in input to prepare 12 bar coded libraries using the Ovation Ultralow Library system. We then performed expression profiling by RNA-seq. The samples were mixed into two pools and run on two 50-nucleotide paired end read rapid run flow cell lanes with the Illumina HiSeq 2500 sequencer. Generating on average 74 and 101 million reads passing filter for brachial and thoracic samples respectively.
Results: This analysis yielded 64 brachial and 124 thoracic genes that were differentially expressed with a stringent cutoff of padj.<0.05. Of these genes, we found 31 genes in common between the two, brachial and thoracic, levels of the spinal cord that may play a role in motor neuron columnar organization. Furthermore our expression profiling of control brachial and control thoracic MNs identified 61 genes with (padj.<0.05), that represent distinct molecular profiles of MNs generated at brachial and thoracic levels which may be used to further characterize MNs involved in forelimb and thoracic innervation.
Conclusions: Our study represents a detailed transcriptional analysis of embryonic spinal motor neurons and revealed a number of novel motor neuron-specific genes that are under transcriptional regulation of Pbx genes.

overall_design: Examination of embryonic spinal MN expression profiles at 2 different spinal cord levels, brachial and thoracic. From RNA collected from 9 pooled Control and 9 PbxMNΔ e12.5 Hb9::GFP FACS MNs.

middle: S

first: Olivia

last: Hanley

first: Lisa

last: Cohen


title: CLIP-seq analysis of integrase-RNA interactions

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: Missouri

address: Washington University School of Medicine

summary: Integrase CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitors and IN K264/266A and R269/K273A mutations

overall_design: Integrase CLIP-seq experiments were conducted by immunoprecipitation of integrase-RNA complexes from fully formed mature and eccentric virus particles. Libraries of RNA molecules bound by integrase were generated and sequenced by Illumina Hi-Seq2000 and 2500 platforms.


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies

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


title: Bulk RNA-seq analysis of Type 5 retinal bipolar cells from the Htr3a-GFP line

city: Cambridge

first: Karthik

last: Shekhar

state: MA

address: 415 Main St.

institute: Broad Institute

summary: 15,000 GFP+ cells were collected from two replicates of the Htr3a GFP line into RNAlater (ThermoFisher, AM7024). RNA was purified and bulk RNA-seq was performed using the Ovation RNA-seq system V2 (Nugen, 7102-32)

overall_design: Bulk RNA-seq analysis of Type 5 retinal bipolar cells (2 biological replicates)


title: ZNF750 is a lineage-specific tumor suppressor in squamous cell carcinoma

first: Phillip

last: Koeffler

overall_design: Refer to individual Series


title: Smart-seq2 analysis of P17 FACS sorted retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line

summary: Three Vsx2-GFP mouse retinas were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 288 single cells and 3 bulk libraries using Smart-seq2 (~10,000 cells each)

overall_design: Three mouse retinas (labeled 1a, 2a, 2b) were used, and 96 single cells from each were processed using Smart-seq2. A bulk RNA-seq control of 10,000 cells from each retina was also prepared


title: XRN2 Autoregulation and Control of Polycistronic Gene Expression in Caenorhabditis elegans

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

institute: Friedrich Miescher Institute

summary: XRN2 is a conserved 5’-->3’ exoribonuclease that complexes with XTB-domain containing proteins. Thus, in Caenorhabditis elegans (C. elegans), the XTBD-protein PAXT-1 stabilizes XRN2 to retain its activity. XRN2 activity is also promoted by 3'(2'),5'-bisphosphate nucleotidase 1 (BPNT1) through its hydrolysis of 3’-phosphoadenosine-5'-bisphosphate (PAP), an endogenous XRN inhibitor. Here, we find through unbiased screening that loss of bpnt-1 function suppresses lethality caused by paxt-1 deletion. This unexpected finding is explained by XRN2 autoregulation, which occurs through repression of a cryptic promoter activity and destabilization of the xrn-2 transcript. Autoregulation appears to be triggered at different thresholds of XRN2 inactivation, such that more robust XRN2 perturbation, by elimination of both PAXT-1 and BPNT1, is less detrimental to worm viability than absence of PAXT-1 alone. Like more than 15% of C. elegans genes, xrn-2 occurs in an operon, and we identify additional operons under its control, consistent with a broader function of XRN2 in polycistronic gene regulation. Regulation occurs through intercistronic regions that link genes in an operon, but similar mechanisms may allow XRN2 to operate on monocistronic genes in organisms lacking operons.

overall_design: Wild-type C. elegans worms were subjected to mock or xrn-2 RNAi from L1 to L4 stage at 20°C. Total RNA was extracted from the worms, and polyadenylated RNA was analyzed.

first: Takashi

last: Miki

first: Helge

last: Grosshans


title: Massively parallel interrogation of the effects of gene expression levels on cellular fitness

city: Rehovot

first: Leeat

last: Keren

state: Israel

address: Herzl 706

department: Mathematics and Computer Science

country: Israel

institute: Weizmann Institute of Science

summary: Data of gene expression levels across individuals, cell types, and disease states is rapidly expanding, yet we have limited understanding of how expression levels impact cellular and organismal phenotypes. Here, we present a massively parallel system for assaying the effect of gene expression levels on cellular fitness in Saccharomyces cerevisiae by systematically altering the expression level of each of ~100 endogenous genes at ~100 distinct expression levels spanning a 500-fold range at high resolution. Our results show that the relationship between expression levels and growth is gene- and environment-specific, with the specific relationship exhibited by each gene being highly informative on its function, stoichiometry within complexes, and interaction with other genes. Notably, in one of the two environmental conditions that we tested, we find that ~20% of the genes have expression levels where fitness is greater than that at wild-type expression levels, indicating that wild-type expression is not optimal for growth in that condition. We find that genes whose fitness is greatly affected by small changes in expression level tend to exhibit lower cell-to-cell variability in expression, suggesting that noise in gene expression is shaped in part by the relationship between expression and fitness. Overall, our study addresses a fundamental gap in our understanding of the functional significance of gene expression regulation and offers a powerful framework for evaluating the phenotypic effects of expression variation.

overall_design: 130 synthetic promoters were genomically integrated upstream of 96 endogenous yeast genes to span an expression range for each gene. Fitness as a function of the expression level of each gene was computed by a pooled growth competition assay.

first: Jean

last: Hausser

first: Maya

last: Lotan-Pompan

first: Ilya

last: Vainberg Slutskin

first: Hadas

last: Alisar

first: Sivan

last: Kaminski

first: Adina

last: Weinberger

first: Uri

last: Alon

first: Ron

last: Milo

first: Eran

last: Segal


title: Complement protein C1q modulates macrophage molecular signaling and inflammatory responses during ingestion of atherogenic lipoproteins

city: Long Beach

first: Deborah

middle: A.

last: Fraser

address: 1250 Bellflower Blvd

department: Biological Sciences

institute: California State University, Long Beach

summary: C1q suppresses JAK-STAT signal transduction and activates PPAR-mediated transcription in macrophages during clearance of modified forms of LDL leading to a reduction in inflammatory response.

overall_design: Human monocyte-derived macrophages (HMDM) were incubated with either oxidized (oxLDL) or acetylated low-density lipoprotein (acLDL) in the presence or absence of C1q for 3 hours. Total RNA was extracted using the Qiagen RNeasy Mini Kit. RNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. Sequences were aligned to a reference genome (hg38), RPKM and raw counts were determined using CASAVA version 1.8.2.

first: Minh-Minh

last: Ho


title: Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP X  Thy1-stop-YFP Line#1 mice

first: Karthik

last: Shekhar

summary: Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align.

overall_design:
Four mouse retinas (labeled 1la, 1Ra, and 2la, 2Ra respective from the two mice) were used, and 96 single cells from each were processed using Smart-seq2. Total 384 cells
Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP mice (Kcng4tm1.1(cre)Jrs mice [Duan et al., Cell 158, 793-807, 2015] crossed to the cre-dependent reporter Thy1-stop-YFP Line#1 [Buffelli et al., Nature 424, 430-434, 2003])


title: Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (Bulk RNA-Seq)

first: H. Leighton

last: Grimes

overall_design: Single-cell RNA Seq of 4 different hematopoietic populations, integrated with ChIP Seq involving 4 different markers

first: Andre

last: Olsson

first: Nathan

last: Salomonis

first: Viren

last: Chaudri

first: Bruce

last: Aronow

first: Harinder

last: Singh

first: H


title: Single cell RNA-sequencing of retinal bipolar cells


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [7]

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

summary: The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs.

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [7] contains the sequences of fragments BACs cloned into the STARR-seq plasmid backbone. These STARR-seq plasmid libraries were transfected into A549 cells. The contents of this data set are the sequences encoded on the pool of reporter plasmids that were then transfected into A549 cells. The data set describing the results of that transfection is described in [1].

first: Anthony

last: D'Ippolito

first: Ian

last: McDowell

first: William

last: Majoros

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Gregory

last: Crawford

first: Timothy

last: Reddy


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [5]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
In dataset [5], the files contain RNA-seq from GR-ChIP-reporters that were transfected into A549 cells and treated with DEX or EtOH.
[5] contains the reporter assay specific RNA-seq from plasmids described in [4].


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [4]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [4] contains the sequences of GR ChIP-seq fragments that have been cloned into the STARR-seq backbone.
[4] *.fragments files contain DNA fragments that were cloned into a massively parallel reporter assay. These fragments were generated via ChIP-seq for the glucororticoid receptor. The ChIP-seq library that was used for this source material was sequenced and the data from that sequencing was deposited in [8].   The [4] *.fragments file contains the abundance of each reporter plasmid produced by cloning the GR ChIP-seq library into the reporter vector.


title: Isolation and next generation sequencing of epididymal extracellular vesicles reveals segmental patterns of miRNA expression and a potential mechanism for modification of the sperm epigenome.

city: Newcastle

first: Brett

last: Nixon

address: University Drive, Callaghan

institute: University of Newcastle

summary: Interest in the sperm epigenome continues to grow in view of the realization that it is vulnerable to dynamic modifications arising from a variety of paternal environment exposures and that this legacy can serve as an important determinant of intergenerational inheritance. It has been postulated that such exchange may be communicated to maturing populations of spermatozoa via the transfer of small non-coding RNAs in a mechanism involving epididymosomes; small membrane bound vesicles secreted by the soma of the male reproductive tract (epididymis).  Herein we confirm that mouse epididymosomes encapsulate an impressive repertoire of >350 microRNA (miRNA), a majority (~60%) of which are also represented in the miRNA signature of maturing spermatozoa. This includes >50 miRNAs that were found exclusively in epididymal sperm and epididymosomes, but not in the surrounding soma, thus supporting the notion that epididymosomes may selectively deliver regulatory non-coding RNA cargo to maturing sperm. Interestingly, we also documented substantial plasticity in terms of the epididymosome-borne miRNAs, including significant fold changes in the relative abundance of almost half of the miRNAs along the length of the epididymis.  Finally, we provide the first direct evidence for the transfer of several prominent miRNAs between mouse epididymosomes and spermatozoa, and in so doing afford novel insight into a mechanism of intercellular communication through which the RNA payload of sperm can be modified during their post-testicular development.

overall_design: Examination of the microRNA expression profile of mouse epididymal epididymosomes using next generation sequencing in triplicate.

first: Jackson

last: Reilly

first: Simone

middle: J

last: Stanger

first: Amanda

last: Anderson

first: Kate

last: Chamberlain

first: Kiralee

last: Church

first: Bettina

last: Mihalas

first: Sonika

last: Tyagi

first: Janet

last: Holt

first: Eileen

last: McLaughlin


title: Direct GR binding sites potentiate clusters of TF binding across the human genome

address: 101 Science Drive

department: Center for Genomic and Computational Biology

overall_design: Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour. Dnase-seq was performed on A549 cells treated for 1 h with dexamethasone or ethanol.

first: Christopher

last: Vockley

first: D’Ippolito

last: Anthony

first: McDowell

last: Ian

first: Majoros

last: William

first: Safi

last: Alexias

first: Song

last: Lingyun

first: Crawford

last: Gregory


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [2]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [2] contains the sequences obtained from plasmids transfected into A549 cells isolated from the nuclei of cells treated with DEX or ETOH. [2] contains the abundance of plasmids that cover same overall region as [1], but were not redundant with the content of [1] and were generated in independent experimental steps.

first: Anthony

last: D'Ippolito

first: Ian

last: McDowell

first: William

last: Majoros

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Gregory

last: Crawford

first: Timothy

last: Reddy


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [3]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [3] contains the results of RNA-seq performed on A549 cells treated with DEX or EtOH for 3 hours.


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [6]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functioal analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [6] contains the ChIP exo data from cells treated with 100 nM DEX.


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [1]

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [1] contains rna seq from BAC DNA tagments (nucleic acids that have been treated with  Nextera transposase to fragment the nucleic acids and add sequencing adapters) cloned into the STARR-seq plasmid backbone, transfected into A549 cells and treated with DEX or ETOH.


title: Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing.

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

summary:
Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology.
Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified ≈ 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel.
In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown

overall_design: Total RNA was extracted from two independent experiments with different time-points of hypoxia exposure (1% oxygen). HUVEC were exposed to 24h normoxia and 24h hypoxia or to 24h normoxia and 48h hypoxia. Each experiment was performed in duplicate.

first: Jose

last: Garcia-Manteiga

first: Christine

last: Voellenkle


title: Med12 and p300 chips in HSPCs

city: New York

first: Beatriz

last: Aranda-Orgilles

address: 522 First Avenue

institute: NYU School of Medicine

summary: We characterized the genome wide occupancy of Med12 and p300 in mouse HSPCs. We also characterize p300 occupancy upon shRNA against control or Med12.

overall_design: ChIP-seq analysis of Med12 and/or p300 in untreated HSPCs

first: Iannis

last: Aifantis


title: Genome-wide characterization of MED12 occupancy in human CD34+ cells

summary: We report ChIP-Seq data for MED12 in human CD34+ cells.  Med12 occupies promoter distal regions that regulate specific transcriptional programs required for the homeostasis of the hematopoietic system.

overall_design: 50 milion cells were used to perform ChIP from CD34+ cells with 10 ug of antibody


title: Histone chromatin modifications in control and Med12-deficient mouse HSPCs

summary:
Using iChIP, we map H3K27Ac, H3K4me3 and H3K4me1 in small populations (HSPCs) in the presence or absence of Med12 and identify affected super-enhancers.
iChIP was performed using previously published protocols (Lara-Astiaso et al, 2014 Immunogenetics. Chromatin state dynamics during blood formation - Science, 345, 6199)

overall_design: Examination of histone modification in mouse HSPCs with and without Med12


title: RNAPol2 accounts for tumor cells liability to JQ1 [ChIP-Seq]

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

summary: We here use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor.

overall_design:
Examination of transcription factor chromatin binding sites and histone marks in RAJI cells upon JQ1 treatment

Please note that only a graphical output (i.e. an enrichment plot over genes) was generated using raw BAM files for the following samples (i.e. no processed data file);
Pol2SerP2_DMSO_ChIP
Pol2SerP5_DMSO_ChIP
Pol2SerP2_JQ1_ChIP
Pol2SerP5_JQ1_ChIP
Raji_ChIPSeq_Pol2_JQ1_6h

first: Stefano

last: Campaner

first: Ottavio

last: Croci

first: Elisa

last: Donato


title: RNAPol2 accounts for tumor cells liability to JQ1

overall_design: Refer to individual Series


title: Drop-Seq analysis of  P17 FACS sorted retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line

first: Karthik

last: Shekhar

summary: Vsx2-GFP mouse retinas were dissected, FACS sorted for GFP+ cells and single-cell mRNAseq libraries generated with Drop-Seq

overall_design: Drop-Seq was performed on two different batches. Bipolar1-Bipolar4 are replicates from batch 1 and Bipolar5-6 are replicates from Batch 2


title: Cell type-specific alternative splicing of cytoskeletal domains governs cell fate in the developing cerebral cortex

city: Chicago

first: Xiaochang

last: Zhang

state: IL

address: 920 E 58th St, CLSC 507A

department: Human Genetics

institute: The University of Chicago

summary: Alternative splicing regulates over 90% of multiexon mammlian genes, but its role in specifying neural progenitor cell (NPC) fates has not been explored. Our analyses of purified mouse NPCs and neurons from developing cerebral cortices revealed hundreds of conserved and differentially spliced exons that add or remove key protein domains, especially in genes regulating the cytoskeleton.

overall_design: TBR2-EGFP BAC transgenic mice, generated by GENSAT and outcrossed to FVB strain for 2 generations, drives EGFP expression in the vast majority of intermediate progenitors and neurons at E14.5. We FACS sorted EGFP positive (differentiating and differentiated neurons) and negative (neural progenitors) cells from the dorsal cerebral cortices of E14.5 TBR2-EGFP. Two replicates for each population were subjected to RNA sequencing. Alternatively spliced exons between the two populations (NPCs and neurons) were identified using MISO.

first: Christopher

last: Walsh


title: Enterococcus faecalis downregulates virulence genes of EHEC

status: Public on Aug 24 2016

city: Freising

first: Klaus

last: Neuhaus

address: Weihenstephaner Berg 3

department: Core Facility Microbiome/NGS

institute: Technische Universität München

summary: The transcriptome of EHEC grown in vitro with or without Symbioflor® was analyzed using RNA-seq. The analysis revealed downregulation of several virulence-associated genes in the presence of Symbioflor®, including virulence key genes (e.g., LEE, flagellum, quorum-sensing).

overall_design: EHEC were grown on LB medium, either with or without Symbioflor added.

first: Marina

last: Lamparter

first: Richard

last: Landstorfer

first: Svenja

last: Simon

first: Rudi

middle: F

last: Vogel


title: Regulation of enhancer dynamics by MED12

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Direct GR binding sites potentiate clusters of TF binding across the human genome [8]

last: Vockley

overall_design:
Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [8] contains ChIP-seq data for A549 cells treated with DEX or EtOH for 3 hours.

first: Anthony

last: D'Ippolito

first: Ian

last: McDowell

first: William

last: Majoros

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Gregory

last: Crawford

first: Timothy

last: Reddy


title: Root adaptive responses to aluminum-toxicity revealed by RNA-Seq in two citrus species with contrasting aluminum tolerance

city: fuzhou

first: peng

last: guo

address: shangxiadian road

institute: Fujian Agriculture and Forestry University

summary:
Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq.
Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis.
Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.

sample_organism:
Citrus sinensis
Citrus maxima

platform_organism:
Citrus sinensis
Citrus maxima

overall_design: Examination of mRNA levels in control and Al-treatment roots of C. grandis and C. sinensis with two biological replicates were generated by deep sequencing, using Illumina HiSeq 2000 device.

first: Peng

last: Guo

first: Li-Song

last: Chen


title: The conserved role of the RSC chromatin remodeler in the establishment of nucleosome depleted regions

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodeling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation is dependent on RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits define alternate versions of the complex.

overall_design: Samples from mononucleosomal DNA from S. pombe strains h- kanR-tetO-snf21-Tap-natR ura4::rTetR-tup11 were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol

first: Carlo

last: Yague-Sanz

last: Vázquez

first: Mar

last: Sánchez

first: Francisco

last: Antequera

first: Damien

last: Hermand


title: Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4

city: Columbus

first: Scott

middle: Q

last: Harper

state: Ohio

address: 700 Children's Drive

department: Gene Therapy

institute: Nationwide Children's Hospital

summary: We report the RNA-seq experiments performed in human myoblasts transfected with human DUX4 and mouse Dux.

overall_design: Comparison of genes up- and down-regulated by DUX4 and Dux in human myoblasts to identify pathways similiarly regulated by both transcription factors.

first: Jocelyn

middle: O

last: Eidahl

first: Carlee

middle: R

last: Giesige

first: Jacqueline

last: Domire

first: Lindsay

last: Wallace

first: Allison

last: Fowler

first: Susan

last: Guckes

first: Sara

last: Garwick-Coppens

first: Paul

last: Labhart


title: Transcriptome profile of murine bone marrow-derived macrophages treated with 15d-PGJ2 or 15d-PGJ2-PC

city: Shanghai

first: Huiyong

last: Yin

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Institute for Nutritional Sciences

summary:
Purpose: The goal of this study is to investigate the alteration of gene expression pattern induced by 15d-PGJ2 or 15d-PGJ2-PC in BMDMs.
Method: BMDMs obtained from C57BL/6 mice were treated with 15d-PGJ2, 15d-PGJ2-PC or media control for 6h. Then RNA sequence was generated by using the Illumina system.
Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome and identified about 14,500 transcripts in the macrophage mRNAs. Among them, 719 and 286 genes were differentially expressed in 15d-PGJ2 and 15d-PGJ2-PC group respectively.
Conclusions: Deoxy-A2/J2-IsoP-PC are a novel series of oxidation products we identified in atherosclerotic plaques. 15d-PGJ2-PC is a representative compound of these oxidation products we chemically synthesised. Using RNA-seq technology, we provided 15d-PGJ2-PC induced gene expression profile and could contribute to  study the roles of these novel oxidation products in the atherosclerosis.

overall_design: mRNA profiles of BMDMs from C57B/L6 mice were generated by deep sequencing, in triplicate, using Illumina.

first: Jianhong

last: Lu


title: Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

state: Utah

department: Chemistry

country: USA

institute: University of Utah


title: Transcriptomic analysis of inter- and intra-patient variation in human iPSC cardiomyocytes: Platform for precision medicine to predict drug toxicity

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: In the present study we created and analyzed cardiomyocytes from two separate iPSC clones from the fibroblasts of five different female individuals and two male individuals, using footprint-free Sendai virus

overall_design: RNA-seq of iPSC cardiomyocytes, Ampli-seq of heart left ventricle and iPSC cardiomyocytes (with and without drug treatment) and Exome-seq of patient fibroblasts.

first: Elena

last: Matsa

middle: W

last: Burridge

first: Kun-Hsing

last: Yu

first: Ningyi

last: Shao


title: Direct GR binding sites potentiate clusters of TF binding across the human genome

first: Christopher

last: Vockley


title: IL-15 activates mTOR and primes stress-activated gene-expression leading to prolonged anti-tumor capacity of NK cells

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23

institute: Karolinska Institutet

summary: Treatment of hematological malignancies by adoptive transfer of activated natural killer (NK) cells is limited by poor post-infusion persistence. We compared the ability of interleukin-2 (IL-2) and IL-15 to sustain human NK cell functions following cytokine withdrawal to model post-infusion performance. In contrasts to IL-2, IL-15 mediated stronger signaling through the IL-2/15 receptor complex and provided functional advantages. Genome-wide analysis of cytosolic and polysome-associated mRNA revealed cytokine dependent differential mRNA levels and translation during cytokine activation but also that most gene expression differences were primed by IL-15 and only manifested after cytokine withdrawal. IL-15 augmented mTOR signaling, which correlated with increased expression of genes related to cell metabolism and respiration. Consistently, mTOR inhibition abrogated IL-15-induced functional advantages. Moreover, mTOR-independent STAT-5 signaling contributed to improved NK cell function during cytokine activation but not following cytokine withdrawal. The superior performance of IL-15 stimulated NK cells was also observed using a clinically applicable protocol for NK cell expansion. Finally, expression of IL-15 correlated with cytolytic immune functions in patients with B cell lymphoma and favorable clinical outcome. These findings highlight the importance of mTOR regulated metabolic processes for immune cell functions and argue for implementation of IL-15 in adoptive NK cell cancer therapy.

overall_design: Freshly isolated NK cells from 6 donors were activated with IL-2 or IL-15 for 48 hours, followed by cytokine withdrawal for 24 hours, resulting in four RNA samples per donor. From each sample, both the cytosolic as well as the polysomal fraction were collected. Donor 3 contains activation and post withdrawal data from two different donors due to poor RNA-quality obtained for some samples which did not allow for processing of the complete set of 6 donors (resulting in a total of 40 samples).

first: Yumeng

last: Mao

first: Vincent

last: van Hoef

first: Xiaonan

last: Zhang

first: Erik

last: Wennerberg

first: Julie

last: Lorent

first: Laia

last: Masvidal Sanz

first: Shuo

last: Liang

first: Rolf

last: Kiessling

first: Andreas

last: Lundqvist


title: Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes

city: Bar Harbor

first: Gregory

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: The juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis, resulting in meiotic substage-specific transcriptomes and the discovery of a transcription factor network that regulates the substages of meiosis.

overall_design: Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), with five biological replicates at each age (samples 8_1 through 18_5). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. A novel permutation-based maximum covariance analysis (PMCA) method was developed to deconvolve genes into meiotic substages. To verify PMCA derived pachytene/diplotene substage-specific genes, we isolated enriched populations of adult pachytene germ cells (samples rep1 through rep4), followed the same RNA-seq protocol, and compared the PMCA derived substage-specific gene lists to the genes expressed in the pachytene/diplotene enriched germ cells.

first: Robyn

last: Ball

first: Yasuhiro

last: Fujiwara

first: Fengyun

last: Sun

first: Jianjun

last: Hu

first: Matthew

last: Hibbs

first: Mary

middle: A

last: Handel


title: Input Strategy for Improving Analysis of ChIP-exo Data and Beyond [RNA-Seq]

first: Bethany

last: Buck-Koehntop

summary: Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data.

overall_design: HeLa cells were transfected with either a scrambled siRNA or one of two CTCF siRNAs (Thermo Fisher Scientific ? Life technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific - Life technologies) and incubated for 24 hr.

first: Tommy

last: Terooatea


title: Identification of TWIST1 transcriptional targets in the cranial mesoderm [ChIP-Seq]

status: Public on Aug 23 2016

city: WESTMEAD

first: PIERRE

last: OSTEIL

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

summary: TWIST1, a basic helix-loop-helix transcription factor is essential for the development of cranial mesoderm and cranial neural crest-derived craniofacial structures. Our previous work showed that, in the absence of TWIST1, some cells within the cranial mesoderm adopt an abnormal epithelial configuration. Here, we show by transcriptome analysis that loss of TWIST1 in the cranial mesoderm is accompanied by a reduction in the expression of genes that are associated with cell-extracellular matrix interactions and the acquisition of mesenchymal characteristics. By comparing the transcriptional profiles of cranial mesoderm-specific Twist1 loss-of-function mutant and control mouse embryos, we identified a set of genes that are both TWIST1-dependent and predominantly expressed in the mesoderm. By ChIP-seq in a cell line model of a TWIST1-dependent mesenchymal state, we identified, among the downstream genes, three direct transcriptional targets of TWIST1: Ddr2, Pcolce and Tgfbi.  Our findings show that the mesenchymal properties of the cranial mesoderm is likely to be regulated by a network of TWIST1 targets genes that influence the extracellular matrix and cell-matrix interactions, and collectively they are required for the morphogenesis of the craniofacial structures.

overall_design: Chromatin extracts were subject to chromatin immunoprecipitation with anti TWIST1 monoclonal antibody (ChIP-seq). Input chromatin, not subject to ChIP was used as the negative control. Two independent replicate experiments were performed. Purified, immunoprecipitated DNA was sequenced at Australian Genome Research facility.

first: Patrick

last: Tam


title: PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

summary: Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.

overall_design: Designed novel method for generation of a ChIP-exo input control


title: Molecular Signatures Associated with ZIKV Exposure in Human Cortical Neural Progenitors

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

institute: Emory University

summary: Zika virus (ZIKV) infection causes microcephaly and has been linked to other brain abnormalities. How ZIKV impairs brain development and function remains elusive. Here we systematically profiled transcriptomes of human neural progenitor cells (hNPCs) exposed to Asian ZIKVC, African ZIKVM, and Dengue virus (DENV). DENV causes distinct gene expression changes; and ZIKV has a broader impact on the expression of gene involved in DNA replication and repair. While overall expression profiles are similar, ZIKVC, but not ZIKVM, induces upregulation of viral response genes. Our analyses reveal virus- and strain-specific molecular signatures associated with ZIKV infection. Further investigation of ZIKV-host interactions based our transcriptomic datasets may help to illuminate neural virulence determinants of ZIKV in patients.

overall_design: Gene Expression Analyses of the cells infected with different flaviviruses


title: Identification of TWIST1 transcriptional targets in the cranial mesoderm

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus


title: Defining AP4- and MYC-regulated gene expression programs in germinal center B cells during cyclic re-entry

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: B cells diversify and affinity-mature their antigen receptor repertoire in germinal centers (GC). GC B cells receive help signals during transient interaction with T cells, yet it remains unknown how these transient T-B interactions sustain the subsequent proliferative program of selected B cells. Here we show that the transcription factor AP4 is required for sustained GC B cell proliferation and subsequent establishment of a diverse and protective antibody repertoire. AP4 is induced by c-MYC during the T-B interactions and maintained by T cell-derived IL-21. B cell-specific deletion of AP4 resulted in reduced GC sizes and somatic hypermutation and a failure to control chronic viral infection. These results indicate that AP4 integrates T cell-mediated selection and sustained expansion of GC B cells for humoral immunity.

overall_design: Splenic B cells activated with anti-IgM and CD40L in vitro and germinal center B cells sorted from C57BL/6 mice eight days after immunization with sheep red blood cells (SRBCs) were obtained and genome-wide occupancy of c-MYC, AP4 and active histone marks was profiled by chromatin immunoprecipitation and high-throughput sequencing. Gene expression in MYC–AP4– LZ, MYC+AP4+ LZ, AP4+ DZ, and AP– DZ GC B cells from SRBC-immunized AP4-mCherry / c-MYC-GFP dual reporter mice was profiled by RNA-seq.

first: Chun

last: Chou


title: 4C-seq analysis of the c-Kit locus

first: Beatriz

last: Aranda-Orgilles

summary: We characterize the transcriptional loop from c-Kit promoter and a novel c-Kit enhancer

overall_design: 10 millions of cells were use to generate replicate libraries

first: Iannis

last: Aifantis


title: A developmental coordinate of the spectrum of pluripotency among  mice, monkeys, and humans

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: The epiblast (EPI) is the origin of all somatic and germ cells in mammals, and of the spectrum of pluripotent stem cells (PSCs) in vitro. To explore the ontogeny of human/primate pluripotency, we performed comprehensive single-cell RNA sequencing for pre- and post-implantation EPI development in cynomolgus monkeys. Here we show that after specification in the blastocysts [embryonic day (E)7], cyEPI undergoes major transcriptome changes upon implantation. Thereafter, cyEPI, while generating gastrulating cells (~E13), maintains its transcriptome relatively stably over a week, retaining a unique set of pluripotency genes while acquiring properties for “neuron differentiation.” h/cyPSCs show the highest similarity to post-implantation late cyEPI (~E17), which, despite co-existing with gastrulating cells, bears characteristics of pre-gastrulating mouse EPI (E5.5) and epiblast-like cells (EpiLCs) in vitro. These findings not only reveal divergence/coherence of EPI development, but also identify a developmental coordinate of the spectrum of pluripotency among key species, providing a basis for better regulation of human pluripotency in vitro.

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus

overall_design: Single cell transcriptome analysis of cynomolgus monkey embryo E6-17 and mouse embryo E4.5 - E6.5 as well as of cynomogus monkey embryonic stem cells (ESCs) and mouse ESC, epiblast like cells (EpiLCs), using SC3-seq technology.

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Kotaro

last: Sasaki

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

city: Pingtung County

first: Chi-Chu

last: Tsai

address: 2-6 Dehe Rd., Dehe Village, Changjhih Township

department: Crop Improvement Section

country: Taiwan

institute: Kaohsiung District Agricultural Research and Extension Station

summary: Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 582 differentially expressed unigenes, of which 415 and 167 genes were, respectively up-regulated (fold-change ≥ 2, p-value < 0.05) and down-regulated (fold-change ≤ 0.5, p-value <0.05) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, forty-seven up-regulated unigenes with enzyme commission (EC) were assigned to 269 isogroups involved in 100 different pathways, and twenty-four down-regulated unigenes with enzyme commission (EC) were assigned to 586 isogroups, involved in 167 different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes at locus 25,051 (one of monooxygenases) and locus 22,288 (one of glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed.

sample_organism:
Armillaria mellea
Gastrodia elata

platform_organism:
Armillaria mellea
Gastrodia elata

overall_design: Transcriptome comparative between vegetative propagation corms and tubers of G. elata, and between tubers of G. elata (symbiosis A. mellea) and A. mellea

first: Keh-Ming

last: Wu

first: Tzen-Yuh

last: Chiang

first: Chun-Yen

last: Huang

first: Chang-Hung

first: Shu-Ju

last: Li

first: Yu-Chung