title: Vitamin C and L-Proline antagonistic effects capture alternative states in the pluripotency continuum [RRBS]

city: Naples

first: Cristina

last: D'Aniello

address: Via Pietro Castellino, 111

institute: IGB-CNR

summary: RRBS analysis identified ~1000 differentially methylated regions (DMRs), distributed throughout all chromosomes Interestingly, the majority of DMRs (77% at day 2 and 96% at day 5) that were hypomethylated in VitC-, were conversely hypermethylated in L-Pro-treated ESCs, thus indicating that VitC and L-Pro modulate methylation at the same DNA regions in an opposite manner. Of note, a high fraction of DMRs (50%) laid in promoters (mostly HCPs) and ~20% in enhancers. Moreover, DMRs-associated genes are highly enriched in genes related to developmental process (p=6,3E-38) and DNA-binding transcriptional regulators (p=9,7E-34). Our findings provide the first evidence that L-Pro availability regulates DNA methylation in ESCs and leads to the hypothesis that the antagonistic effects of VitC and L-Pro on DNA methylation pattern might regulate pluripotency.

overall_design: DNA methylation profile of L-Pro- and VitaminC-treated  and untreated cells at day 2 and day 5 using the Illumina HiSeq platform

first: Gabriella

last: Minchiotti


title: Effect of 48h treatment with 100nM GSK2879552 on T-ALL cell lines LOUCY and PEER

status: Public on Feb 03 2017

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was performed on biological triplicates of LOUCY and PEER cells treated with 100nM GSK2879552 for 48h versus their corresponding DMSO treatment controls. GSK2879552 is a potent, selective and orally bioavailable inhibitor of the lysine-specific histone demethylase 1 (LSD1). Gene expression was severely affected by LSD1 inhibition.  Pathway analysis performed on the differentially expressed genes following 48hrs of LSD1i treatment clearly showed an increased apoptotic gene signature (CASP3, CASP8) and enhanced expression of genes associated with TRAIL signaling. Furthermore, pre-ranked Gene Set Enrichment Analysis (GSEA) revealed that genes upregulated after LSD1 inhibition in  LOUCY showed significant enrichment for transcripts that are down in hematopoietic stem cells and early T lymphocytes. In contrast, important components of the Notch, WNT and SMAD signalling complex were significantly down regulated upon short-term LSD1i treatment in LOUCY  cells. In line with this notion, pre-ranked GSEA also revealed that LSD1i resulted in decreased expression of genes that significantly overlap with an oncogenic MYC signature.

overall_design: LOUCY and PEER cells were treated with 100nM GSK2879552 or DMSO for 48h. Three biological replicates of this treatment were performed for each celline.

first: Steven

last: Goossens

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Jody

last: Haigh


title: Vitamin C and L-Proline antagonistic effects capture alternative states in the pluripotency continuum [RNA-Seq]

country: Italy

summary: Samples 1-4 report RNA-seq transcriptome profiling of the L-Proline- (L-Pro) and bFgf/ActivinA- (F/A) derived mCherry+/eGFP+ (yellow) ESC population, using the Illumina HiSeq platform. Whole-genome expression revealed that more than 1000 genes were significantly deregulated in L-Pro- and F/A-induced cells compared to control (mCherry+/eGFP− red cells) and the two population shared up to 75% of deregulated genes with the same deregulation trend. Specifically, the pluripotency-associated genes were downregulated either at similar level (Nanog, Klf2, Klf4 and Gbx2) or at lower levels (up to 10 times) (Dppa 2, 3, 4, 5a, Rex1, Esrrb) in F/A- compared to L-Pro-treated cells.  Interestingly, mesendodermal-related genes (e.g. Brachyury, Cer1, Dkk1, Eomes, Foxa2, and Sox17) were induced in both conditions but at significant higher levels in F/A- compared to L-Pro-treated cells. The transcriptome analysis of mCherry+/eGFP+ (yellow) cells supported the idea that L-Pro mimics F/A in inducing a naïve to primed transition, and suggested that it exerted a milder (weaker) effect.                            Samples 5-14 report RNA-seq transcriptome profiling of the mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs) bulk culture, grown in FBS/LIF ± VitaminC (VitC) and L-Proline (L-Pro) and compared them to the standard naive/2i and primed/bFgf/ActivinA-EpiSCs (F/A), using the Illumina HiSeq platform. Whole-genome expression identified around 7900 deregulated genes in the different conditions, (fold change≥2 and pvalue<0.05). Principal component analysis (PCA) placed VitC between 2i and untreated control, and L-Pro between control and F/A.  Accordingly, a set of pluripotency-associated genes was expressed at higher level in 2i and VitC conditions, while downregulated in L-Pro and F/A, compared to control. Conversely, priming markers were downregulated in 2i and VitC and upregulated in L-Pro and F/A compared to control  The transcriptome analysis supported that VitC- and L-Pro captured alternative pluripotency states that can be likely placed between naïve/2i and primed/F/A states.

overall_design: RNA-seq  profiling of ESCs grown in FBS/LIF ± VitC, 2i, L-Pro or F/A, using the Illumina HiSeq platform


title: Vitamin C and L-Proline antagonistic effects capture alternative states in the pluripotency continuum

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of 24h treatment with 100nM GSK2879552 on the murine T-ALL cell with and without Zeb2 overexpression

summary: RNA sequencing was performed on biological triplicates of p53 null T-ALL cells with ZEB2 overexpression (P53/R26-Zeb2tg/tg) versus p53 null T-ALL cells without Zeb2 overexpression (P53/R26+/+) treated with 100nM GSK2879552 for 24h versus their corresponding DMSO treatment controls. P53/R26+/+ and P53/R26-Zeb2tg/tg tumor lines displayed a very distinct gene expression signature under baseline (DMSO) conditions in line with our previous observations that Zeb2 driven thymomas reflect a more immature T-ALL subtype. GSK2879552 is a potent, selective and orally bioavailable inhibitor of the lysine-specific histone demethylase 1 (LSD1). LSD1i treatment in control P53/R26+/+ cell lines only caused limited effects on overall transcription. In contrast, gene transcription was more severely affected by LSD1 perturbations in the P53/R26-Zeb2tg/tg lines with significant changes in the expression transcripts enriched for signalling pathways essential for embryonic development (like TGFbeta and Wnt signalling), genes involved in transcriptional repression/regulation, apoptosis and DNA replication/repair. All together, these results demonstrate that Zeb2 overexpression modulates murine T-ALL responsiveness to LSD1 inhibitors.

overall_design: p53 null T-ALL cells with ZEB2 overexpression (P53/R26-ZEB2tg/tg) versus p53 null T-ALL cells without Zeb2 overexpression (P53/R26+/+) were treated with 100nM GSK2879552 or DMSO for 24h. Three biological replicates of this treatment were performed.


title: polyA mRNA RNA-seq from Ishikawa (ENCSR000BYC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

summary:
RNA-seq on ECC-1 greater than 200bp polyA+ treated with genistein at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.

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


title: polyA mRNA RNA-seq from Jurkat clone E61 (ENCSR000BXX)

summary:
RNA-seq on Jurkat greater than 200bp polyA+

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


title: ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Genome binding/occupancy profiling by high throughput sequencing


title: Effect of 48h treatment with 100nM GSK2879552 on T-ALL cell lines HSB2 and RPMI8402

summary: RNA sequencing was performed on biological triplicates of HSB2 and RPMI8402 cells treated with 100nM GSK2879552 for 48h versus their corresponding DMSO treatment controls. GSK2879552 is a potent, selective and orally bioavailable inhibitor of the lysine-specific histone demethylase 1 (LSD1). Gene expression was severely affected by LSD1 inhibition.  Pathway analysis performed on the differentially expressed genes following 48hrs of LSD1i treatment clearly showed an increased apoptotic gene signature (CASP3, CASP8) and enhanced expression of genes associated with TRAIL signaling. Furthermore, pre-ranked Gene Set Enrichment Analysis (GSEA) revealed that genes upregulated after LSD1 inhibition in  HSB2 showed significant enrichment for transcripts that are down in hematopoietic stem cells and early T lymphocytes. In contrast, important components of the Notch, WNT and SMAD signalling complex were significantly down regulated upon short-term LSD1i treatment in HSB2  cells. In line with this notion, pre-ranked GSEA also revealed that LSD1i resulted in decreased expression of genes that significantly overlap with an oncogenic MYC signature.

overall_design: HSB2 and RPMI8402 cells were treated with 100nM GSK2879552 or DMSO for 48h. Three biological replicates of this treatment were performed for each celline.


title: RNA-seq of abscisic acid-reponsive transcription factors [DIG]

summary: Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community.  Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.

overall_design: Three-day old etiolated seedlings were treated by 10 uM Dex for 4 hours in dark. Light-grown seedlings were grown on plates containing 500 nM Dex for 10 days.

first: Liang

last: Song

first: Shao-shan

middle: C

last: Huang

first: Rosa

last: Castanon


title: ChIP-seq of abscisic acid-reponsive transcription factors [DIG]

overall_design: Identification of binding sites for 21 transcription factors using both mock- and ABA-treated conditions with mock IP of wild-type Col-0 ChIPped by anti-GFP antibody as control. Each experiment was carried out with at least two replicates.


title: RNA-seq of abscisic acid-reponsive transcription factors

overall_design: Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment. 10 uM ABA treatment or ethanol mock treatment for 1 to 60 hours.


title: Identification of endogenous changes in the transcriptome of young versus old Drosophila intestinal stem cells using Next Generation RNA Sequencing

status: Public on Feb 02 2017

city: Ulm

first: Petra

last: Pandur

address: Albert-Einstein-Allee 11

department: Institute for Biochemistry and Molecular Biology

country: Germany

institute: University of Ulm

summary: The Drosophila midgut is an ideal model system to study molecular mechanisms that interfere with the intestinal stem cells’ (ISCs) ability to function in tissue homeostasis.    Due to the lack of a combination of molecular markers suitable to isolate ISCs from aged intestines, it has been a major challenge to study endogenous molecular changes of ISCs during aging. Our FACS-based approach using the esg-GAL4, UAS-GFP fly line allowed the isolation of a cell population enriched for ISCs from young and old midguts by their small size, little granularity and low GFP intensity. The isolated ISCs were subsequently used for RNA sequencing to identify endogenous changes in the transcriptome of young versus old ISCs.

overall_design: Cell populations enriched for ISCs isolated from young (6-8 days old) and old (59-65 days old) midguts were sorted. Cells from three different batches of young and old midguts were subjected to Next Generation Sequencing using Illumina Genome Analyzer IIx.

first: Helen

middle: M

last: Tauc

first: Alpaslan

last: Tasdogan


title: downregulation of DDX5 and DDX17

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

summary: RNAseq : MCF-7 cells were transfected with siRNA targeting both DDX5 and DDX17 RNA helicases, and total RNA were extracted as described previously (Dardenne Cell Rep 2014).

overall_design: siRNA control (2 replicates) + siRNA DDX5/DDX17 (2 replicates)

first: Cyril

last: Bourgeois

first: Didier

last: Auboeuf

first: Clara

last: Benoit-Pilven

first: Sophie

last: Terrone


title: RNA sequencing of primary human platelets and in vitro cell lines

city: Baltimore

first: Eric

middle: W

last: Mills

state: Maryland

address: 725 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary: Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes. We use RNA sequencing of synchronized populations of in vitro derived platelet-like particles (PLPs) to show that mRNA decay strongly shapes the nascent platelet transcriptome. Our data suggests that the decay of platelet mRNAs is slowed by the natural loss of the mRNA surveillance and ribosome rescue factor Pelota (PELO).

overall_design: Analysis of RNA sequencing data from primary human platelets and in vitro derived platelet-like particles; manipulation by overexpression of Pelota (PELO) in Meg01/platelet-like particles.

first: R

last: Green

first: Nicholas

middle: T

last: Ingolia


title: Ribosome profiling and RNA-Sequencing of wild type and Pelota knockout mouse epidermis

summary: mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes.  Here we show that Pelo is required for mammalian epidermal homeostasis. Conditional deletion in murine epidermal stem cells expressing Lrig1 results in hyperproliferation and abnormal differentiation, whereas deletion in other stem cells does not. Loss of Pelo results in truncated ribosome footprints and global upregulation of translation. Translational inhibition by rapamycin-mediated down regulation of mTOR rescues the epidermal phenotype. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.

overall_design: Analysis of ribosome profiling and RNA sequencing data from primary mouse epidermis; manipulation by transgenic knockout of Pelota (PELO).

first: Kifayathullah

last: Liakath-Ali

first: Inês

last: Sequeira

first: Beate

last: Lichtenberger

first: Ajay

last: Mishra

first: Angela

middle: O

last: Pisco

first: Ibrahim

last: Adham

first: Rachel

first: Fiona

last: Watt


title: Subpopulations of mouse beta cells

city: Cambridge

first: Arnon

last: Arazi

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Type 1 diabetes (T1D) is a chronic autoimmune disease that involves immune mediated destruction of β cells. How β cells respond to immune attack is unknown. We identified a population of β cells during the progression of T1D in non-obese diabetic (NOD) mice that survives immune attack. This population develops from normal β cells confronted with islet infiltrates. Pathways involving cell movement, growth and proliferation, immune responses, and cell death and survival are activated in these cells. There is reduced expression of β cell identity genes and diabetes antigens and increased immune inhibitory markers and stemness genes. This new subpopulation is resistant to killing when diabetes is precipitated with cyclosphosphamide. Human β cells show similar changes when cultured with immune cells. These changes may account for the chronicity of the disease and the long term survival of β cells in some patients.

overall_design: mRNA profiles of top and bottom beta cells were generated by RNA-seq. 4 samples were processed from each population of cells.

first: Jinxiu

last: Rui

first: Kevan

last: Herold


title: Pubertal Ductal Morphogenesis: Isolation and Transcriptome Analysis of the Terminal End Bud.

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

summary: The terminal end buds (TEB) are the growing part of the ductal mammary epithelium during puberty, which enable the formation of the primary mammary epithelial network. These bulbous end structures are highly proliferative, and this allows the ductal expansion into the mammary fat pad. The TEB comprise of an outer cap cell layer, which include the progenitor cells of the myoepithelium, and the body cells, which are  thought to be the progenitors from which the luminal epithelium is formed. Since TEBs make up only a minute part of the whole mammary tissue, associated factors can be easily missed in whole-tissue section analysis. We have therefore optimised a method to enzymatically separate TEB and ducts, respectively, from the surrounding stroma of pubertal mice and performed transcriptome analysis on the isolated structures to identify potential novel regulators of epithelial outgrowth.

overall_design: TEBs and duct fragments were isolated through collagenase-II digestion and microdissection from pubertal female C57/BL6 mice (for detailed protocol see Stein and Morris, Methods Mol Biol. 2017;1501:131-148.). Samples were analysed in technical replicates from pooled samples, representing ~300-400 isolated TEBs or ducts each.

first: Daria

last: Olijnyk

first: Joanna

middle: S

last: Morris

first: Barry

middle: A

last: Gusterson


title: ChIP-seq of abscisic acid-reponsive transcription factors

first: Joseph

last: Ecker

first: Liang

last: Song

first: Shao-shan

last: Huang

first: Rosa

last: Castanon


title: Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Adenosquamous lung tumors may result from cellular plasticity. We demonstrate lineage switching of KRAS+ lung adenocarcinomas (ADC) to squamous cell carcinoma (SCC) through deletion of Lkb1 (Stk11) in autochthonous and transplant models.  Chromatin analysis reveals loss of H3K27me3 and gain of H3K27ac and H3K4me3 at squamous lineage genes, included Sox2, ΔNp63 and Ngfr.  SCC lesions have higher levels of the H3K27 methyltransferase EZH2 than the ADC lesions, but there is a clear lack of the essential Polycomb Repressive Complex 2 (PRC2) subunit EED in the SCC lesions.

overall_design:
We performed chromatin immunoprecipitation (ChIP) on microdissected tumors confirmed to be either ADC or SCC by histology and qPCR.  The two activating marks, histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), and the PRC2 derived silencing mark, histone H3 lysine 27 tri-methylation (H3K27me3) were immunoprecipitated, followed by sequencing the chromatin bound DNA.
Examination of 3 different histone modifications in 2 histological subtypes of mouse tumors

first: Kwok-kin

last: Wong


title: Analysis of DNA Methylation in replication and cell cycle arrest.

first: Andrew

last: Feinberg

address: 855 N. Wolfe St

summary: In order to determine the effects of cell cycle and cell cycle arrest on DNA methylation, whole genome bisulfite sequencing was performed on primary fibroblasts sorted based on DNA content and Ki67.

overall_design: Three sets of adult primary dermal fibroblasts were cultured for 4 passages in DMEM with 15% FBS, stained with propidium iodide and anti-Ki67 and sorted into "G0" (2N DNA, Ki67 -), "G1" (2N DNA, Ki67 +) and "G2" (4N DNA, Ki 67 +) using FACS. A subset of passage 4 cells were grown to contact inhibition and maintained for 1 week, then "Ext_G0" cells were isolated. DNA was extracted from all sorted groups, bisulfite converted and sequenced using Illumina HiSeq 2000.

first: Amy

last: Vandiver


title: Genome-wide map of Pol II and Flag-LARP7 in human HeLa cells

city: Toulouse

first: Beata

last: Jady

address: 118 route de Narbonne

department: Laboratoire de Biologie Moléculaire Eucaryote

institute: CNRS

summary: We generated genome-wide maps of Pol II and Flag-LARP7 in human HeLa cells. We find that Flag-LARP7 and Pol II co-locolize on Pol II-specific sn/snoRNA genes.

overall_design: 5 samples were analyzed: Input, two controls, Pol II and Flag-LARP7

first: S

last: Egloff

first: P

last: Vitali

first: R

last: Raffel

last: Murphy

first: T

last: Kiss


title: Paternal nicotine exposure alters hepatic xenobiotic metabolism in offspring

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Although it is increasingly accepted that some paternal environmental conditions can influence phenotypes in future generations, it remains unclear whether phenotypes induced in offspring represent specific responses to particular aspects of the paternal exposure history, or whether they represent a more generic response to paternal “quality of life”. To establish a paternal effect model based on a specific ligand-receptor interaction and thereby enable pharmacological interrogation of the offspring phenotype, we explored the effects of paternal nicotine administration on offspring phenotype in mouse. We show that paternal exposure to chronic nicotine induced a broad protective response to xenobiotic exposure in the next generation. This effect manifested as increased survival following an injection of toxic levels of nicotine, was specific to male offspring, and was only observed after these offspring were first acclimated to low levels of nicotine for a week. Importantly, offspring xenobiotic resistance was documented not only for toxic nicotine challenge, but also for toxic cocaine challenge, indicating that paternal nicotine exposure reprograms offspring to become broadly resistant to environmental toxins. Mechanistically, the reprogrammed state was characterized by enhanced clearance of nicotine in drug-acclimated animals, and we found that isolated hepatocytes displayed upregulation of enzymes that metabolize xenobiotics. Taken together, our data show that paternal nicotine exposure induces a protective phenotype in offspring by enhancing metabolic tolerance to xenobiotics in the environment.

overall_design: Hepatocytes were isolated from eight week-old male F1 animals from control (TA) and nicotine-exposed fathers, 4 biological replicates each.

first: Oliver

middle: J

last: Rando

first: Xin

middle: Y

last: Bing


title: Genome wide analyses of Su(Hw)M393 binding in the Drosophila ovary

city: Iowa City

first: Ryan

last: Baxley

state: IA

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

summary: The Suppressor of Hairy-wing [Su(Hw)] protein is a twelve zinc-finger DNA binding transcriptional regulator. Here, we map the genome wide association of Su(Hw) protein expressed from the novel su(Hw)M393 allele, which encodes a protein with a C350S substitution that inactivates ZF4. These analyses demonstrate that ZF4 is required for association with a subset of Su(Hw) binding sites and suggests that these sites may be primarily associated with insulator function.

overall_design: Mapping the genome wide localization of Su(Hw) carrying a disruption of ZF4 in ovaries from Drosophila females that were less than 6 hours old .

first: Pamela

middle: K

last: Geyer


title: Stable Binding of the Conserved Transcription Factor Grainy Head to Its Target Genes Throughout Drosophila melanogaster Development

city: Madison

first: Melissa

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.

overall_design: Examination of Grainy head binding in Drosophila melanogaster embryos during four stages of development, and the effect of depletion on gene expression at three stages.

first: Markus

last: Nevil

first: Eliana

last: Bondra

first: Katharine

middle: N

last: Shulz

first: Tommy

last: Kaplan


title: Not All H3K4 methylations are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The spatiotemporal regulation of gene expression is central for cell-lineage specification during embryonic development and is achieved through the combinatorial action of transcription factors/co-factors and the epigenetic states at cis-regulatory elements. Previously, we reported that Mll2 (KMT2B)/COMPASS is responsible for the implementation of H3K4me3 at promoters of bivalent genes. Here, we show that Mll2/COMPASS can also implements H3K4me3 at some of the non-TSS regulatory elements, a subset of which share epigenetic signatures of active enhancers. Our mechanistic studies reveal that the association of Mll2’s CXXC domain with CpG-rich regions plays an instrumental role for chromatin targeting and subsequent implementation of H3K4me3. Although Mll2/COMPASS is required for H3K4me3 implementation on thousands of sites, it appears to be essential for the expression of a subset of genes, including those functioning in the control of transcriptional programs during embryonic development, indicating that not all H3K4 trimethylations implemented by MLL2/COMPASS are functionally equivalent.

overall_design: Characterization of H3K4me3 and Mll2 occupancy by ChIP-seq in mouse embryonic stem cells and identifying their role in gene expression and during differentiation by RNA-seq studies. A high resolution 4C-seq experiments involving two restriction digests (HindIII and NlaIII) were performed to investigate the interaction bewteen promoters of Prdm1 and Prdm14 (viewponts) and cis-regulatory elements whose H3K4me3 is catalyzed by Mll2 in mouse embryonic stem cells.

first: Deqing

last: Hu

last: Gao


title: Genomewide nucleosome occupancy and DNA methylation analysis on normal and prostate cancer cells

status: Public on Feb 01 2017

city: Aarhus N

first: Søren

last: Vang

address: Palle Juul-Jensens Boulevard 99

country: Denmark

institute: Department of Molecular Medicine (MOMA)

summary: The goal of this study was to compare the nuclosome occupancy and DNA methylation patterns in prostate cancer cells compared to normal prostatic cells

overall_design: Nuclosome occupancy and DNA methylation sequencing (NOMe-seq) analysis of two cell lines (LNCaP and PrEC)

first: Karina

last: Dalsgaard Sørensen

first: Kamilla

last: Mundbjerg


title: Liver of MAT1A WT and MAT1A KO mice treated with placebo or SAMe during 8 weeks

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

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

overall_design: Refer to individual Series


title: Multilayered control of alternative splicing regulatory networks by transcription factors (ChIP-Seq)

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.

overall_design: ChIP-Seq and input control of Nacc1 in N2A cells

first: Hong

last: Han

first: Thomas

last: Gonatopoulos-Purnatzis

first: Robert

last: Weatheritt

first: Calley

middle: L

last: Hirsch

first: Kevin

last: Ha

first: Ernest

last: Radovani

first: Syed

last: Nabeel-Shah

first: Timothy

last: Sterne-Weiler

first: Juli

last: Wang

first: Dave

last: O'Hanlon

first: Qun

last: Pan

first: Debashish

last: Ray

last: Zheng

first: Frederick

last: Vizeacoumar

first: Alessandro

last: Datti

first: Lilia

last: Magomedova

first: Carolyn

last: Cummins

last: Hughes

first: Jack

middle: F

last: Greenblatt

first: Jeffrey

last: Wrana

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Maturation of human iNSCs

city: Chapel Hill

first: Shawn

middle: D.

last: Hingtgen

state: NC

address: 4212 Marsico Hall, 125 Mason Farm Road

department: UNC Eshelman School of Pharmacy, UNC Biomedical Research Imaging Center

institute: University of North Carolina at Chapel Hill

summary: The expression profiles of human iNSCs were compared to skin fibroblasts and brain-derived neural progenitor cells

overall_design: Each cell line was expanded in culture, replicates were collected and analyzed

last: Bago

first: Ralf

last: Schmid

first: C

last: Miller

first: Onyi

last: Okolie

first: Ryan

last: Van der Werff

first: T

last: Underhill

first: Joel

last: Parker


title: Potential of epigenetic therapy of acute myeloid leukemia using 5-aza-2'-deoxycytidine (decitabine) and 3-deazaneplanocin-A

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary:
Background:Aberrant DNA methylation that silences tumor suppressor genes occurs frequently in patients with acute myeloid leukemia (AML). Treatment of AML patients with the inhibitor of DNA methylation, 5-aza-2'-deoxycytidine (5-AZA-CdR) can induce complete remissions, but most patients will relapse. The clinical efficacy of 5-AZA-CdR may be influenced by its limited capacity to activate tumor suppressor genes silenced by methylation of lysine 27 histone H3 (H3K27) by EZH2. In order to overcome this limitation, we investigated previously the antileukemic action of 5-AZA-CdR in combination with the EZH2 inhibitor, 3-deazaneplanocin A (DZNep) on HL-60 AML cells. We observed a remarkable synergistic interaction against these AML cells for this combination. In this study, we investigated in more depth the action of 5-AZA-CdR plus DZNep on gene expression in AML cells using RNA sequence analysis
Result:In a colony assay, 5-AZA-CdR in combination with DZNep exhibited also a potent synergy against another human AML cell line: AML-3. The induction of apoptosis in HL-60 and AML3 leukemic cells by 5-AZA-CdR plus DZNep was also synergistic. RNA sequence analysis on HL-60 leukemic cells showed that the combination of 5-AZA-CdR plus DZNep increased the expression of thousands of genes. The genes upregulated by this combination included genes related to differentiation, development, senescence, apoptosis, and tumor suppressor function. Many of the genes activated by 5-AZA-CdR plus DZNep have the potential to suppress leukemogenesis.
Conclusion: The activation of many genes by the combination of 5-AZA-CdR plus DZNep correlates with its synergistic antileukemic action. The block in differentiation is one of the hallmarks of AML.The activation of many genes that program differentiation and development by this combination of epigenetic agents has the potential to reverse this block. The reversal of these two epigenetic genesilencing mechanisms by 5-AZA-CdR plus DZNep merits clinical investigation in patients with AML

first: Richard

last: Momparler

first: Sylvie

last: Côté

first: Louise


title: Sociality and DNA methylation are not evolutionary dependent

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: DNA methylation is an important chromatin modification that is necessary for the structural integrity and proper regulation of the genome for many species. Despite its conservation across the tree of life, little is known about its contribution to complex traits. Reports that differences in DNA methylation between castes in closely related Hymenopteran insects (ants, bees and wasps) contributes to social behaviors has generated hypotheses on the role of DNA methylation in governing social behavior. However, social behavior has evolved multiple times across insecta, and a common role of DNA methylation in social behavior remains outstanding. Using phylogenetic comparative methods we sought to better understand patterns of DNA methylation and social behavior across insects. DNA methylation can be found in social and solitary insects from all orders, except Diptera (flies), which suggests a shared loss of DNA methylation within this order. The lack of DNA methylation is reflected in the absence of the maintenance and de novo DNA methyltransferases (DNMT) 1 and 3, respectively. Interestingly, DNA methylation is found in species without DNMT3. DNA methylation and social behavior (social/solitary) or with division of labor (caste+/caste–) for 123 insect species analyzed from 11 orders are not evolutionary dependent, which is further supported by sequencing of DNA methylomes from 40 species.

sample_organism:
Blattella germanica
Periplaneta americana
Acyrthosiphon pisum
Heliothis virescens
Helicoverpa zea
Aedes aegypti
Aedes albopictus
Anopheles gambiae
Culex quinquefasciatus
Anastrepha suspensa
Aedes atropalpus
Copidosoma floridanum
Eublaberus posticus
Rhyparobia maderae
Reticulitermes flavipes
Aphidius ervi
Toxorhynchites amboinensis
Reticulitermes virginicus
Microplitis demolitor
Cryptocercus garciai
Polistes carolina
Pemphigus obesinymphae
Blaptica dubia
Blattella asahinai
Pemphigus populitransversus
Pemphigus populicaulis
Aphis craccivora
Microplitis mediator
Pyractomena borealis
Chrysodeixis includens

overall_design: MethylC-Seq collected from a diverse collection of social and solitary insects


title: The use of cold active proteases can dramatically reduce single cell RNA-seq gene expression artifacts

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Single cell RNA-seq is a powerful methodology, but with important limitations. In particular, the process of enzymatic separation of cells at 37O C can be expected to result in artifact changes in gene expression patterns. We here describe a dissociation method that uses protease from a psychrophilic microorganism with high activity in the cold. The entire procedure is carried out at 6O C or colder, where mammalian transcriptional machinery is largely inactive. To test this method we carry out single cell RNA-seq on about 9,000 cells, comparing the results of the cold method with a method using 37O C incubations for multiple times. We show that the cold active protease method results in a great reduction in gene expression artifacts.

overall_design: Whole mouse post natal day 1 kidney cells were dissassociated by either a cold active protease or an enzyme cocktail for varying lengths of time. The gene expression profiles of the four groups of cells were determined by drop-seq / RNA-seq.

first: S

last: Potter


title: DNA methylation status of the liver of MAT1A WT and MAT1A KO mice treated with placebo or SAMe during 8 weeks

first: Jose

last: Lavin

summary: Methionine adenosyltransferase (MAT) enzymes generate SAMe (S-adenosylmethionine), the main biological methyl donor. There are two MAT encoding genes in mammals (Mat1a and Mat2a), which show different activities and cellular distribution. Mat1a encodes the enzyme mainly expressed in normal liver. Mat1a ablation in mice results in the spontaneous development of non-alcoholic steatohepatitis (NASH). We observed that SAMe depletion in Mat1a KO mice had three main effects on hepatic lipid metabolism: 1) impaired TG (triglyceride) export via VLDL; 2) impaired mitochondrial FA (fatty acid) oxidation (as evidenced by membrane depolarization, downregulation of Phb1 (prohibitin 1, a mitochondrial chaperone protein) and Mcj/Dnajc15 (endogenous mitochondrial repressor of respiratory chain), and accumulation of long-chain acylcarnitines); and 3) increased FA uptake. The convergence of these three factors induced TG accumulation in LD (lipid droplets). LD expansion confronts hepatocytes with a high demand of PC (phosphatidylcholine) molecules to cover the LD surface since other phospholipids, such as PE (phosphatidylethanolamine), cannot stabilize LD and prevent coalescence. In Mat1a KO this situation is aggravated, since SAMe-dependent PC synthesis via PE methylation is decreased, the PC/PE ratio reduced and mitochondrial FA oxidation impaired. To put a brake to this drain of PC molecules to LD, FA are rerouted in Mat1a KO mice liver to other catabolic (endoplasmic reticulum and peroxisome oxidation) and biosynthetic (ceramides synthesis) pathways, causing oxidative stress, inflammation and fibrosis. SAMe treatment for two months in 8-9 month old Mat1a KO mice ameliorated mitochondrial dysfunction (reduces membrane depolarization, improves Phb1 and Mcj expression, and increases SAMe transport to mitochondria) improving FA oxidation efficiency (FA and acylcarnitine levels decrease), which results in a drastic reduction in TG accumulation. SAMe treatment in Mat1a KO mice resulted in more PC available for proper membrane function, improving liver lipid homeostasis, histology (H&E, Sudan red, Sirius red) and liver injury (ALT, AST).

overall_design: DNA methylome maps of MAT1A WT and KO mice treated or not with SAMe

first: José

last: Mato


title: Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)

first: Ulrich

last: Braunschweig

overall_design:
RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each)
vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns
vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns
AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns
AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns
Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns
Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns

first: Hong

last: Han

first: Thomas

last: Gonatopoulos-Purnatzis

last: Weatheritt

first: Calley

last: Hirsch

first: Kevin

last: Ha

first: Ernest

last: Radovani

first: Syed

last: Nabeel-Shah

first: Timothy

last: Sterne-Weiler

first: Juli

last: Wang

first: Dave

last: O'Hanlon

first: Qun

last: Pan

first: Debashish

last: Ray

last: Zheng

first: Frederick

last: Vizeacoumar

first: Alessandro

last: Datti

first: Lilia

last: Magomedova

first: Carolyn

last: Cummins

last: Hughes

first: Jack

last: Greenblatt

first: Jeffrey

last: Wrana

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Human Adult Sorted Live Cell Erythroblasts transduced with Sigma non-targeting shRNA negative control (SHC002V) with puromycin selection RNAseq

city: Bethesda

first: Jeffery

middle: L.

last: Miller

state: MD

address: 10 Center Drive Room 9N311

department: NIDDK

institute: NIH

summary:
Erythroblasts cultured from mobilized CD34+ cells from six healthy adult human donors were used to generate an erythroblast transcriptome transduced with Sigma non-targeting shRNA negative control . Cellular maturation was maintained including enucleation.  On culture day 14 total RNA was isolated (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter).
We would like to thank Gerard Bouffard and the National Human Genome Research Institute for their expertise and assistance with RNA-seq.

overall_design: Human CD34+ cells from health donor transduced with lentivirus expressing Sigma non-targeting shRNA negative control in serum free culture.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.

first: Y

last: Lee

first: Colleen

last: Byrnes

first: Raymond

last: Guo


title: BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1 [EuMyc_ChIP-seq]

summary: BET inhibitors (BETi) target bromodomain-containing proteins and are currently being evaluated as anti-cancer agents. We discovered that the maximal therapeutic effects of BETi in a Myc-driven B cell lymphoma model required an intact host immune system. Genome-wide analysis of the BETi induced transcriptional response identified the immune checkpoint ligand Cd274 (Pd-l1) as a Myc-independent, BETi target-gene. BETi directly repressed constitutively expressed and IFN-γ induced CD274 expression across different human and mouse tumor cell lines and primary patient samples. Mechanistically, BETi decreased Brd4 occupancy at the Cd274 locus without any change in Myc occupancy, resulting in transcriptional pausing and rapid loss of Cd274 mRNA production. Finally, targeted inhibition of the PD1/PD-L1 axis by combining anti-PD1 antibodies and the BETi JQ1 caused synergistic responses in mice bearing Myc-driven lymphomas. Our data uncovers a novel interaction between BETi and the PD-1/PD-L1 immune-checkpoint and provides novel insight into the transcriptional regulation of CD274.

overall_design: ChIP-Seq analysis of Eμ-Myc lymphoma cell lines AT3 mammary tumor cell line

first: Stephin

last: Vervoort

first: Jake

last: Shortt

first: Ricky

last: Johnstone


title: N4- cytosine DNA methylation epigenetically regulates gene expression and pathogenesis in Helicobacter pylori

city: Bangalore

first: Sumith

last: Kumar

state: Karnataka

address: Department of Biochemistry, Indian Institute of Science, Bangalore, India

country: India

institute: Indian Institute of Science

summary: Next-generation sequencing (NGS) can reveal putative target which can be regulated by m4C modification. Comparison of wild-type strain with the strain harboring deleted M2.hpyAII mtase gene was done to identify the differentially expressed gene.

overall_design: Transcriptome sequencing of exponentially growing H. pylori 26695 wild-type strain and R-hpyAII-M2.hpyAII deletion strain (biological replicates) was carried out by Illumina HiSeq 2500

first: S

first: N

middle: R

last: Desirazu


title: Human Cord Blood Sorted Live Cell Erythroblasts RNA-Seq

summary: Erythroblasts cultured from six healthy commercial available cord blood CD34+ cells were used to generate an cord blood erythroblast transcriptome. Cellular maturation was maintained including enucleation.  On culture day 14 total RNA was isolated (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter).

overall_design:
Human CD34+ cells from health donor cultured in serum free medium.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.
We would like to thank Gerard Bouffard and the National Human Genome Research Institute for their expertise and assistance with RNA-seq.


title: BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1 [EuMyc_RNA-seq]

overall_design: RNA Sequencing of Eμ-Myc lymphoma cell lines treated for 2 hours with JQ1, or DMSO vehicle.


title: LIN28A Over-expression RNAseq

summary:
To explore the effects of LIN28Ain human erythroid cell development, lentiviral transduction was used for LIN28A over-expression in erythroblasts cultured from mobilized CD34+ cells from six healthy adult human donors. LIN28A over-expression in cultured adult erythroblasts reduced the expression of let-7 and significantly increased HbF expression. Cellular maturation was maintained including enucleation. LIN28Aexpression in adult erythroblasts increased the expression of gamma-globin, and the HbF content of the cells rose to levels >30% of their hemoglobin. mRNA was isolated on culture day 14 (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter).
[Acknowledgement] We would like to thank Gerard Bouffard and the National Human Genome Research Institute for their expertise and assistance with RNA-seq.

overall_design: Human CD34+ cells from healthy donor transduced with lentivirus expressing human LIN28A in serum free culture.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.


title: Conservation and innovation in the DUX4-family gene network [MMH6 RNA-Seq]

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Facioscapulohumeral dystrophy (FSHD; OMIM #158900, #158901) is caused by mis-expression of the DUX4 transcription factor in skeletal muscle1. Animal models of FSHD are hampered by incomplete knowledge of the conservation of the DUX4 transcriptional program in other species. Despite divergence of their binding motifs, both mouse Dux and human DUX4 activate genes associated with cleavage-stage embryos, including MERV-L and ERVL-MaLR retrotransposons, in mouse and human muscle cells respectively. When expressed in mouse cells, human DUX4 maintained modest activation of cleavage-stage genes driven by conventional promoters, but did not activate MERV-L-promoted genes. These findings indicate that the ancestral DUX4-factor regulated genes characteristic of cleavage-stage embryos driven by conventional promoters, whereas divergence of the DUX4/Dux homeodomains correlates with retrotransposon specificity. These results provide insight into how species balance conservation of a core transcriptional program with innovation at retrotransposon promoters and provide a basis for animal models that recreate the FSHD transcriptome.

overall_design: We generated a new RNA-seq dataset in mouse myoblasts and compared them to a published dataset for human DUX4 in human myoblasts (GSE85461; DOI:10.1093/hmg/ddw271). This new dataset (and the dataset we compared to) used a doxycycline-inducible system and a codon-altered transgene. This new datasets reflects three separate cell cultures of a clonal cell line induced with doxycycline for eighteen hours, independently barcoded and sequenced in parallel; doxycycline induction caused expression of MMH in mouse myoblasts. MMH is a chimeric gene whose N-terminus is codon-altered mouse Dux through the mouse Dux homeodomains and its C-terminus is codon-altered human DUX4 starting just after human DUX4's homeodomains. The MMH-chimera maintained the DNA binding domain of Dux and the carboxy-terminal epitopes of DUX4, permitting us to use the same DUX4 antisera to immunoprecipitate the MMH-chimera and DUX4 (see related ChIP-seq dataset). We also generated a matched control dataset by preparing three more cell cultures of this same MMH cell line and harvesting them in parallel at eighteen hours, but not treating with doxycycline.

first: Jennifer

last: Whiddon

first: Ashlee

last: Langford

first: Chao-Jen

last: Wong

first: Jun

last: Zhong


title: Multilayered control of alternative splicing regulatory networks by transcription factors (iCLIP-Seq)

first: Ulrich

last: Braunschweig

overall_design:
iCLIP-seq of Nacc1 (2 replicates and input) and Flag-Zfp871 (2 replicates of 2 clones each) in N2A cells
------------------------------------------
Authors state that the 'processed data' consist of a plot only since the analyses (including the plots as supplementary files) were done directly from raw data.

first: Hong

last: Han

first: Thomas

last: Gonatopoulos-Purnatzis

first: Robert

last: Weatheritt

first: Calley

last: Hirsch

first: Kevin

last: Ha

first: Ernest

last: Radovani

first: Syed

last: Nabeel-Shah

first: Timothy

last: Sterne-Weiler

first: Juli

last: Wang

first: Dave

last: O'Hanlon

first: Qun

last: Pan

first: Debashish

last: Ray

last: Zheng

first: Frederick

last: Vizeacoumar

first: Alessandro

last: Datti

first: Lilia

last: Magomedova

first: Carolyn

last: Cummins

last: Hughes

first: Jack

last: Greenblatt

first: Jeffrey

last: Wrana

first: Jason

last: Moffat

first: Benjamin


title: small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Iconisemion striatum
Nothobranchius furzeri
Nothobranchius kuhntae
Nothobranchius rachovii
Nothobranchius pienaari
Nothobranchius kadleci
Nothobranchius korthausae

first: Mario

last: Baumgart

first: Emanuel

last: Barth

first: Philipp

last: Koch

first: Manja

last: Marz

first: Matthias

last: Platzer

last: Cellerino


title: Conservation and innovation in the DUX4-family gene network [MMH6 ChIP-Seq]

first: Stephen

last: Tapscott

overall_design: We generated one new ChIP-seq dataset in mouse myoblasts and compared it to a published ChIP-seq dataset for human DUX4 expressed in human myoblasts (GSE33838; 10.1016/j.devcel.2011.11.013). This new dataset was generated from a monoclonal cell line using a doxycycline-inducible system and a MMH transgene. MMH is a chimeric gene whose N-terminus is codon-altered mouse Dux through the mouse Dux homeodomains and its C-terminus is codon-altered human DUX4 starting just after human DUX4's homeodomains. The MMH-chimera maintained the DNA binding domain of Dux and the carboxy-terminal epitopes of DUX4, permitting us to use the same DUX4 antisera to immunoprecipitate the MMH-chimera and DUX4. For MMH peaks, we compared MMH-expresssing cells at 18-hours of induction immunoprecipitated with a 50:50 mixture of the DUX4 antibodies MO488 and MO489 to MMH-expressing cells immunoprecipitated with an antibody to GFP, which was not present in these cells.

first: Jennifer

last: Whiddon

first: Ashlee

last: Langford

first: Chao-Jen

last: Wong

first: Jun

last: Zhong


title: Intergenerational programming of hepatic xenobiotic response by paternal Nicotine exposure

city: Worcester

first: Shweta

last: Kukreja

address: Aaron Lazare Medical Research Building (LRB) 364 Plantation Street, LRB 9th Floor

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: Although it is increasingly accepted that some paternal environmental conditions can influence phenotypes in future generations, it generally remains unclear whether the phenotypes induced in offspring represent specific responses to particular aspects of the paternal exposure history, or whether they represent a more generic response to paternal “quality of life”. To establish a paternal effect model based on a known ligand-receptor interaction and thereby enable pharmacological interrogation of the specificity of the offspring response, we explored the effects of paternal nicotine administration on offspring phenotype in mouse. We show that chronic paternal exposure to nicotine prior to reproduction induced a broad protective response to multiple xenobiotics in the next generation. This effect manifested as increased survival following an injection of toxic levels of either nicotine or of cocaine, was specific to male offspring, and was only observed after offspring were first acclimated to sublethal doses of nicotine or cocaine. Mechanistically, the reprogrammed state was characterized by enhanced clearance of nicotine in drug-acclimated animals, accompanied by hepatic upregulation of genes involved in xenobiotic metabolism. Surprisingly, this protective effect could also be induced by paternal exposure to a nicotinic receptor antagonist as well as to nicotine, suggesting that paternal xenobiotic exposure, rather than nicotinic receptor signaling, is likely to be responsible for programming of offspring drug resistance. Taken together, our data show that paternal drug exposure can induce a protective phenotype in offspring by enhancing metabolic tolerance to xenobiotics in the environment.

overall_design: Hepatocytes were isolated from 8 week-old male F1 animals from control (TA) and nicotine-exposed (NIC) fathers, and allowed to adhere to the bottom of the well for three hours. Nonadherent cells were then removed, and fresh culture medium was then added. Cells were harvested at different time points in Trizol, and total RNA was extracted. Strand specific libraries were prepared from all samples, and sequenced on Illumina NextSeq500.

first: Markus

middle: P

last: Vallaster

first: Oliver

last: Rando


title: Metabolic origins of spatial organization in the tumor microenvironment

city: New York City

first: Carlos

last: Carmona-Fontaine

address: 31 Washigton Place

institute: New York University

summary: We report the transcriptional changes induced by hypoxia and/or lactate on bone marrow-derived macrophages (BMDMs)

overall_design: Untreated macrophages as well as macrophages treated with lactate, cultured in hypoxia (1% oxygen) or both were cultured in vitro. Then total mRNA was sequenced.


title: Human Adult Sorted Live Cell Erythroblasts RNA-Seq.

first: Jeffery

last: Miller

summary: Erythroblasts cultured from mobilized CD34+ cells from six healthy adult human donors were used to generate an erythroblast transcriptome. Cellular maturation was maintained including enucleation.  On culture day 14 total RNA was isolated (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter).

overall_design: Human CD34+ cells from health donor cultured in serum free medium.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.

first: Y

last: Lee

first: Colleen

last: Byrnes


title: BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1 [3mRNA-seq]

first: Simon

last: Hogg

overall_design: RNA Sequencing (3'-mRNA-Seq, QuantSeq) of AT3 (mouse mammary tumor cell line) and ALF1 (human plasma cell leukaemia line) treated for 2 hours with JQ1, interferon-gamma, JQ1+interferon-gamma, or DMSO vehicle.

first: Stephin

last: Vervoort

first: Jake

last: Shortt

first: Ricky

last: Johnstone


title: Circulating CXCR5+CXCR3+PD-1Lo Tfh-like cells in HIV-1 controllers with neutralizing antibody breadth

city: Cambridge

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

summary: HIV-1-specific broadly-neutralizing antibodies (bnAb) typically develop in individuals with continuous high-level viral replication and increased immune activation, conditions that cannot be reproduced during prophylactic immunization. Understanding mechanisms supporting bnAb development in the absence of high-level viremia may be important for designing bnAb-inducing immunogens. Here, we show that the breadth of neutralizing antibody responses in HIV-1 controllers was associated with a relative enrichment of circulating CXCR5+ CXCR3+ PD-1Lo CD4 T cells. These CXCR3+ PD-1Lo Tfh-like cells were preferentially induced in vitro by functionally superior dendritic cells from controller neutralizers, and able to secrete IL-21 and support B cells. In addition, these CXCR3+ PD-1Lo Tfh-like cells contain higher proportions of stem cell-like memory T cells, and upon antigenic stimulation differentiated into PD-1Hi Tfh-like cells in a Notch-dependent manner. Together, these data suggest that CXCR5+ CXCR3+ PD-1Lo cells represent a dendritic cell-primed precursor cell population for PD-1Hi Tfh-like cells that may contribute to the generation of bnAbs in the absence of high–level viremia.

overall_design: We analyzed transcriptional profiles of mDC from 4 neutralizer controllers compared to cells from 4 non-neutralizer controllers.

first: Enrique

last: Gayo-Martin

first: Jacqueline

last: Cronin

first: Taylor

last: Hickman

first: Zhengyu

last: Ouyang

first: Madelene

last: Lindqvist

first: Kellie

middle: E

last: Kolb

first: Julian

last: Schulze zur Wiesch

first: Rafael

last: Cubas

first: Filippos

last: Porichis

first: Alex

last: Shalek

first: Jan

last: van Lunzen

first: Elias

last: Haddad

first: Bruce

middle: D

last: Walker

first: Daniel

last: Kaufmann

first: Mathias

last: Lichterfeld


title: Generation and regulation of the electrical membrane potential (Δψ) in Campylobacter jejuni, the major constituent of the proton motive force

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary: The generation of an electrical membrane potential (Δψ), the major constituent of the proton motive force (pmf) is crucial for the ATP synthesis, bacterial growth and motility. The pmf drives the rotation of flagella and is vital for the microaerophilic human pathogen Campylobacter jejuni to colonize the mucus layer of the gut of warm-blooded animals. C. jejuni harbors a branched electron transport chain, enabling respiration with different electron donors and acceptors to generate a Δψ. Here, we demonstrate which electron donor/acceptor couples generate a Δψ and show the impact of the Δψ on the growth performance and motility of this bacterium. In the absence of both oxygen and formate or hydrogen, no Δψ is generated, which strongly reduced the growth rate and the number of motile bacteria. ATP generation is driven either by the pmf, or by substrate level phosphorylation if pyruvate is present. In response to low oxygen tension, C. jejuni upregulates the transcription of the alternative respiratory acceptor complexes and increases the transcription and activity of the donor complexes formate dehydrogenase (FdhABC) and hydrogenase (HydABCD). In conclusion, C. jejuni is dependent on oxygen as electron acceptor or formate/hydrogen as electron donor to generate a pmf that sustains efficient growth and motility performance.

overall_design: Comparison of growth conditions, C. jejuni strain 81116 grown under microaerophilic (5% Oxygen) condition compared to  C. jejuni strain 81116 grown under oxygen limited (0.3% oxygen) conditions with or without 10mM nitrate.

first: A

middle: X

last: van der Stel

first: S

last: Huynh

first: C

first: M

middle: M

last: Wösten


title: Transcriptomic Profiling of Developing Human Paraxial Mesoderm from 4.5-5 Weeks of Gestation Human Embryos

city: Los Angeles

first: Haibin

last: Xi

address: 615 Charles E Young Dr South, BSRB 257

department: MIMG

institute: UCLA

summary: Somites form during embryonic development and give rise to unique cell and tissue types, such as skeletal muscles and bones and cartilages of the vertebrae. Using somitogenesis stage human embryos, we performed the first ever transcriptomic profiling of human presomitic mesoderm as well as nascent and developed somites. Using this approach we uncovered novel regulators unique duing human somitogensis, and efficiently guided human pluripotent stem cells to differentiate to somite cells and downstream progeny. This work improves our understanding of human somite development and may enhance our ability to model and treat diseases affecting somite derivatives.

overall_design: Human embryos of 4.5-5 weeks of gestation were obtained from electively aborted fetuses following informed consent and de-identification. After procurement, tissues were immediately washed in sterile PBS, placed in PBS supplemented with 5% fetal bovine serum, 1% Penicillin-Streptomycin and 2.5 µg/mL Amphotericin B, and shipped on ice. Within 48 hours, targeted tissues were micro-dissected from the embryos. Developed somites (SM Dev) included the two somite pairs at the forelimb bud level, nascent somites (SM) included the two somite pairs just anterior to the most caudal segmentation border that was visible, and presomitic mesoderm (PSM) included the tail region mesoderm posterior to SM. Duplicates were used for each sample type for RNA-seq.

first: April

last: Pyle


title: Conservation and innovation in the DUX4-family gene network (ChIP-seq)

first: Stephen

last: Tapscott

overall_design: We generated three new ChIP-seq datasets in mouse myoblasts and compared them to a published ChIP-seq dataset for human DUX4 expressed in human myoblasts (GSE33838; 10.1016/j.devcel.2011.11.013). All datasets were generated from monoclonal cell lines using a doxycycline-inducible system and codon-altered transgenes. For DUX4 peaks, we compared DUX4-expresssing cells at 24-hours of induction immunoprecipitated with a 50:50 mixture of the DUX4 antibodies MO488 and MO489 to DUX4-expressing cells immunoprecipitated with an antibody to an HA-tag, which was not present in these cells. For Dux peaks, we compared Dux-expressing cells at 24-hours of induction immunoprecipitated individually with each of two Dux antibodies (A-19 and S-20) to Dux-expressing cells immunoprecipitated with an antibody to IgG.

first: Jennifer

last: Whiddon

first: Ashlee

last: Langford

first: Chao-Jen

last: Wong

first: Jun

middle: W

last: Zhong

middle: J


title: Conservation and innovation in the DUX4-family gene network (RNA-seq)

overall_design: We generated two new RNA-seq datasets in mouse myoblasts and compared them to a published dataset for human DUX4 in human myoblasts (GSE85461; DOI:10.1093/hmg/ddw271). All of our datasets (and the dataset we compared to) used a doxycycline-inducible system and codon-altered transgenes. Both new datasets reflect three separate cell cultures of clonal cell lines induced with doxycycline for thirty-six hours, independently barcoded and sequenced in parallel; doxycycline induction caused expression of mouse Dux in one dataset and human DUX4 in the second dataset, both in mouse myoblasts. We also generated four control datasets, each dataset of which reflects three separate cell cultures independently barcoded and sequenced in parallel. Specifically, two control datasets were generated to match the induced datasets mentioned above (i.e. the same mouse myoblast clonal cell lines were used, but these cells were not treated with doxycycline, instead simply harvested at the same thirty-six hour time point). Finally, two more control datasets were generated from clonal mouse myoblasts with an integrated, doxycycline-inducible firefly luciferase transgene, induced and un-induced for thirty-six hours.


title: Identification of quiescent and spatially-restricted mammary stem cells that are hormone responsive

city: Melbourne

first: Casey

last: Ah-Cann

state: Victoria

address: 1G Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to explore histone modification in four basal cell populations defined by Lgr5 and Tspan8 expression taken from adult mouse mammary glands using chromatin immunoprecipitation sequencing (ChIP-seq).
Methods: The ChIP DNA samples were prepared and indexed for Ilumina sequencing using the TruSeq DNA sample Prep Kit (Ilumina) as per manufacturer's instruction. The library was quantified using the Agilent Tapestation and the Qubit's RNA assay kit for Qubit 2.0 Fluorometer (Life Technologies). The indexed libraries were then prepared for paired-end 75bp sequencing on a NextSeq500 instrument using the 150 cycle kit v2 chemistry (Ilumina) as per manufacturer's instructions. Reads were aligned to the mouse genome (mm10) using the subread algorithm by Liao et al. (2013) and counted into bins associated with Entrez gene identifiers (27080 genes in total) using featureCounts in two different ways. Genebody counts summarised the number of reads overlapping anywhere between the first and last base of a given gene while promoter counts summarized the number of reads overlapping a region 3000 bases upstream to 2000 bases downstream of the TSS of each gene. For downstream analysis, genebody counts were used for the H3K27me3 marks and promoter counts were used for the H3K4me3 marks.

overall_design: Enrichment of H3K4me3 and H3K27me3 epigentic marks are shown in the four mammary basal cell populations defined by the expression of Lgr5 and Tspan8.

first: Nai

middle: Y

last: Fu

first: Anne

middle: C

last: Rios

first: Bhupinder

last: Pal

first: Charity

last: Law

first: Paul

last: Jamieson

first: Ruijie

last: Liu

first: François

last: Vaillant

first: Felicity

last: Jackling

first: Kevin

middle: H

first: Gordon

middle: K

last: Smyth

first: Geoffrey

last: Lindeman

first: Matthew

last: Ritchie

first: Jane

last: Visvader


title: The isoxazoloanthrone Y100 perturbs proteostasis and mitochondrial function in NF1 dysregulated cells

city: Hanover

first: Robert

last: Allaway

state: New Hampshire

address: Vail 501A, 72 College St

department: Department of Molecular and Systems Biology

institute: Geisel School of Medicine

summary: We identified a molecule in a synthetic lethal screen with ira2Δ in yeast called Y100. Y100 targets ira2Δ deficient yeast and inhibits NF1-deficient tumor cells. Y100 disrupts proteostasis, metabolic homeostasis, and induces the formation of mitochondrial superoxide in NF1 deficient cancer cells. Here, we examined the transcriptional response following treatment with Y100 or a vehicle control.

overall_design: RNA expression data was obtained from immortalized mammary epithelial cells (IMECs) that were treated for 8 hours with 1 micromolar Y100 or a vehicle control.

first: Jason

last: Wells

first: Carol

last: Ringelberg


title: Cell-type-specific gene expression profiling using ribosome affinity purification

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary:
Post-transcriptional regulation including mRNA binding to ribosomes plays an important role in determining cell-type-specific gene expression patterns.
Here, we applied an approach that profiles cell-type-specific mRNAs. The Translating Ribosome Affinity Purification method (TRAP; Heiman et al., Cell, 2008 and Doyle et al., Cell, 2008) was developed in mice and has been combined with the UAS/Gal4 system in Drosophila (Thomas et al., PLoS ONE, 2012). TRAP is a powerful method to find cell-type-specific differences at the level of the 'translatome' (Dougherty, Schmidt, Nakajima, & Heintz, Nucleic Acids Research, 2010). In parallel to published efforts, we developed and implemented the method for the fly and compared distinct head cell types and identified cell-type-specific transcript classes with neuronal (e.g. receptor-, neuropeptide- or hormone activity) or glial function (e.g. transporter activity). Neuronal TRAP genes are over-represented in the brain, larval CNS and thoracico-abdominal ganglion (Chintapalli, Wang, & Dow, Nature Genetics, 2007). Using cell-type-to-cell-type comparisons (e.g. neurons vs. glia), instead of a given cell population to the total (e.g. neurons vs. head), the differences could be identified with greater resolution. TRAP uncovered more neuronal genes compared to neuronal RNA polymerase II ChIP-seq data (Schauer et al., Cell Reports, 2013). Thus, TRAP data confirm the importance of post-transcriptional regulation in defining cell identity.
TRAP is one of the best methods to reveal differential "omics" data among distinct cell types by profiling ribosome-bound mRNAs. TRAP is a promising tool to reveal cell-type-specific transcriptional and translational changes in a perturbed environment.

overall_design: This dataset contains cell-type-specific ribosome-bound mRNA-seq profiles. Input and IP samples from Drosophila adult head neurons, glia and fat body.

first: Carla

last: Margulies

first: Andreas

last: Ladurner


title: Influence of green light on the transcriptome of Pseudomonas cichorii JBC1

city: Iksan-si

first: Yong

middle: Hoon

last: Lee

state: Jeollabuk do

address: 79, Gobong-ro, Madong

department: Division of Biotechnology

country: South Korea

institute: Chonbuk National University

summary: Pseudomonas cichorii JBC1 was cultured in LB media till it reached exponential phase and the bacterial cells were collected and resuspended in minimal media and treated under green light and dark condition for 12 hours at 30°C. After treatment, the RNA from each sample was collected and sequenced.

overall_design: The experiment was conducted with 3 replicates under two different light conditions and the sample from the 3 replicates were pooled together and sequenced

first: Nagendran

last: Rajalingam

middle: S

last: Park


title: polyA mRNA RNA-seq from liver (ENCSR000CHB)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
RNA-seq on 8 week adult mouse liver

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


title: Effects of IFN-a and IFN-b on ex vivo ATL patient pbmcs

city: Leuven

first: Tim

last: Dierckx

state: Vlaams Brabant

address: Herestraat 49 - 1040

department: Microbiology and Immunology

institute: KU Leuven

summary: The data contained in this record are used to differentiate between the effects of IFN-a and IFN-b on 48h cultures of the ex vivo pbmcs of ATL patients, using Affymetrix microarrays (HuGene 1.0).

overall_design: We used microarrays to identify differentially expressed genes between ex vivo PBMCs of ATL patients, cultured in parallel for 48h with either no treatment, 1000 IU IFN-a treatment or 1000 IU of IFN-b treatment

first: Johan

last: Van Weyenbergh

first: Wouter

last: Van Delm


title: H3K36me2 occupancy profiling by high throughput sequencing from control and WHSC1 knockdown PC3 cells.

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: WHSC1 catalyzes dimethylation of lysine 36 on histone H3, which is profoundly upregulated in prostate cancer patients especially in metastatic PCa patients. We conduct ChIP sequencing in chromatin landscape induced by WHSC1 depleted in prostate cancer cell PC3 to understand the H3K36me2 genome-wide alterations.

overall_design: Lentivirus-mediated RNA interference was used to knockdown WHSC1 expression in prostate cancer cell line PC3. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K36me2 (Millipore).

first: Jun

last: Qin


title: Mutant p53 R270H induces invasion and metastasis of mouse intestinal tumor organoids through gain-of-function mechanism

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

country: Japan

institute: kanazawa university

summary: Apc(D716) mutant mice develop benign intestinal adenoma, while Apc(D716) and p53 R270H compound mutant mice develop invasive adenocarcinoma in the intestine.  We examined expression profile of tumor-derived organoids using Apc(D716),  Apc(D716) p53 Null, Apc(D716) p53 R270H mutant mice by RNA sequencing, and identified mutant p53-induced gene set.

overall_design: Total RNA was extracted from Apc(D716) p53(+/+) tumor organoids, Apc(D716) p53(flox/flox) tumor organoids, and Apc(D716) p53(M/M) tumor organoids.  For each genotype, two mice were used and organoids were prepared independently.  p53(flox) allele is null mutation, whereas p53(M) allele carrys R270H mutation.  We used Illumina HiSeq 2500, and examined expression profiles.

first: Mizuho

last: Nakayama

first: Kanae

last: Echizen

first: Yoichi

last: Yamada

first: Masanobu

last: Oshima


title: GlpR functions as a global DeoR-type regulator of metabolic gene transcription in the haloarchaeon Haloferax volcanii

city: Durham

first: Amy

last: Schmid

address: 125 Science Dr.

institute: Duke University

summary: Investigation of gene expression in ∆glpR mutant strains vs wild type in response to glycerol and glucose.

overall_design: H. volcanii H26 (∆pyrF parent strain) and KS8 (∆glpR) transcriptomes were compared following growth in minimal medium supplemented with glucose and glycerol. Three biological replicate trials were performed for each strain under each condition.

first: Julie

last: Maupin-Furlow


title: Conservation and innovation in the DUX4-family gene network

first: Stephen

last: Tapscott

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

overall_design: Refer to individual Series


title: Organ-specific gene expression in single differentiating Drosophila embryos

first: David

last: Molnar

address: Tennis Court Road

department: Genetics / Systems Biology Centre

institute: University of Cambridge

summary: Age-matched stage 13 embryos were dissected and cDNA of 8 organs from each embryo were sequenced. The organs were foregut, anterior midgut, posterior midgut, hindgut, Malpighian tubules, left salivary gland, right salivary gland, ventral nerve cord. Gene expression, transcription start and stop sites, and strands of termini were analysed. SMART amplification adapters were used for finding transcript termini and for phasing.

overall_design: 3 embryos, 8 organs from each. PolyA RNA was reverse transcribed and amplified using an improved SMART protocol.


title: Genome-wide map of MCM3 and GFP-tagged ESCO2 mutants' binding in human fibroblast cell line vu1199-F SV40

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

summary: Differential co-localization of ESCO2 mutants with MCM3 in the human genome.

overall_design: MCM3-ChIP and GFP-ChIP was performed on vu1199-F cells arrested in G1/S with aphidicolin.

first: Miroslav

last: Ivanov

first: Jan-Michael

last: Peters


title: Whole-genome landscape PARP1 in HEK293T cells

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: Poly [ADP-ribose] polymerase 1 (PARP1) is involved in differentiation, proliferation, tumor transformation, in repair of single-stranded DNA and double-stranded DNA breaks (DSBs) in conjunction with BRCA. PARP1 enzyme works modifying nuclear proteins by poly ADP-ribosylation. It was found that PARP1 and HNRNPA2B1 bind at termini of forum domains and may play a role in coordinated regulation of genes in forum domains (Tchurikov et al., 2013). Forum domains are long DNA fragments of excised chromosomal DNA. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. The domains are delimited by hot spots of double-strand breaks (DSBs). This ChIP-Seq is aimed to compare genome-wide binding sites of PARP1 with different genomic features, including the hot spots of DSBs.

overall_design: Profile of PARP1 in HEK293T cells

middle: A

first: Yuri

middle: V

last: Kravatsky


title: microRNA-seq and RNA-seq reveals changes in the astrocyte transcriptome following Borrelia burgdorferi infection

city: Grand Forks

first: Archana

last: Dhasarathy

state: North Dakota

address: 501 N Columbia Rd.

institute: University of North Dakota


title: RNA-seq reveals changes in the astrocyte transcriptome following Borrelia burgdorferi infection

summary: mRNA profiles of astrocytes infected with Borrelia burdorferi for 24 hours, 48 hours, and 24 hour  uninfected controls  were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Humaira

last: Qureshi

first: Elizabeth

last: Peterson

first: Danielle

last: Perley

first: Emily

last: Blake

first: Bradley

last: Jokinen

first: Attas

last: Abbas

first: Sergei

last: Nechaev

first: John

last: Watt

first: Catherine

last: Brissette


title: microRNA changes in astrocytes following Borrelia burgdorferi infection

summary: miRNA profiles of astrocytes infected with Borrelia burgdorferi for 24 hours, 48 hours, and 24 hour uninfected controls  were generated by deep sequencing, in duplicate, using Illumina MiSeq.


title: LncRNA based TOBF1 chromatin recruitment in early G1 modulates mouse embryonic stem cell identity

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden


title: A comparison of gene expression between lesional and non-lesional derived keratinocytes of Hailey-Hailey disease patients.

city: ROME

first: Claudio

last: Talora

address: Viale Regina ELENA 291

department: Molecular Medicine

institute: Sapienza University of ROME

summary:
Purpose: The goal of this study was to compare NGS-derived keratinocytes transcriptome profiling (RNA-seq) between non lesional and lesional derived keratinocytes of hailey-Hailey disease patients.
Methods: kerationocytes gene profiles of lesional and non-lesional derived keratinocytes were generated by deep sequencing, in triplicate, using Illumina HIseq2000. The sequence reads that passed quality filters were analyzed at gene level with the following methods: STAR for the alignment; HTSeq for generating raw read counts; edgeR for normalization and differential expression analysis. QRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 45 million sequence reads per sample to the human genome (hg19). Hierarchical clustering of gene expressions clearly showed separation between non-lesional and lesional keratinocytes. A total of 1,453 differentially expressed genes at FDR<0.05 were identified, uncovering several genes that may contribute to Hailey-Hailey manifestation function.
Conclusions: Our study represents the first detailed analysis of keratinocyte gene expression profile, generated by RNA-seq technology.  We conclude that RNA-seq gene based characterization of HHD-keratinocytes would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: non-lesional and lesional  mRNA profiles of Hailey-Hailey Patients- derived kerationocytes  were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Loredana

last: Le Pera


title: The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

summary: In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box helicase DHX15 and the 5’-3’ exonuclease XRN2. Using UV crosslinking and analysis of cDNA (CRAC), we reveal that NKRF binds to the transcribed spacer regions of the pre-rRNA transcript. Consistent with this, we find that depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step (A’). The catalytic activity of DHX15, which we demonstrate is stimulated by NKRF functioning as a cofactor, is required for efficient A’ cleavage, suggesting that a structural remodelling event may facilitate processing at this site. In addition, we show that depletion of NKRF or XRN2 also leads to the accumulation of excised pre-rRNA spacer fragments and that NKRF is essential for recruitment of the exonuclease to nucleolar pre-ribosomal complexes. Our findings therefore reveal a novel pre-ribosomal subcomplex that plays distinct roles in the processing of pre-rRNAs and the turnover of excised spacer fragments.

overall_design: HEK293 cell lines expressing Flag-His-tagged NKRF or the Flag-His tag alone were crosslinked (UV - 254 nm; PAR - 365 nm after growth in media containing 4-thiouridine) and analyzed by CRAC.

first: Indira

last: Memet

first: Carmen

last: Doebele

first: Katherine

last: Sloan


title: ChIRP-Seq of Panct1 lncRNA in mouse ES cells

summary: We report the chromatin binding of the lncRNA (AK156552) in mouse embryonic stem (ES) cells.

overall_design: Chromatin Isolation by RNA purification was done using Glutaraldehyde cross-linking in mouse ES cells. DNA obtained after ChIRP was sequenced.

first: Debojyoti

last: Chakraborty

first: Frank

last: Buchholz


title: RNA-seq analysis of Akt1-mediated muscle growth

city: Boston

first: Chia-Ling

last: Wu

state: MA

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

summary:
Background: Skeletal muscle constitutes a significant portion of total body mass and is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is a preferential loss of fast glycolytic muscle fibers. We previously reported a mouse model in which a constitutively-active Akt transgene is induced to express in a subset of muscle groups leading to the hypertrophy of type IIb myofibers with an accompanying increase in strength. This muscle growth protects mice in various cardio-metabolic disease models, but little is known about the underlying cellular and molecular mechanisms by which fast-twitch muscle impacts disease processes and regulates distant tissues.
Purpose: In the present study, poly(A)+ tail mRNA-seq was performed to characterize the transcriptome of the hypertrophic gastrocnemius muscle from Akt1-transgenic mice.
Results: Pathway analysis for the 3,481 differentially expressed genes in muscle identified enriched signaling pathways involving growth, cell cycle regulation, and inflammation. Combined metabolomics and transcriptomic analyses revealed that Akt1-induced muscle growth mediated a metabolic shift involving reductions in glycolysis and oxidative phosphorylation, but enhanced pentose phosphate pathway activation and increased branch chain amino acid accumulation. Signal peptide prediction analysis revealed 241 differentially expressed in muscle transcripts that potentially encode secreted proteins. A number of these secreted factors have signaling properties that are consistent with the myogenic, metabolic and cardiovascular-protective properties that have previously been associated with type IIb muscle growth.
Conclusions: These data reveal that enhanced Akt signaling promotes the activation of the pentose phosphate and the accumulation of branched amino acids that are important for the production of nucleic acids and proteins. Numerous known and novel transcripts potentially encoding muscle secreted proteins were identified, indicating the importance of fast-twitch muscle in inter-tissue communication.

overall_design: mRNA profiles of adult muscle growth from four muscle-specific conditional Akt transgenic (DTG) and four littermate control mice (1256[3Emut]Mck-rtTA) were generated by deep sequencing using Illumina HiSeq.

first: Kenneth

last: Walsh


title: ChIP-Seq of TOBF1 (A830080D01Rik) in mouse ES cells

summary: We report the chromatin binding of a novel protein TOBF1 (encoded by A830080D01Rik) in mouse embryonic stem (ES) cells.

overall_design: Chromatin Immunoprecipitation was done using Formaldehyde-DSG cross-linking in mouse ES cells. DNA obtained after ChIP was sequenced.


title: The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL (RNA-seq)

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: This study shows how the way by which the RNA-Seq data is analyzed affects the resulting gene expression profile. Three parameters were explored: the RNA-Seq analysis algorithm pipeline (cufflinks – Cuffdiff 2 or HTSeq & DESeq), sequencing depth and sequencing protocol: single or paired end, 100 or 50 bases. For comparison, the same samples were processed by gene microarrays.

overall_design: RNA-Seq and gene microarray was conducted on four acute lymphoblastic leukemia (ALL) precursor B cell lines, two lines carrying the chromosome translocation t(4;11) in which the human MLL gene is rearranged, and two lines lacking this abnormality.

first: Eli

last: Canaani


title: The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL


title: Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

status: Public on Jan 31 2017

city: Chicago

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Tuberculosis is a deadly infectious disease, which kills millions of people every year. The causative pathogen, Mycobacterium tuberculosis (MTB), is estimated to have infected up to a third of the world’s population; however, only approximately 10% of healthy individuals progress to active TB disease. Despite evidence for heritability, it is not currently possible to predict whether a healthy person is susceptible to TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from a past episode of active TB. We measured genome-wide gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms in proximity to the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. By intersecting the gene expression and GWAS data, we identified two promising candidate genes: CCL1 and UNC13A. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated decent performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.

overall_design: We obtained whole blood samples from 25 healthy male Caucasian individuals. Six of the donors had recovered from active TB, and are thus putatively susceptible. The remaining 19 tested positive for latent TB without ever experiencing symptoms of active TB, and are thus putatively resistant. We isolated dendritic cells (DCs) and treated them with Mycobacterium tuberculosis (MTB) or a mock control for 18 hours. To measure genome-wide gene expression levels in infected and non-infected samples, we isolated and sequenced RNA using a processing pipeline designed to minimize the introduction of unwanted technical variation. There are a total of 50 samples (25 individuals x 2 treatments).

first: Ludovic

last: Tailleux

first: Marsha

last: Myrthil

first: Cécile

last: Charlois

first: Emmanuel

last: Bergot

first: Aurélien

last: Dinh

first: Gloria

last: Morizot

first: Olivia

last: Chény

first: Cassandre

last: Von Platen

first: Jean-Louis

last: Herrmann

first: Roland

last: Brosch

first: Luis

middle: B

last: Barreiro

first: Yoav

last: Gilad


city: Münster

first: Shirin

last: Glander

state: Deutschland (DEU)

address: Domagkstraße 3

institute: University Münster

summary:
Comparative genomic analysis of basal and LPS-induced expression patterns of bone marrow derived macrophages and bone marrow resident macrophages demonstrates completely divergent transcriptome profile and indicates/confirms the existance of two distinct monocyte/macrophage populations in murine bone marrow.
Most resident tissue macrophages descent from embryonic precursors of the yolk sac but inflammatory and bone marrow (BM) macrophages are considered to develop from hematopoietic stem cells (HSCs) in the BM. We now identified a novel subpopulation of resident CD163+ macrophages in the BM which were phenotypically and functionally distinct from classical BM-derived macrophages. Bioinformatics analysis of transcriptoms indicated a unique immune-modulatory phenotype of CD163+ macrophages. Cell fate studies in Csf1rMer-iCre-Mer;RosaLSL-GFP mice demonstrated that resident CD163+ macrophages of the BM do not develop from HSCs but descent from embryonic progenitors in the yolk sac strictly dependent on transcription factor IRF8. In contrast to other yolk sac derived tissue macrophages CD163+ cells seem to play a relevant role in infections and sterile inflammation. IRF8-/- mice lacking this population are highly sensible to S. aureus infections. Thus, CD163 defines a macrophage population resident in the bone marrow but originating from yolk sac progenitors which exhibits immune-modulatory properties under different inflammatory conditions. We used quantitative RNA-seq to perform whole transcriptome analysis and compare the transcriptomes of resident CD163+ BM macrophages and classical CD163- BMDM in steady state and after LPS stimulation.

overall_design: Murine resident CD163+ macrophages from BM and classical CD163- BMDM were stimulated with LPS or left untreated and subsequently selected for RNA extraction and transcriptome comperative analysis using Illumina mRNA-sequencing (RNA-seq).

first: L

last: Fischer-Riepe

first: J

last: Schulte-Schrepping

first: N

last: Daber

first: A

middle: I

last: Chasan

first: M

last: Pohlen

last: Wolf

last: Fischer

first: T

last: Ulas

first: S

first: C

last: Schulz

last: Vettorazzi

first: F

last: Rosenbauer

last: Stoll

middle: L

last: Schultze

last: Niemann

last: Tuckermann

last: Roth

first: K

last: Barczyk-Kahlert


title: ATR Mutations Promote the Growth of Melenama Tumor by Modulating the Immune Microenvironment [skin]

city: Irvine

first: Anand

last: Ganesan

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

summary: Melanomas accumulate a high burden of mutations that could potentially generate neoantigens, yet these tumors are still able to suppress the immune response in order to facilitate their continued growth. In this study, we identify subsets of human melanoma tumors that have partial loss of function mutations in ATR, a kinase that recognizes and repairs UV-induced DNA damage and is required for cellular proliferation. ATR mutant tumors exhibit both the accumulation of multiple mutations and the altered expression of inflammatory genes, resulting in decreased T-cell recruitment and increased recruitment of macrophages known to spur tumor invasion. Taken together, these studies identify a novel mechanism by which melanoma cells modulate the immune microenvironment to allow continued tumor growth.

overall_design: RNA-sequencing analysis was performed on ATR wild type and ATR mutant mouse nevi. 3 control (ATR wild type) and 3 experimental (ATR mutant mouse nevi) samples were compared.

first: Chi-Fen

last: Chen

first: Rolando

last: Ruiz-Vega

first: Priya

last: Vasudeva

first: Francisco

last: Espitia

first: Tatiana

last: Krasieva

first: Sebastien

last: de Feraudy

first: Bruce

last: Tromberg

first: Sharon

last: Huang

first: Dave

last: Hoon

first: Chad

middle: P

last: Garner

first: Jie

last: Wu


title: ATR Mutations Promote the Growth of Melenama Tumor by Modulating the Immune Microenvironment [tumor]


title: A Molecular Census of Arcuate Hypothalamus and Median Eminence Cell Types

first: Linus

middle: Tzu-Yen

last: Tsai

address: 330 Brookline Avenue

department: Medicine, Division of Endocrinology, Diabetes, and Metabolism

institute: Beth Israel Deaconess Medical Center

summary:
Drop-seq and single cell sequencing of mouse arcuate nucleus and median eminence.

Please see below link for searchable cluster-based gene expression.

overall_design: Drop-Seq was performed on six separate days using mice in C57BL6/J background at various ages/sex noted. On day 1, Chow_1 replicate was obtained. On day 2, Chow_2 replicate was  obtained. On day 3, Chow_3 replicate was obtained.  On day 4, 10% Diet_1 and HFD_1 replicates were obtained. On day 5, Fast_1 and Refed_1 replicates were obtained. On day 6,  Fast_2, Fast_3, Chow_4, and Chow_5 replicates were obtained

middle: T

first: John

middle: N

last: Campbell


title: ATR Mutations Promote the Growth of Melenama Tumor by Modulating the Immune Microenvironment