title: Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

institute: Univeristy of Geneva

summary: The transcriptional co-activators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, play global roles in transcriptional activation. Here we explore the relative contributions of these factors to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. We show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect. Relative dependence on Esa1 and Tra1, a shared component of NuA4 and SAGA, distinguishes two large groups of co-regulated growth-promoting genes. In contrast, we show that the activity of Mediator is particularly important at a separate, small set of highly transcribed TATA box-containing genes. Our analysis indicates that at least three distinct combinations of co-activator deployment are used to generate moderate or high transcription levels, and suggests that each may be associated with distinct forms of regulation.

overall_design: Histone acetylation, nucleosome occupancy, RNA Polymerase II binding as well as metabolic labeled RNA was measured upon nuclear depletion of Esa1, Gcn5, Tra1 and Med17. Med8 binding was measured by ChEC-Seq upon nuclear depletion of Med17, Esa1 and Gcn5.  IMPORTANT: The S.pombe spike control normalization of the metabolic labeled RNA-Seq (4-tU RNA-Seq) data revealed to be unreliable due to the reduced number of reads uniquely assigned to the S.pombe transcriptome. Therefore, we advise against making any quantitative interpretation of the data. Furthermore, the 4-tU RNA-Seq experiment has been performed only once. For these reasons, the 4-tU RNA-Seq data are not included in the publication linked to this study. Nevertheless, we think these data could be potentially useful for the scientific community and we deposit them here to make them publicly available.

first: Sebastian

last: Gruenberg

first: Slawomir

last: Kubik

first: Gabriel

middle: E

last: Zentner

first: David

last: Shore


status: Public on Aug 15 2018

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

country: USA

institute: Marshall University School of Medicine

type: Expression profiling by high throughput sequencing

summary: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds pollutants, therapeutic drugs and endogenous ligands.  The AHR is expressed in all breast cancer subtypes and it can switch the aggressiveness of breast cancer cells from low to high depending on the ligand that it binds.  Jagged 1 (JAG1) is a NOTCH receptor ligand that is overexpressed in basal-like breast cancer.  JAG1 promotes breast cancer progression in part by increasing the migratory and invasive activity of breast cancer cells (BCCs).  The regulation of JAG1 by AHR in MCF-7 and MDA-MB-231 BCCs by two AHR ligands (TCDD and ITE) was investigated in this report.  TCDD is the prototype AHR ligand, and ITE is a non-toxic endogenous AHR ligand with anti-cancer activity.  Ingenuity pathway analysis (IPA) revealed a significant association between TCDD-regulated genes (TRGs) and cell movement.  Short interfering RNA (siRNA)-directed knockdown of AHR confirmed TCDD-stimulated decreases in JAG1 required AHR expression.  TCDD-induced reductions in JAG1 were inhibited by the AHR antagonist CH-223191.  The endogenous non-toxic AHR ligand ITE also reduced JAG1 by activating AHR in BCCs.  MDA-MB-231 are basal-like BCCs that are highly migratory and invasive, and these cancer cell attributes were significantly inhibited by ITE.  We reduced JAG1 with targeting siRNA, and the outcome mirrored ITE, it suppressed TNBC cell migration and invasive activity.  Collectively, these findings are the first showing that ITE is a tumor-suppressing AHR ligand in TNBC cells in part because it reduces JAG1 expression

overall_design: Expression profiling of four replicates of MCF-7 cells treated with 100nM TCDD were compared to expression profiles of four control replicates of MCF-7 cells treated with DMSO by RNA-Seq

first: Sean

last: Piwarski

first: Donald

middle: A

last: Primerano

first: Jun

last: Fan

first: Travis

middle: B

last: Salisbury


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [CAGE]

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood.

overall_design: CAGE assays in different developmental stages of european amphioxus

first: Malcom

last: Perry

first: Piotr

last: Balwierz

first: Ge

last: Tan

first: Piero

last: Carninci

first: Boris

last: Lenhard


title: MLL1 is essential for retinal development

city: St. Louis

first: Philip

last: Ruzycki

state: MO

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

summary: By removing MLL1 from mouse retinal progenitors, we discovered that MLL1 plays multiplex roles in retinal development by regulating: 1) progenitor cell proliferation and cell cycle progression; 2) retinal cell composition; 3) maintenance of horizontal neurons; 4) formation of functional synapses between neuronal layers; and 5) visual function development. Altogether, our results suggest that MLL1 is an indispensable regulator for the development of retinal structure and function.

overall_design: Triplicate mutant (MLL1 fl/fl Chx10-Cre) and triplicate WT samples were compared

first: Diana

middle: S

last: Brightman

first: Rachel

middle: L

last: Grant

first: Ray

last: Suzuki

first: Anne

middle: K

last: Hennig

first: Shiming

last: Chen


title: Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state

status: Public on Aug 14 2018

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: During early mammalian development transient pools of pluripotent cells emerge that can be immortalised upon stem cell derivation. The pluripotent state, "naïve" or "primed", depends on the embryonic stage and derivation conditions used. Here we analyse the temporal gene expression patterns of mouse, cattle and porcine embryos at stages that harbour different types of pluripotent cells. We document conserved and divergent traits in gene expression, and identify predictor genes shared across the species that are associated with pluripotent states in vivo and in vitro Amongst these are the pluripotency-linked genes Klf4 and Lin28b The novel genes discovered include naïve- (Spic, Scpep1 and Gjb5) and primed-associated (Sema6a and Jakmip2) genes as well as naïve-to primed transition genes (Dusp6 and Trip6). Both Gjb5 and Dusp6 play a role in pluripotency since their knockdown results in differentiation and downregulation of key pluripotency genes. Together, our interspecies comparison revealed new insights of pluripotency, pluripotent stem cell identity and a new molecular criterion for distinguishing between pluripotent states in various species including human.

sample_organism:
Sus scrofa
Bos taurus
Mus musculus

platform_organism:
Sus scrofa
Bos taurus
Mus musculus

overall_design: RNA-Seq profiles of three embryonic stages, 3 replicas per stage. This profiling is performed for mouse (mus musculus), pig (sus scrofa) and cow (bos taurus). Furthermore 4 RNA-Seq samples on mouse liver RNA to investigate various methods of amplification for small quantities of RNA.

first: Andreia

last: Bernardo

first: Alice

last: Jouneau

last: Kensche

first: Kristine

last: Freude

first: Yan

first: Julianna

last: Kobolak

first: Anita

last: Feher

first: Zsuzsanna

last: Polgar

first: Chiara

last: Sartori

first: Istvan

last: Bock

first: Claire

last: Louet

first: Tiago

last: Faial

first: Vanessa

last: Hall

first: Kaveh

last: Maseyakhi

first: Martijn

last: Huynen

first: Giovanna

last: Lazzari

first: Poul

last: Hyttel

first: Henk

last: Stunnenberg

first: Roger

last: Pedersen

first: Andras

last: Dinnyes


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ChIP-Seq]

first: Juan

last: Tena

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIPseq assays in different developmental stages of european amphioxus

first: Elisa

middle: d

last: la Calle-Mustienes

first: Ignacio

last: Maeso

first: Panos

last: Firmpas

middle: J

first: José

last: Gómez-Skarmeta


title: Reprogramming oncogene levels through gene body hypermethylation in RTK-driven cancer

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

type: Methylation profiling by high throughput sequencing

summary: While promoter epigenetic modifications have been linked to tumor suppressor silencing in cancers, modifications in gene body regions has been largely neglected. Using a genetic setting in which subtle enhanced levels of non-oncogenic receptor tyrosine kinases (RTKs) become progressively pathological, we show that reprogrammed CpG island (CGI) methylation locks cells into tumorigenicity. By focusing on gene bodies, we found an enrichment of hypermethylated CGI similar to that reported in cancer patients. Gene body CGI hypermethylation correlates with decreased H3K27me3 modification and enhanced transcription for a proportion of genes, which act as oncogenes in cancer cells. Collectively, our results illustrate that tumorigenesis is ensured by an increase dosage of a set of oncogenes through an epigenetic reprogramming involving gene body CGI hypermethylation.

overall_design: Genomic DNA from dissected Alb-R26Met tumors (n=10) and control livers (n=3) was used to analyze the DNA methylation profile

first: Maria

last: Arechederra

first: Fabrice

last: Daian

first: Sylvie

last: Richelme

first: Rosanna

last: Dono

first: Andrew

last: Saurin

first: Flavio

last: Maina


title: Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing

status: Public on Aug 13 2018

city: Debrecen

first: Lilla

last: Ozgyin

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary:
Purpose: We aimed to examine whether eukaryotic cell lyophilization and long-term storage would be feasible as an environmentally friendly and cheap alternative to cryogenic storage or the use of FFPE samples for large-scale RNA profiling studies.
Brief method: On three different days three million GM12873 cells were taken up in 0.1 M trehalose, subjected to lyophilization (freeze-drying) and then stored for two weeks at room temperature in the presence of CaCl2 in a dark, tightly sealed box. Fresh paired control cells were pelleted and taken up in trizol without lyophilization. Total RNA was isolated using a modified trizol method, quantified and subjected to mRNA-Seq library preparation. Samples were sequenced using a NextSeq 500 instrument to 75 bp (single-end). Raw reads were aligned to the hg19 genomic build with TopHat 2.0.7 and gene expression quantification was performed using Cufflinks.
Results: We found that lyophilized cells are highly similar in all inferred RNA-Seq quality metrics compared to their non-lyophilized controls and are useful sources of high-quality RNA for both small and large-scale studies.
Conslusion: Lyophilization might be the preservation technique of choice in the future for studies aiming to involve large sample sets, such as clinical studies.

overall_design: mRNA profiles of three paired control and lyophilized cells stored at room temperature for two weeks.

first: Attila

last: Horvath

first: Balint

last: Balint


title: Discovery of a periosteal stem cell mediating intramembranous bone formation and fracture healing (single cell RNA-Seq)

city: New York

first: Matthew

last: Greenblatt

state: NY

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

summary: CTSK-mGFP positive cells from Day 6 old mouse femurs were sorted as single cells into 384 well plates pre-loaded with unique barcoded RT-primers. After sorting, cells were snap frozen on dry ice before being submitted to the New York Genome Center (NYGC) for cDNA synthesis and library preparation. The FACS profile for all the sored cells were collected to co-relate with gene expression.

overall_design: Mouse femur was obtained from mice within the same litter. Femur samples was subjected to collagenase digestion, and single cell suspension was obtained. The samples were stained for FACS antibodies and single cell sorting was performed into two individual 384 well plates. The experiment has two replicates from two independant animals. The samples were always kept discrete.

first: Shawon

last: Debnath

first: Jason

last: McCormick


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [RNA-seq]

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

summary: Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the putative tumor suppressor proteins PBRM1 (BAF180) and ARID2 (BAF200) that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). Here, we integrate RNA-seq, ARID2 and histone mark ChIP-seq, and ATAC-seq data to show that PBAF acts to enhance or repress gene expression depending on the genomic context. At baseline, ARID2 binds to areas of open chromatin at both active enhancers and promoters. Depletion of PBRM1 leads to attenuated and redistributed ARID2 chromatin binding that correlates significantly with gene expression changes. At enhancers, ARID2 binding loss leads to diminishment of the histone mark H3K4me1 and gene downregulation. Alternatively, at a subset of promoters, ARID2 binding loss derepresses gene expression. Interestingly, ARID2, which remains bound to other PBAF subunits after loss of PBRM1, is essential for many of the pro-tumorigenic transcriptional changes observed after loss of PBRM1, whereas other core SWI/SNF components are dispensable. Upon loss of PBRM1, ARID2 positively regulates cancer-related genes and pathways, including the cancer stem cell marker ALDH1A1 and EGF signaling, to stimulate tumor cell growth. Therefore, ARID2 is crucial for maintaining the transformed state of PBRM1-deficient ccRCC cells. In total, this study suggests a novel mechanism of transcriptional control by PBRM1, whereby its loss alters the chromatin distribution of the residual PBAF complex leading to altered transcription that promotes tumorigenesis.

overall_design: RNA-seq was performed at high and low serum concentrations in the the human clear cell renal cell carcinoma cell line 786-O in which PBRM1 had been stably knocked down with two different lentiviral vectors containing shRNA targeting PBRM1 (sh1 or sh2), or with a lentiviral vector containing an off-target control shRNA (control). RNA-seq at high and low serum concentration was also performed in another human clear cell renal cell carcinoma cell line, A-704, which harbors a homozygous truncating mutation of PBRM1. These cells had been stably transduced with either an empty-vector containing retrovirus (EV) or a retrovirus containing wild-type PBRM1 with a C-terminal V5 tag (V5).

first: Sakellarios

last: Zairis

first: William

last: Su

first: Nicole

last: Steinbach

first: Dan

last: Hasson

first: Deepti

last: Mathur

first: Asif

last: Chowdhury

first: Bertilia

last: Tavarez

first: Emily

last: Bernstein

first: Raul

last: Rabadan

first: Ramon

last: Parsons


title: Discovery of a periosteal stem cell mediating intramembranous bone formation and fracture healing (batch RNA-Seq)

summary: FACS sorted 4 bulk cell population from mouse femur (P6)  were subjected to RNA sequencing. The samples were periosteal stem cell (PSC), progenitor population type 1 (PP1), progenitor population 2 (PP2) and CTSK-mGFP negative mesenchymal stem cells (MSC). The aim of this project was to obtain Differentially expressed gene list for each cell types as well as compare transcriptinal profile between each population.

overall_design: All samples for RNA seq were obtained on the same day from mouse femur  within the same litter. Cells were sorted into 4 populations by FACS. No samples were pooled. There are 4 Replicates for each populaton.


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits

first: Juan

last: Tena

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

sample_organism:
Branchiostoma lanceolatum
Danio rerio
Oryzias latipes

overall_design: Refer to individual Series


title: RNA-seq analysis in the Tas2r143-reporter mice (Tas2r143-CreERT2;Rosa26flox-mT-stop-flox-mG)

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: RNA-seq analysis of Tas2r143-expressing cells in the trachea and stomach of adult Tas2r143-reporter mice

overall_design: EGFP- and Tomato-positive cells were isolated from the trachea and stomach of tamoxifen-treated Tas2r143- reporter mice to validate the Tas2r143-CreERT2 mouse line and to characterize Tasr143-expressing cells.

first: Shuya

last: Liu


title: Mechanosensitive Gene Regulation by Myocardin-Related Transcription Factors is Required for Cardiomyocyte Integrity in Load-Induced Ventricular Hypertrophy

city: Rochester

first: Eric

last: Small

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

summary: Cardiac-restricted deletion of myocardin-related transcription factors (MRTFs) in adult mice leads to partially penetrant lethality and rapid deterioration in cardiac physiology in response to trans-aortic constriction (TAC). The goals of the RNA-seq are to define the gene programs altered in MRTF-depleted cardiomyocytes compared to control cardiomyocytes 7 days after TAC surgery.

overall_design: MRTF double knockout (called "MRTF dKO" or "dKO") and control mice were subject to TAC or sham surgery at 8 weeks of age. Cardiomyocytes were isolated from knockout or control hearts 7 days after surgery and RNA was isolated using Trizol for RNA-seq analysis.

first: Michael

last: Trembley

last: Myers


title: Algesic MBP peptide induce pain-specific signaling in rodent Schwann Cells

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: We demonstrated the pain-specific response to the algesic peptide fragment MBP84-104 of myelin basic protein that induces pain if injected into sciatic nerve of rats and mice. We used the wild-type peptide MBP 84-104, H89G mutant peptide (MBP84-104-H89G), scramble peptide (MBP84-104-SCR) and phosphomimetic peptide MBP84-104-mimTT to stimulate the primary rat Schwann cell cultures. After 24h we isolated total RNA and conducted genome wide RNA-seq. In addition, we performed RNA-seq using Schwann cells constitutively expressing an MBP84-104-mCherry construct. The gene expression data was analyzed using Ingenuity Pathway Analysis software. We conclude that the Schwann cells expressing MBP84-104 constructs stimulate pain-specific signaling pathways thus representing a relevant model to study neuropathic pain.

overall_design: examination of gene expression in Schwann cells stimulated by MBP fragment

middle: V

first: Alex

middle: Y

last: Strongin

first: Veronica

last: Shubayev


title: Next Generation Sequencing Facilities Quantitative Analysis of Wild type iNKT cells at stage2 and stage3 transcriptomes

status: Public on Aug 10 2018

city: Shanghai

first: Yu

last: Xu

address: 320 Yueyang Road

country: China

institute: Shanghai Institue of Biochemistry and Cell Biology

summary:
Purpose:Next Generation Sequencing applying for compare the iNKT cells at stage2 and stage3 distict transcriptome, included pathway-enrichment analysis and genes expression of interests
Methods:iNKT cells at stage2 and stage3 were isolated from thymus in 6 week old wild type mice by cell sorting. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer.
Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse
Conclusions:Our study represents the detailed analysis of iNKT cells at stage2 and stage3 transcriptomes, with biologic replicates

overall_design: iNKT cells at stage2 and stage3 mRNA profiles of 6 week old wild type mice were generated by deep sequencing with three replications

first: Yang

last: Sun


title: Discovery of a periosteal stem cell mediating intramembranous bone formation and fracture healing

first: Matthew

last: Greenblatt


title: Retinoic acid suppresses MYB in adenoid cystic carcinoma [RNA-seq]

status: Public on Aug 11 2018

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Translocations that drive overexpression of the oncogenic transcription factor MYB are molecular hallmarks of adenoid cystic carcinoma (ACC), a malignant salivary gland tumor. Surgical resection, whenever possible, is the standard therapy for ACC, but there are no available therapeutic options available if surgery fails. Here we performed a chemical genetic screen using a zebrafish embryo culture system and identified retinoic acid agonists as potent suppressors of c-myb. Retinoic acid treatment strongly decreased c-myb gene expression in U937 cells and suggested a direct transcriptional mechanism of regulation. Retinoic acid agonists strongly inhibited tumor growth in vivo in different ACC patient derived xenograft models. Analysis of the xenografts revealed a significant decrease in MYB binding at translocated enhancers, thereby disrupting the MYB positive feedback loop that drives ACC. Our findings identify an important role of retinoic acid in MYB regulation and as a potential new effective therapy for ACC.

overall_design: RNA-seq analysis of ACC xenograft samples treated with vehicle or ATRA

first: Joseph

last: Mandelbaum

middle: I


title: Integrative analysis of the genomic architecture of a complex kidney damage QTL in inbred hypertensive rats implies Tmem63c for translational research

city: Muenster

last: Barysenka

address: Domagkstrasse 3

department: Genetic Epidemiology

institute: Institute of Human Genetics, University of Muenster

summary: Despite recent advances in genomics, the identification of genes underlying complex diseases remains challenging. Inbred rat strains offer well-established experimental models to support the identification of susceptibility genes for diseases such as kidney damage associated with elevated blood pressure or hypertension. Here, we combined quantitative trait locus (QTL) mapping in two contrasting inbred rat strains with targeted next generation sequencing (NGS), compartment-specific transcriptome sequencing (RNA-Seq), and phenotype directed follow-up translational analysis.

overall_design: mRNA profiles of spontaneously hypertensive rats and Munich Wistar Frömter rats were generated by deep sequencing, in triplicate, using NextSeq 500

first: Angela

last: Schulz

first: Nina

last: van de Lest

first: Andreas

last: Eisenreich

first: Martina

last: Schmidbauer

first: Nicola

last: Müller

first: Theodor

last: Lorenzen

first: Alexander

last: Meyer

first: Laura

last: Herlan

first: Anika

last: Witten

first: Frank

last: Rühle

first: Weibin

last: Zhou

first: Emile

last: de Heer

first: Marion

last: Scharpfenecker

first: Daniela

last: Panakova

first: Monika

last: Stoll

first: Reinhold

last: Kreutz


title: Inactivation of transcription factor HNF-1β with CRISPR/Cas9 induces epithelial-mesenchymal transition

city: Minneapolis

first: Siu Chiu

last: Chan

state: MN

address: MCB-5148 420 Washington Ave SE

department: Medicine

institute: University of Minnesota

summary: Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is essential for the development of the kidney. Mutations of HNF-1β produce autosomal dominant tubulointerstitial kidney disease (ADTKD) characterized by tubular cysts, renal fibrosis, and progressive decline in kidney function. To understand the functions of HNF-1β, we generated HNF-1β-deficient mIMCD3 renal epithelial cells. Gene editing with CRISPR/Cas9 was used to delete exon 1 of HNF-1β by non-homologous end joining (NHEJ). We performed RNA-seq on three independent HNF-1β-deficient mIMCD3 cell lines and three paired control cell lines. Our RNA-seq of HNF-1β-deficient cells showed upregulation of 1,135 genes and repression of 759 genes compared to control cells. Pathway analysis revealed that fibrosis and epithelial-mesenchymal transition (EMT) pathways were highly activated in HNF-1β-deficient cells. We conclude that loss of HNF-1β in renal epithelial cells leads to the activation of a transcriptional network that induces EMT and aberrant TGFβ signaling. Targeting this network may inhibit fibrosis in ADTKD and other chronic kidney diseases.

overall_design: RNA-seq of three independent HNF-1β-deficient mIMCD3 cell lines and three paired control cell lines.

first: Peter

last: Igarashi

first: Siu

middle: C


title: A novel role for Lyl1 in primitive erythropoiesis

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: Stem Cell Leukemia (Scl or Tal1) and Lymphoblastic Leukemia 1 (Lyl1) are highly related members of the basic helix-loop-helix (bHLH) family of transcription factors that are co- expressed in hematopoietic stem cells and the erythro-megakaryocytic lineages. Previous studies suggest that Scl is essential for hematopoietic development including primitive erythropoiesis. However, analysis of single-cell RNA-sequencing data of early embryos showed that primitive erythroid cells express both Scl and Lyl1. Therefore, to determine whether Lyl1 has a functional role in erythropoiesis, we crossed conditional Scl mice with transgenic mice expressing a Cre recombinase under the control of the Epo receptor, active in erythroid progenitors. Surprisingly, embryos with markedly reduced expression of Scl from E9.5 survived to adulthood. In contrast, mice with reduced expression of Scl and absence of Lyl1 (double knockout; DKO) died at E10.5 due to progressive loss of erythropoiesis. Consistent with a phenocopy of Gata1-null mice, gene expression profiling of DKO yolk sacs prior to the loss of erythrocytes (E9.5) revealed loss of Gata1 and many of the known target genes of the SCL-GATA1 complex. ChIP-seq analyses showed that LYL1 exclusively bound a small subset of SCL targets including GATA1. Together, these data show for the first time that Scl and Lyl1 share functional roles in primitive erythropoiesis.

overall_design: RNA-Seq analysis of WT, LYL1 KO, SCL KO, LYL1 SCL DKO e9.5 embryos

first: David

last: Curtis

first: Sung

last: Chiu


title: Proteus mirabilis MrpJ ChIP-seq

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (UTIs) and urolithiasis. The transcriptional regulator MrpJ inversely modulates two critical aspects of P. mirabilis UTI progression: fimbria-mediated attachment to the urinary tract, and flagella-mediated motility. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was used for the first time in a CAUTI pathogen to probe for in vivo direct targets of MrpJ. ChIP-seq revealed 81  78 direct MrpJ targets, including genes for motility, fimbriae and a type VI secretion system (T6SS), and the putative MrpJ binding sequence ACnCnnnnnnnGnGT.

overall_design: Four types of P. mirabilis samples were sequenced:1) empty vector with no ChIP antibody (control); 2) pMrpJ (produces His-tagged MrpJ) with no ChIP antibody (control); 3) empty vector with anti-His ChIP (control) and 4) pMrpJ with anti-His ChIP (experimental sample). Two biological replicates were sequenced for each sample type, for a total of 8 samples.

first: Irina

last: Debnath

first: Joseph

middle: T

last: Wade

first: Anne

last: Stringer


title: Rapid CLIP Dissociation from MHC II Promotes an Unusual Antigen Presentation Pathway in Autoimmunity

status: Public on Aug 09 2018

city: Cambridge

first: Orr

last: Ashenberg

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary: A number of autoimmunity-associated MHC class II proteins interact only weakly with the invariant chain-derived class II-associated invariant chain peptide (CLIP).  CLIP dissociates rapidly from I-Ag7 even in the absence of DM, and this property is related to the type 1 diabetes-associated b57 polymorphism.  We generated knock-in Non-obese Diabetic (NOD) mice with a single amino acid change in the CLIP segment of invariant chain in order to moderately slow CLIP dissociation from I-Ag7.  These knock-in mice had a significantly reduced incidence of spontaneous type 1 diabetes and diminished islet infiltration by CD4 T cells, in particular T cells specific for fusion peptides generated by covalent linkage of proteolytic fragments within b cell secretory granules.  Rapid CLIP dissociation enhanced presentation of such extracellular peptides, thus bypassing the conventional MHC class II antigen processing pathway.  Autoimmunity-associated MHC class II polymorphisms therefore not only modify binding of self-peptides, but also alter the biochemistry of peptide acquisition.

overall_design: Mouse pancreatic tissue was digested by collagenase, and islets were isolated and dissociated into single cells. Beta-cell-specific CD4 T cells were single-cell sorted by FACS based on tetramer labeling, and individual cells were profiled with a modified full length SMART-Seq2 protocol.

first: Yoshinaga

last: Ito

first: Jason

last: Pyrdol

first: Adrienne

last: Luoma

first: Orit

last: Rozenblatt-Rosen

first: Matan

last: Hofree

first: Elena

last: Christian

first: Lucas

last: Ferrari de Andrade

first: Rong

last: En Tay

first: Luc

last: Teyton

first: Aviv

last: Regev

first: Stephanie

last: Dougan

first: Kai

middle: W

last: Wucherpfennig


title: Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

summary: N6-methyladenosine (m6A) is the most prevalent internal modification of mammalian messenger RNAs (mRNAs) and long non-coding RNAs. The biological functions of this reversible RNA modification can be interpreted by cytoplasmic and nuclear "m6A reader" proteins to fine-tune gene expression, such as mRNA degradation and translation initiation. Here we profiled transcriptome-wide m6A sites in adult mouse cerebral cortex, underscoring that m6A is a widespread epitranscriptomic modification in brain. Interestingly, the mRNA targets of fragile X mental retardation protein (FMRP), a selective RNA-binding protein, are enriched for m6A marks. Loss of functional FMRP leads to Fragile X syndrome (FXS), the most common inherited form of intellectual disability. Transcriptome-wide gene expression profiling identified 2,035 genes differentially expressed in the absence of FMRP in cortex, and 92.5% of 174 downregulated FMRP targets are marked by m6A. Biochemical analyses indicate that FMRP binds to the m6A sites of its mRNA targets and interacts with m6A reader YTHDF2 in an RNA-independent manner. FMRP maintains the stability of its mRNA targets while YTHDF2 promotes the degradation of these mRNAs. These data together suggest that FMRP regulates the stability of its m6A-marked mRNA targets through YTHDF2, which could potentially contribute to the molecular pathogenesis of FXS.

overall_design: Gene expression analyses were performed on mRNA samples isolated from the cerebral cortex of 6-week-old wild-type and Fmr1 KO male mice. N6-methyladenosine (m6A) epitranscriptome profiling was performed on the same mRNA samples. Six mice were pooled for each biological repilcate.

first: Peng

last: Jin


title: Atherosclerosis-driven Treg plasticity results in the formation of a dysfunctional subset of plastic IFNγ+ Th1/Tregs.

city: Norfolk

last: Galkina

state: VA

address: 700 West Olney Road

department: Microbiology and Molecular Cell Biology

institute: Eastern Virginia Medical School

summary: Here, we used single cell RNA-seq to compare the transcriptomes of Tregs, Th1, and plastic Th1/Tregs co-isolated from atherosclerotic Apoe-/- mice.

overall_design: 271 single T cell RNAseq libraries were generated from FACS sorted Apoe-/- splenic CD4+CD73+PD1+CD25+CCR5+ T cells via fluidigm C1, SMARTer, and NexteraXT reagents to compare gene expression between co-isolated Th1, Treg, and Th1/Treg cells.

first: Matthew

last: Butcher

first: Christopher

last: McGary

first: Adam

middle: R

last: Filipowicz

first: Patric

last: Lundberg


title: RNA sequencing of germinating Rhizopus delemar strain RA 99-880

city: Birmingham

first: Poppy

last: Sephton Clark

state: West Midlands

address: University of Birmingham

department: IMI

country: United Kingdom

institute: University of Birmingham

summary: Rhizopus delemar is an invasive fungal pathogen, responsible for the frequently fatal disease mucormycosis. Germination, a crucial mechanism by which spores of Rhizopus delemar infect and cause disease, is a key developmental process that transforms the dormant spore state into a vegetative one. Understanding the molecular mechanisms which underpin this transformation may be key to controlling mucormycosis; however, the regulation of germination remains poorly understood. This study describes the transcriptional changes which take place over the course of germination.

overall_design: mRNA sequenced from R. delemar germinated for: 0, 1, 2, 3, 4, 5, 6, 12, 16 and 24 hours. Three biological replicates were produced for each time point, mRNA from each sample was sequenced with Illumina HiSeq technology, with 100bp paired end reads.

last: Sephton-Clark

first: Jose

middle: F

last: Munoz

first: Elizabeth

last: Ballou

first: Christina

middle: A

last: Cuomo

first: Kerstin

last: Voelz


title: Human lymph nodes maintain a unique subset of resident memory T cells with high functional potential important for protective immunity and immunotherapies

first: Donna

last: Farber

department: Department of of Surgical Sciences and Microbiology and Immunology

institute: Columbia University

summary: Tissue resident memory T cells (TRM) predominate in barrier sites and mediate protective immunity, while their role in lymphoid tissues is undefined. Here we analyzed memory CD8+ T cells in different lymphoid compartments including bone marrow, spleen, and lymph nodes (LN) relative to lung within diverse individuals. We identify an organ-specific subset in human LN (TLN) not found in blood or other tissues, expressing high levels of TCF-1 and transcriptionally enriched for markers of quiescence, self-renewal and follicular-helper cells. High dimensional CyTOF analysis reveals TLN as intermediate in differentiation between naive and TRM cells, with circulating memory T cells the most differentiated. TLN exhibit higher TCR diversity, lower in vivo turnover, yet higher proliferative responses compared to memory cells in other lymphoid or mucosal sites. These findings establish human LN as reservoirs for diverse memory T cells poised for high expansion and TLN as important targets for in vivo immunotherapies.

overall_design: Here we did RNA-sequencing of T cell subsets isolated from human tissues. We isolated memory T cells (CD3+CD4-CD8+CD45RO+) that were either CD69+ or CD69- from either bone marrow or lymph nodes from the same individual and isolated RNA for RNA-seq. We did this from three different individuals, totaling 12 samples (2 from bone marrow (CD69 pos and neg) and 2 from lymph nodes(CD69 pos and neg) of three individuals). All RNA-seq samples were sequenced in the same batch.

first: Michelle

last: Miron


title: Sorted BCC timecourse after Vismo treatment - MCT, 6d, 14d

status: Public on Aug 08 2018

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP mice were aged until the appropriate tumor density was achieved. Skin samples were taken from control mice (untreated) or mice treated for 6 days or 14 days at twice a day dosing with vismodegib (75mg/kg body weight). RNA was extracted from freshly FACS sorted tumor cells based on GFP intensity.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0014328

overall_design: Gene expression profiling of tumor cells from BCC mice sorted at 6 days and 14 days of vismodegib treatment compared to sorted tumor cells from untreated mice.

first: Brian

last: Biehs


title: Dietary effect on mouse intestinal Bmi1 stem cells

city: Bronx

first: Wenge

last: Li

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

overall_design: Examination of transcriptomic profiles of intestinal stem cells fed with different diets

first: Leonard

last: Augenlicht


title: Dietary effect on mouse intestinal Lgr5 stem cells


title: CHD7 deficiency delays leukemogenesis in mice induced by CBFB-MYH11

city: Bethesda

first: Pu

middle: Paul

last: Liu

state: MD

address: 49 Convent Dr.

department: TFGB

institute: NHGRI/NIH

summary: CHD7 interacts with CBFb-SMMHC through RUNX1 and modulates their gene expression regulation and is important for CBFB-MYH11 leukemogenesis in the mouse model.

overall_design: RNA-seq of bone marrow c-KIT+ cells from 3 groups of mice: (1) WT, (2) Chd7f/f, Mx1-Cre, Cbfb+/56M, and (3) Mx1-Cre, Cbfb+/56M.

first: Tao

last: Zhen

first: P

middle: P


title: RNA-seq of genes mis-regulated in WT and the bpc1,2,3,4,6 loss-of-function mutant in response to cytokinin in roots of Arabidopsis thaliana

city: Chapel Hill

first: Carly

middle: Michelle

last: Shanks

state: NC

address: Genome Sciences Building, Room 4163

department: Biology

institute: UNC Chapel Hill

summary: We find that sub-set of cytokin repsonse genes are not regulated at WT levels in the bpc1,2,3,4,6 mutant.

overall_design: Whole ten-day-old seedlings of WT and the bpc1,2,3,4,6 mutant were treated with synthetic cytokinin (benzyladenine) or a vehicle control (NaOH) for 1 hour and root tissue was isolated.


title: TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells [4C-seq]

status: Public on Aug 07 2018

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

summary: We report the 4C-Seq profile of the IGFBP3 transcriptional start site in MCF7 and MCF7 TRPS1 CRISPR KO cell lines.

overall_design: Investigation of TRPS1- and YAP-dependent transcriptional programs.

first: Dana

last: Elster

first: Marie

last: Tollot


title: TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells [ATAC-seq]

summary: We report the ATAC-Seq profiles of TRPS-depleted T47D cells.


title: Hedgehog gradient in the stroma maintains niche diversity and organ function [RNA-seq]

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: We disrupted the spatial Hh activation gradient in murine lung by inducing the constitutively active form of the Hh effector, Smo (SmoM2), throughout the entire GLI2+ stroma and performed RNA-seq on the bulk GLI2+ population. Whole adult murine lung tissue was dissociated to single cells and subjected to fluorescence activated cell sorting (FACS) to select all live GLi2+ cells. The bulk RNA-sequencing library was then subsequently generated. Cells were sequenced at a depth of average of 45 million reads/sample. The results reveal that expansion of Hh activation in the GLI2+ domain in the murine lung resulted in upregulation of genes that are expressed in the proximal stroma fibroblasts. Conversely, Hh activation downregulated genes enriched in the distal stroma as well as mesothelial cells.

overall_design: Four Gli2creERT2-tdt:R26RYFP/SmoM2 mice were administered intraperitoneally with tamoxifen for labelling the Hh-activated GLI2+ cells with yellow fluorescent protein (YFP) reporter expression, and four Gli2creERT2-tdt:R26RYFP mice were used as control. Whole adult murine lung tissue was dissociated to single cells, and subjected to FACS to select all live YFP+ cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. The GLI2+ cells were sorted by endogenous YFP fluorescence. Then the RNA of the samples were extracted and sent to GENEWIZ company for sequencing o the Illumina HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.

first: Chaoqun

last: Wang

first: Tien

last: Peng


title: Regulated Capture of Vk Gene Topologically Associating Domains by Transcription Factories

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Antigen receptor gene recombination requires stochastic, monoallelic choice of a single variable gene in each lymphocyte progenitor. However, how this occurs remains unknown. Herein, we report that prior to Vκ to Jκ gene recombination, Igκ alleles reside within spatially different nuclear niches defined by elongating RNA Polymerase II (e-Pol II) and cyclin D3 complexes assembled on the nuclear matrix. Upon cell cycle exit, and cyclin D3 downregulation, only the Vκ allele in the more constrained e-Pol II niche was transcribed. Chromatin modeling and single cell RNA-seq revealed that the nuclear niche favored Vκ flanking CTCF sites, thus shaping the transcribed repertoire. Furthermore, multiple contiguous Vκs oriented away from CTCF sites were preferentially transcribed. Cyclin D3 also repressed monoallelic protocadherin and olfactory genes. These studies of Igκ reveal a general mechanism by which regulated, stochastic chromatin loop capture by fixed e-Pol II complexes generates diversity and couples cell cycle exit to monogenic choice.

overall_design: Bulk and Single Cell RNA-seq of B6 x CAST F1 hybrid small pre-B cells and bulk RNA-seq of Ccnd3-/- pro-B cells

first: Sophiya

last: Karki

first: Domenick

last: Kennedy

first: Kaitlin

last: Mclean

first: Adrian

last: Grzybowski

first: Shiladitya

last: Banerjee

first: Heping

last: Xu

first: Elizabeth

last: Davis

first: Malay

last: Mandal

first: Christine

last: Labno

first: Sarah

middle: E

last: Powers

last: Le Beau

first: Aaron

last: Dinner

first: Harinder

last: Singh

first: Alexander

last: Ruthenburg

first: Marcus

last: Clark


title: TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells

first: Bjoern

last: von Eyss

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

overall_design: Refer to individual Series


title: TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells [ChIP-seq]

summary: We report the ChIP-Seq profiles for TRPS1 and TEAD1 in MCF7 and T47D cell lines, and for YAP in MCF7 cells.

first: Dana

last: Elster

first: Marie

last: Tollot


title: Genome-wide chromatin accessibility profiling in adult human heart using DNase-seq

city: Baltimore

first: Dongwon

last: Lee

address: 733 N Broadway, MRB 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: We performed DNase-seq to identify open chromatin regions in adult human hearts as potential cis-regulatory elements

overall_design: We collected two adult female human heart left ventricle samples, one from an autopsy accessed 5 hours postmortem and one from an explant accessed 12 hours post-surgery, respectively. To evaluate the effect of postmortem or post-surgery time interval on DNaseI hypersensitivity, two pieces were dissected from each sample, both snap frozen but either immediately after dissection or after being left at room temperature for 19 hours and 12 hours, respectively

first: Ashish

last: Kapoor

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Marc

middle: K

last: Halushka

first: Gregory

last: Crawford

first: Aravinda

last: Chakravarti


title: TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells [RNA-seq]

summary: We report the gene expression profiles of TRPS-depleted and YAP 5SA overexpressing breast cancer cell lines.


title: Uridilation by TUT4/7 restricts retrotransposition of human Line-1s

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary:
Purpose: the goal of this study was to test whether the amounts of genome-encoded Line-1s are influenced by TUTases and Mov10
Methods: RNA-Seq data were obtained for PA-1 or Hek293 Flp-IN T-Rex cells in which wild-type or mutant TUTases or Mov10 were overexpressed or the proteins were depleted by RNA interference
Results: Minor changes (less than 0.4-fold) were observed in the amounts of mRNAs of Homo sapiens-specific Line-1 families in Hek293 Flp-IN T-Rex and PA-1 either overexpressing or depleted of TUTases and Mov10

overall_design: LINE-1 repetitive elements profiles of Hek293 Flp-IN T-Rex and PA-1 generated by deep sequencing, in triplicate, using Illumina NextSeq 500 and Illumina HiSeq 2500.

first: Zbigniew

last: Warkocki

first: Pawel

middle: S

last: Krawczyk

first: Dorota

last: Adamska

first: Krystian

last: Bijata

first: José

middle: L

last: Garcia-Perez


title: A super carbonate apatite (sCA) could deliver sufficient amounts of miRNA into the colorectum inflamed by dextran sodium sulfate (DSS) treatment

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary:
Purpose: A super carbonate apatite (sCA) nanoparticle is an in vivo pH-sensitive delivery system for siRNA and microRNA. These carriers accumulate specifically in tumors, yet they cause no serious adverse events in mice and monkeys. Systemic administration of sCA incorporating siRNA and microRNA has demonstrated superb tumor suppressive effects in vivo. We recently observed that sCA could deliver abundant nucleic acids to the inflammatory sites in rheumatoid arthritis mouse model. Based on the success, we tried to examine whether sCA could deliver sufficient amounts of miRNA into the colorectum inflamed by dextran sodium sulfate (DSS) treatment.
Methods: We performed a RNA sequencing analysis of the DSS-treated colon walls. DSS was administered for 4 days and sCA-miR-29a, sCA-miR-29b, sCA-NC-miR was injected on days 1, 2, 3. On day 4, colorectum was removed and the mRNA samples were subject to the RNA sequencing analysis.
Results: RNA sequencing of the rectum samples showed a number of enhanced or reduced gene expression in DSS treated NC-miR group on day 4 compared to normal mice. Such tendency of upregulation or downregulation was also noted in DSS-treated NC-miR group on day 2. Comparison of DSS treated samples on day 4 among NC-miR, miR-29a and miR-29b groups, revealed that several gene expression related to the interferon pathway was reversed by miR-29a or miR-29b towards the normal controls. These include Stat1, Stat2, IRF7, IRF9, and IFIT1.
Conclusions: Many molecules in the interferon signaling pathway were activated in DSS-induced colitis on day 4 and Stat1, Stat2, IRF7, IRF9, and IFIT1 were key molecules in the interferon related pathways. These findings suggest that sCA-miR-29a or sCA-miR-29b may inhibit type 1 IFN and type 2 IFN pathways which are otherwise activated by DSS treatment.

overall_design: ΜiR-29a and miR-29b, NC-miR loaded in sCA were systemically administered from the tail vein on the 1st, 2nd and 3rd days after the 2% DSS administration was started, and the rectum of the mouse was collected on the 4th day. RNA was extracted from the harvested colorectum. For these four conditions (n = 2) and normal mice (n = 2), ten samples were subjected to RNA sequencing.

first: Tadafumi

last: Fukata

first: Xin

last: Wu

first: Hirofumi

last: Yamamoto


title: Genome-wide Dppa4 binding in E14 mESC, 3T3, and P19 cells

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: DPPA4 is a DNA-associated factor that is highly and selectively expressed in embryonic stem cells. DPPA4 expression is strikingly downregulated upon loss of pluripotency, but is reactivated in a number of cancer cell types. It has recently been identified as an oncogene and shown to promote cell proliferation and anchorage independent growth; Dppa4-transformed cells can form tumors in vivo in mice. DPPA4 has been shown to associate with active chromatin and histone H3, but the global binding dynamics of DPPA4 are unknown. Additionally, only several DPPA4 gene targets are known. To better understand the role of DPPA4 in embryonic stem cell pluripotency and oncogenesis, we performed ChIP-Seq in E14 mouse embryonic stem cells (mESC), 3T3 cells ectopically expressing DPPA4, and P19 embryonic carcinoma cells.

overall_design: ChIP-Seq was performed in duplicate on E14 mouse embryonic stem cells, 3T3 cells ectopically expressing Dppa4, and P19 embryonic carcinoma cells

first: Rachel

last: Klein

first: Po-Yuan

last: Tung


title: Human Oral and Cutaneous Wound Healing Transcriptomes

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

summary: Comparative analysis between oral and cutaneous wound healing in humans using paired and sequential biopsies during the repair process.

overall_design: mRNA profiles of Oral/Skin Wound Healing human sample  were generated by sequencing using Illumina

first: Stephen

last: Brooks


title: Human normal oral keratinocytes (NOK) siRNA and Human epidermal keratinocytes (HEK) overexpression RNA-Seq

summary: Transcriptome of si-RNA transfected NOK  cells and adenovirus-transduced HEK cells

overall_design: mRNA profiles of HEK (human epidermal keratinocytes) transduced with adenoviruses and NOK (human normal oral keratinocytes) transfected with siRNAs.


title: Transcriptomes of human cutaneous and oral mucosa determine that rapid wound healing in the oral mucosa is predetermined by transcriptional networks that control keratinocyte differentiation and the inflammatory response


title: Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration

status: Public on Aug 06 2018

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute


title: Huntingtin aggregation impairs autophagy leading to Argonaute-2 accumulation and global microRNA dysregulation

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

type: Non-coding RNA profiling by high throughput sequencing

summary: Many neurodegenerative diseases are characterized by the presence of intracellular protein aggregates resulting in alterations in autophagy. However, the consequences of impaired autophagy on neuronal function remain poorly understood. In this study, we used cell culture and mouse models of huntingtin protein aggregation, as well as post-mortem material from patients with Huntington's disease to demonstrate that Argonaute-2 (AGO2) accumulates in the presence of neuronal protein aggregates and that this is due to impaired autophagy. Accumulation of AGO2, a key factor of the RNAinduced silencing complex that executes microRNA functions, results in global alterations of microRNA levels and activity. Together these results demonstrate that impaired autophagy found in neurodegenerative diseases not only influences protein aggregation, but also directly contributes to global alterations of intracellular posttranscriptional networks.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of mRNA sequencing of i) lentiviral mediated overexpression of wtHTT (18Q) and mHTT (66Q) in 293T cells, ii) striatal tissue collected from AAV-wtHTT and AAV-mHTT injected mice and examination of small RNA sequencing from i) lentiviral mediated overexpression of wtHTT (18Q) and mHTT (66Q) in 293T cells and ii)  AGO2-RIP and total RNA samples obtained from AAV-wtHTT and AAV-mHTT injected mice.

first: Karolina

last: Pircs

first: Rebecca

last: Petri

first: Sofia

last: Madsen

last: Brattås

first: Romina

last: Vuono

first: Daniella

last: Ottosson

first: Isabelle

last: St-Amour

first: Bob

last: Hersbach

first: Monika

last: Matusiak-Brückner

last: Hult Lundh

first: Åsa

last: Petersén

first: Nicole

last: Déglon

first: Sébastien

last: Hébert

first: Malin

last: Parmar

first: Roger

last: Barker

first: Johan

last: Jakobsson


title: In vivo evidence for ATPase-dependent DNA translocation by the Bacillus subtilis SMC condensin complex

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

summary: Structural maintenance of chromosomes (SMC) complexes shape the genomes of virtually all organisms but how they function remains incompletely understood. Recent studies in bacteria and eukaryotes have led to a unifying model in which these ring-shaped ATPases act along contiguous DNA segments processively enlarging DNA loops. In support of this model, single-molecule imaging experiments indicate that Saccharomyces cerevisiae condensin complexes can extrude DNA loops in an ATP hydrolysis dependent manner in vitro. Here, using time-resolved high-throughput chromosome conformation capture (Hi-C) we investigate the interplay between ATPase activity of the Bacillus subtilis SMC complex and loop formation in vivo. We show that point mutants in the SMC nucleotide binding domain that impair but do not eliminate ATPase activity not only exhibit delays in de novo loop formation but also have reduced rates of processive loop enlargement. These data provide in vivo evidence that SMC complexes function as loop extruders.

overall_design: Hi-C experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich media.

first: X

first: D

middle: Z

last: Rudner


title: Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration [bulk RNA-seq]

city: Cambridge

first: Chandra

last: Chilamakuri

summary: To compare secretory signatures of wildtype and mutant mice, the transcription profiles of tdTom+ cells from Atoh1(WT)CreERT2 R26RtdTom and Atoh1(9S/T-A)CreERT2 R26RtdTom mice were generated. The profiles were obtained for both small intestine (SI) and colon.

overall_design: A total of 6 mice were used for this experiment; TdTom+ population was collected from each SI and colon.

first: Goran

last: Tomic

first: Anna

last: Philpott

first: Douglas

middle: J

last: Winton


title: Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration    [colon]

summary: To define Atoh1 secretory signature, transcriptional profiling of secretory cells was performed. The expression profile of Atoh1+ cells from Atoh1(WT)CreERT2 R26RtdTom mice was determined by comparing tdTom+ (secretory) and tdTom- (absorptive) cells to define the baseline pro-secretory signature for both colon and small intestine (SI).

overall_design: A total of 8 mice were used for this experiment; TdTom+ and tdTom- populations were collected from each SI and colon.

first: Sarah

last: Kozar

first: Jing

last: Su


title: Single-cell RNA sequencing of circulating tumor cells in hepatocellular carcinoma

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: The purpose of this experiment is to detect and characterize circulating tumor cells in single cell sequence data and characterize the other cell types in the blood.

overall_design: As a pilot study, two samples coming from two different individuals were analyzed

first: Augusto

last: Villanueva

first: Delia

last: D'Avola


title: Evaluation of Edaphic Microbial Ammonium Oxidizing Communities during a Yellow Potato Cycle Culture

city: Bogotá

first: Sandra

middle: Milena

last: Gonzalez Sayer

state: Cundinamarca

address: 30th Avenue to 45th Street

department: Biotechnology Institute

country: Colombia

institute: National University of Colombia

summary: This study evaluated the ammonium oxidizing communities (COA) associated with a potato crop (Solanum phureja) rhizosphere soil in the savannah of Bogotá (Colombia) by examining the presence and abundance of amoA enzyme genes and transcripts by qPCR and next-generation sequence analysis. amoA gene abundance could not be quantified by qPCR due to problems inherent in the primers; however, the melting curve analysis detected increased fluorescence for Bacterial communities but not for Archaeal communities. Transcriptome analysis by next-generation sequencing revealed that the majority of reads mapped to ammonium-oxidizing Archaea, suggesting that this activity is primarily governed by the microbial group of the Crenarchaeota phylum. In contrast,a lower number of reads mapped to ammonia-oxidizing bacteria.

overall_design: Transcriptome of rhizosphere soil from the potato (Solanum phureja) crop, samples were collected at various growth stages: 20 days after planting (emergence), 50 days after planting (hilling) and 90 days after planting (flower advent); three potato plants with root–soil systems were randomly sampled as biological replicates for each growth stage.

last: Gonzalez

first: Guillermo

last: Torres

first: Laura

last: Ceron

first: Fabio

last: Aristizabal


title: Jun promotes axon regeneration by binding enhancer sites and dimerizing with Atf3

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary: Axon regeneration is a necessary step toward functional recovery after spinal cord injury. The AP-1 transcription factor c-Jun has long been known to play an important role in directing the transcriptional response of Dorsal Root Ganglion (DRG) neurons to peripheral axotomy that results in successful axon regeneration. Here we performed ChIPseq for Jun in mouse DRG neurons after a sciatic nerve crush or sham surgery in order to measure the changes in Jun’s DNA binding in response to peripheral axotomy. We found that the majority of Jun’s injury-responsive changes in DNA binding occur at putative enhancer elements, rather than proximal to transcription start sites. We also used a series of single polypeptide chain tandem transcription factors to test the effects of different Jun-containing dimers on neurite outgrowth in cortical and hippocampal neurons. These experiments demonstrated that dimers composed of Jun and Atf3 promoted neurite outgrowth in rat CNS neurons. Our work provides new insight into the mechanisms underlying Jun’s role in axon regeneration.

overall_design: This study measures two biological conditions: DRG neurons that received a sciatic nerve axotomy (injured), and DRG neurons that received a sham surgery (uninjured). For each condition, three biological replicates were performed. Each biological replicate consists of the pooled sciatic DRGs (L4-L6) of three adult, male, C57Bl/6 mice. For each biological replicate, the eluate of the chromatin immunoprecipitation for c-Jun is provided along with the input control.

first: John

last: Bixby

first: Vance

last: Lemmon


title: Nucleosome profiles for mammalian tissues

city: Irvine

first: Yumei

last: Li

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

sample_organism:
Macaca mulatta
Homo sapiens
Sus scrofa
Mus musculus
Tupaia belangeri


title: Nucleosome profiles for mammalian tissues [RNA-Seq]

summary: Chromatin structure affects gene splicing and nucleosome as the basic packaged unit is associated with exon recognition. But little is known about the function of nucleosome occupancy in the process of exon origination. Here we performed MNase-seq to obtain genome-wide nucleosome profiles for several tissues of human, rhesus monkey, treeshrew, mouse and pig. At the first time we found conserved nucleosome profile for different tissues. By combining RNA-seq data of each species, we traced the nucleosome occupancy changes of human new exons. Surprisingly, we found nucleosomes were higher occupied before exon formation. And this pre-occupancy contributed to the formation of exon-intron GC difference and maintain splice site strength. Thus we proposed a preadaption model for the function of nucleosome occupancy in human exons origination.

platform_organism:
Macaca mulatta
Homo sapiens
Sus scrofa
Mus musculus
Tupaia belangeri

overall_design: Nucleosome profiles and transcriptome for multiple tissues of human, monkey, tree shrew, mouse and pig.

first: Chen

first: Shuxian

first: Qi

last: Peng

first: Aibin

last: He

first: Chuanyun


title: Nucleosome profiles for mammalian tissues [Mnase-Seq]

summary: Chromatin structure affects gene splicing and nucleosome as the basic packaged unit is associated with exon recognition. But little is known about the function of nucleosome occupancy in the process of exon origination. Here we performed MNase-seq to obtain genome-wide nucleosome profiles for several tissues of human, rhesus monkey, tree shrew, mouse and pig. At the first time we found conserved nucleosome profile for different tissues. By combining RNA-seq data of each species, we traced the nucleosome occupancy changes of human new exons. Surprisingly, we found nucleosomes were higher occupied before exon formation. And this pre-occupancy contributed to the formation of exon-intron GC difference and maintain splice site strength. Thus we proposed a preadaption model for the function of nucleosome occupancy in human exons origination.


title: Sox5 and Sox6 direct a cardiac adaptive response to pressure overload

status: Public on Aug 05 2018

city: Dallas

first: Benjamin

last: Nelson

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical School

summary:
Rationale: We previously demonstrated that the transcription factor Sox6 regulates skeletal muscle biology by determining myofiber composition and muscle performance. Although the role of Sox6 and Sox5, its closest paralog, has not been ascertained in the heart, genome-wide association studies linked both Sox5 and Sox6 to cardiovascular disease.
Objective: This study identifies the role of Sox5 and Sox6 in the adult mammalian heart under normal and stress conditions.
Methods and Results: Using Sox5 and Sox6 cardiac-specific and Sox5 conduction system-specific knockout mice, we investigated the role of the two transcription factors in the heart under normal conditions and during cardiac stress. Sox5/6-deficient (DKO) mice displayed blunted cardiac contractility, which was present in Sox5 but not Sox6 single KO mice. DKO mice had a mild reduction in blood pressure, and conduction-specific knockout of Sox5 resulted in a reduced heart rate at baseline. After cardiac pressure overload, DKO mice showed increased lethality compared to control mice and were more prone to develop heart failure. We performed RNA deep sequencing in ventricles from DKO and control mice to identify potential Sox5/6 target genes and found altered expression of genes encoding regulators of calcium handling and cation transporters. Patch-clamping in isolated cardiomyocytes revealed shortened action potential duration in Sox5 KO cells.
Conclusions: Unlike in skeletal muscle, our results suggest Sox5 but not Sox6 to be a major regulator of cardiac function and rhythm. Sox5 is essential to preserve cardiac function under normal conditions by maintaining contractility and to prevent cardiac failure after pressure overload.

overall_design: Examination of 4 cardiac ventricles per genotype (DKO and control).

first: Nadine

last: Beetz

first: Tong

last: Zang

first: Lillian

last: Sutherland

first: Nikhil

middle: V

last: Munshi

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson


title: H3K9me3 ChIP-Seq in BJ-HELT cells

status: Public on Aug 04 2018

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

institute: IRCAN

summary: We generated H3K9me3 profile of reads and peaks of BJ fibroblasts expressing hTERT and SV40 early region (BJ-HELT cell line).

overall_design: Examination of H3K9me3 regions in BJ-HELT cells.

first: Aaron

last: Mendez-Bermudez

last: Gilson


title: RNA-seq for U937 cells with or without 3 day differentiation with PMA and recovery

status: Public on Aug 03 2018

city: South San Francisco

first: Christopher

middle: John

last: Bohlen

address: Room 15-2006, Genentech Building 15

department: Neuroscience

institute: Genentech

summary: Sequencing data related to our manuscript "Systematic identification of general and context-specific regulators of phagocytosis using magnetic genome-wide CRISPR screens"

overall_design: Two groups of U937 cells were sequenced before and after PMA differentiation. One group carried Streptococcus pyogenes Cas9 and a safe-harbor control sgRNA, and the second group was a clonally expanded U937 line expressing GFP. Each group was separated into eight separate wells at d0, and half of the wells were treated with 50 nM PMA. At day 3, undifferentiated cells were split to prevent overcrowding, and differentiated cells were trypsinized and replated. Cells were allowed to recover for 2 additional days before cells were lysed for RNA harvest and sequencing.

first: Michael

last: Haney

last: Bassik


title: Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration[intestine]

first: Chandra

last: Chilamakuri

summary: To define Atoh1 secretory signature, transcriptional profiling of secretory cells was performed. The expression profile of Atoh1+ cells from Atoh1(WT)CreERT2 R26RtdTom mice was determined by comparing tdTom+ (secretory) and tdTom- (absorptive) cells to define the baseline pro-secretory signature for small intestine (SI).

overall_design: A total of 8 mice were used for this experiment; TdTom+ and tdTom- populations were collected from each SI.

first: Sarah

last: Kozar

first: Jing

last: Su

first: Douglas

last: Winton


title: Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells [ATAC-Seq]

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: An IRF8-dependent subset of classical dendritic cells (cDCs), termed DC1, effectively cross-primes CD8+ T cells and facilitates antitumor T cell responses. Etv6 is an ETS family transcription factor that controls hematopoietic stem and progenitor cell (HSPC) function. We report that like HSPC, cDCs express Etv6 but not its antagonist ETS1, whereas interferon-producing plasmacytoid dendritic cells (pDCs) express both factors. Deletion of Etv6 in the bone marrow reduced the generation of DC1-like cells in vitro and the differentiation of DC1 in vivo, including the loss of signature marker CD8a. Global expression and chromatin profiling of Etv6-deficient DCs revealed impaired lineage identity of DC1, including the reduction of cDC signature and upregulation of pDC signature. Accordingly, DC-specific Etv6 deletion impaired CD8+ T cell cross-priming and tumor-specific CD8+ T cell responses. These results identify Etv6 as a regulator of DC1 differentiation and functional fitness that indirectly facilitates T cell cross-priming and antitumor immunity.

overall_design: Examination of chromatin accessibility profiles of Etv6-deficient dendritic cell subtypes

middle: M

first: Boris

last: Reizis


title: A map of gene expression in neutrophil-like cell lines

city: Davis

first: Sean

middle: R.

last: Collins

state: CALIFORNIA

address: One Shields Ave, 334 Briggs Hall

department: Microbiology & Molecular Genetics

institute: UC Davis

summary: We report gene expression data for the human cell lines HL-60 and PLB-985, which serve as models for human neutrophils. We measured gene expression using RNA-Seq for these cell lines both prior and after differentiation into a neutrophil-like state using two differentiation protocols (treatment with DMSO or treatment with DMSO and replacement of serum with Nutridoma).

overall_design: HL-60 and PLB-985 cells grown in culture were processed for RNA-Seq both before and after differentiation for six days in media supplemented with 1.3% dimethyl sulfoxide (DMSO). The cell lines were also analyzed after differentiation for six days in media with 1.3% DMSO, reduced serum (0.5% FBS), and Nutridoma-CS (2%). PLB-985 cells were also analyzed at intermediate time points of 2 days and 4 days with the Nutridoma protocol.

first: Esther

last: Rincón

first: Briana

last: Rocha-Gregg

middle: R


title: Nutritional control of protein translation

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

institute: Deutsches Krebsforschungszentrum

summary: Regulation of protein translation is a key feature of many biological processes. Global protein translation as well as translation at the codon level can be regulated by RNA modifications. These modifications are particularly enriched in tRNAs, where they represent an additional regulatory layer on top of the primary RNA sequence. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the gut microbiota and absorbed in the intestine. We show here that reduced queuine supply results in a strong reduction of tRNA queuosinylation in various cultured human cell lines and mouse tissues. In addition, Dnmt2-dependent tRNA methylation is dynamically modulated by the presence or absence of queuine. Ribosome profiling showed that nutritionally determined queuosine-tRNA (Q-tRNA) levels control the translation speed of Q-tRNA decoded codons. Dysregulation of translation resulted in pronounced endoplasmic reticulum stress and activation of the unfolded protein response, which could be rescued by the addition of queuine. Together, these findings establish a direct link between nutrient availability and the decoding of the transcriptome, thus providing a new perspective in our understanding of translational regulation.

overall_design: Cytoplasmic RNA and Cytoplasmic RNA protected by ribosome from RNase I (Ribonuclease I) cleavage, were sequenced. Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing.

first: Carine

last: Legrand


title: Functional aspects of meningeal lymphatics in ageing and Alzheimer's disease [1 of 3]

city: Charlottesville

last: Overall

state: Virginia

address: 409 Lane Road

institute: University of Virginia

summary: Aging is a major risk factor for many neurological pathologies, including Alzheimer’s disease (AD). However, the mechanisms underlying brain aging and cognitive decline remain elusive. Body tissues are perfused by interstitial fluid (ISF), which is locally reabsorbed via the lymphatic vascular network. In contrast, the parenchyma of the central nervous system (CNS) is devoid of lymphatic vasculature; in the brain, removal of cellular debris and toxic molecules, such as amyloid beta (A) peptides, is mediated by a combination of transcellular mechanisms of transport across the blood−brain and blood−cerebrospinal fluid (CSF) barriers, phagocytosis and digestion by resident microglia and recruited monocytes/macrophages, and CSF influx and ISF efflux through a paravascular route. The recent characterization of meningeal lymphatic vessels prompted a reassessment of the conventional pathways of CNS waste clearance. The role of this vasculature in brain function, specifically in the context of aging and AD, is still poorly understood. Here we show that meningeal lymphatic vessels play an essential role in maintaining brain homeostasis by draining macromolecules from the CNS (CSF and ISF) into the cervical lymph nodes. Using pharmacological, surgical, and genetic models we show that impairment of meningeal lymphatic function in adult mice slows paravascular influx of CSF macromolecules and efflux of ISF macromolecules, and induces cognitive impairment. Treatment with a lymphangiogenic factor, vascular endothelial growth factor C (VEGF-C), enhances meningeal lymphatic drainage of CSF macromolecules, improving brain perfusion and learning and memory performance in aged mice. Disruption of meningeal lymphatic vessels in transgenic mouse models of AD promotes amyloid deposition in the meninges, which closely correlates with human meningeal pathology, and aggravates overall disease severity. Our findings suggest that meningeal lymphatic dysfunction may be an aggravating factor in AD pathology and in age-associated cognitive decline. Thus, augmentation of meningeal lymphatic function might be a promising therapeutic target for preventing or delaying age-associated neurological diseases.

overall_design: Lymphatic endothelial cells (LECs) were isolated from meninges of adult (2-3 months-old) or old (20-24 months-old) male C57BL/6 mice. Cells were sorted by FACS according to the following phenotype: CD45-CD31+PDPN+.

first: Sandro

last: Da Mesquita

first: Antoine

last: Louveau

first: Andrea

last: Vaccari

first: Igor

last: Smirnov

first: R

last: Cornelison

first: Kathryn

last: Kingsmore

first: Christian

last: Contarino

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Daniel

last: Raper

first: Kenneth

last: Viar

first: Romie

middle: D

last: Powell

first: Wendy

last: Baker

first: Nisha

last: Dabhi

first: Robin

last: Bai

first: Rui

last: Cao

first: Song

last: Hu

first: Stephen

last: Rich

first: Jennifer

last: Munson

first: M

middle: B

last: Lopes

first: Scott

middle: T

last: Acton

first: Jonathan

last: Kipnis


title: RNA-sequencing of WT and Asic3-null leukemia-initiating cells (LICs)

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

institute: Tongji hospital

summary: To tease apart the downstream signaling triggered by the Asic3-mediated ion current, RNA-sequencing analyses were conducted with WT and Asic3-null LICs. We found 199 genes were significantly up-regulated, while 587 were down-regulated in Asic3-null LICs. The gene ontology (GO) analysis showed that ASIC3 might mainly be involved in the pattern recognition receptor activity, protein complex binding and calcium ion binding. KEGG further indicated that ASIC3 was required for the glutathione metabolism and hematopoietic cell lineage.

overall_design: WT and Asic3-null YFP+Mac-1+c-Kit+ LICs were purified by flow cytometry for the extraction of total RNA and subjected to RNA-sequencing.

first: Jun-Ke

last: Zheng

first: Hao

last: Gu


title: Identification of relationships between Molecular and Imaging Phenotypes in Non-small cell lung cancer using radiogenomics Map

city: Stanford

first: Shaimaa

last: Bakr

state: CA

address: 4450 Serra Mall, Stanford, CA 94305

department: Electrical Engineering

institute: Stanford University

summary:
Purpose:  To create a radiogenomic map linking computed tomographic (CT) image features and gene expression profiles generated by RNA sequencing for patients with non-small cell lung cancer (NSCLC).
Methods: A cohort of 113 patients with NSCLC diagnosed between April 2008 and September 2014 who had preoperative CT data and tumor tissue available was studied. For each tumor, a thoracic radiologist recorded 87 semantic image features, selected to reflect radiologic characteristics of nodule shape, margin, texture, tumor environment, and overall lung characteristics. Next, total RNA was extracted from the tissue and analyzed with RNA sequencing technology. Ten highly coexpressed gene clusters, termed metagenes, were identified, validated in publicly available gene-expression cohorts, and correlated with prognosis. Next, a radiogenomics map was built that linked semantic image features to metagenes by using the t statistic and the Spearman correlation metric with multiple testing correction.
Results: RNA sequencing analysis resulted in 10 metagenes that capture a variety of molecular pathways, including the epidermal growth factor (EGF) pathway. A radiogenomic map was created with 32 statistically significant correlations between semantic image features and metagenes.
Conclusions: Radiogenomic analysis of NSCLC showed multiple associations between semantic image features and metagenes that represented canonical molecular pathways

overall_design: We studied 130 cases of NSCLC with CT, PET/CT and RNASeq data under IRB approval from Stanford University and the Veterans Administration Palo Alto Health Care System. The collection of tissue samples consisted of a distribution of poorly- to well-differentiated adenocarcinomas and squamous cell cancers. The surgeon had removed necrotic debris during excision and sampled cavitary lesions to include as much solid component as practical. Then, from the excised tumor, he cut a 3 to 5 mm thick slice along its longest axis, and froze it within 30 minutes of excision. We retrieved the frozen tissue and extracted the RNA that was then processed by centrillion genomic services using Illumina Hiseq 2500

first: Olivier

last: Gevaert

first: Sylvia

last: Plevritis


title: Comparison of human brain and spinal cord neural stem cells (NSCs)

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Regional identity of several kind of human neural stem cells were assessed by RNA-Seq

overall_design: We compared whole transcriptome of human fetal spinal cord, fetal brain, fetal spinal cord derived NSCs, H9-derived NSCs, H9-derived spinal cord NSCs, and UCSF4-derived spinal cord NSCs

first: Hiromi

last: Kumamaru

first: Ken

last: Kadoya

first: Ruhel

last: Ahmad

first: Mark

last: Tuszynski


title: Single-Cell RNA-seq study of E13.5 and P7 brain and Spinal Cord Pdgfra-GFP positive samples during development in Mice.

status: Public on Aug 02 2018

city: Stockholm

first: David

last: van Bruggen

state: Stockholm

address: Scheeles väg 2

department: MBB

institute: Karolinska Institutet

summary: In order to elucidate the developmental origin of oligodendrocyte precursor cells (OPCs) and get a better understanding of the several waves of OPC generation, we look at several timepoints and perform single-cell RNA-seq on Pdgfra positive populations in Mice.

overall_design: Mice line used in this study included Pdgfra-cre-ERT/RCE and the Pdgfra-H2BGFP knock-in mouse. Embryos at embryonic day 13.5 and pups from post-natal day 7, from both genders of the  Pdgfra-GFP mice line were used to extract OPCs, as well as E12.5 and P3 tamoxifen injected mice harvested at P7. The single cell suspension from embryonic and post-natal tissue was FACS sorted for GFP positive cells using a BD FACSAria III Cell Sorter B5/R3/V3 system.

first: Gonçalo

last: Castelo-Branco

first: Sueli

last: Marques

first: Darya

last: Vanichkina


title: Transcriptonal profiling of the hippocampus in the CA1 subfield in Fmr1 knockout mouse

first: Rayna

middle: Michelle

last: Harris

address: 1 Shields Ave

institute: University of California Davis

summary: To better understand the effects silencing the Fmr1 gene, we conducted an integrative analysis of learning behavior, synaptic physiology, and hippocampal gene expression.

overall_design: We compared the CA1 transcriptome of wild type and Fmr1 knock out mice that were used as controls in a behavioral experiment testing active place avoidance

first: Hsin-Yu

last: Kao

first: Juan

last: Alarcon

first: Hans

last: Hofmann

first: Andre

last: Fenton


title: miRNAs affected in peripheral blood CD34+ cells by stroke

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: To understand the differentially expressed miRNAs in the peripheral blood CD34+ cells after stroke (first 24 hours after symptom onset), we have employed mRNA sequencing. Among 45 patients included in the study, 6 patients were chosen depending on the clinical outcome (3 patients with "good" and 3 patients with "bad" clinical outcome after 3 months). Immediately after the collection of the peripheral blood from the patients, mononuclear cells (MNCs) were isolated by density centrifugation. Then, CD34+ cells were isolated from MNCs using MACS columns. The cells were immediately frozen in RNAProtect Cell Reagent. The cell samples were shipped to Seqmatic LLC (Fremont, CA, USA) for RNA isolation and miRNA sequencing. RNA integrity measurements, library preparation and next generation sequencing were conducted at Seqmatic LLC, CA, USA.

overall_design: Around 50-60 mL peripheral blood was collected from stroke patients in the first 24 h after the symptom onset. The blood samples were diluted 2 times with dilution buffer (Ca2+/Mg2+-free PBS with 2mM EDTA) and 35 mL of blood was carefully layered on 15 mL of Lymphoprep (Axis-Shield, Oslo, Norway). After 35 min centrifugation at 400xg, the mononuclear cell (MNC) ring was collected and washed with MACS Buffer (Ca2+/Mg2+-free PBS with 2mM EDTA and 0.5% BSA) 3 times by centrifugation at 300xg. After the last centrifugation, the cells were counted and incubated with CD34 micro beads from Miltenyi according to the manufacturer's instructions. Then, the cells were passed through MACS columns 2 times (1 time through LS and 1 time through MS column) to obtain highly pure CD34+ cell population. The cells were centrifugaed at 300xg for 10 min and the cell pellet was frozen in RNAProtect Cell Reagent from Qiagen immediately. The cells were kept -80 celcius degrees until the shipment to Seqmatic LLC (CA, USA) on dry ice.


title: Characterization and Targeting of Malignant Stem Cells in Patients with Advanced Myelodysplastic Syndromes (MDS) [drug]

status: Public on Aug 01 2018

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

summary: In this study we report that during evolution of MDS malignant HSCs activate distinct cellular programs that render such cells susceptible to therapeutic intervention. Specifically, metabolic analyses of the MDS stem cell compartment shows a profound activation of protein synthesis machinery and increased oxidative phosphorylation that occurs during later stages of MDS pathogenesis. Reliance on protein synthesis makes MDS stem cells senstive to translation inhibitors including homoharringtonine.

overall_design: Respective populations were sorted from human bone marrow mononuclear cells, treated with Homoharringtonine for 4 hours at 250 nM and total RNA is isolated and subjected to RNA -seq.

first: Craig

last: Jordan


title: Characterization and Targeting of Malignant Stem Cells in Patients with Advanced Myelodysplastic Syndromes (MDS) [cell population]

summary: In this study we report that during evolution of MDS malignant HSCs activate distinct cellular programs that render such cells susceptible to therapeutic intervention. Specifically, metabolic analyses of the MDS stem cell compartment shows a profound activation of protein synthesis machinery and increased oxidative phosphorylation that occurs during later stages of MDS pathogenesis.

overall_design: Respective populations were sorted from human bone marrow mononuclear cells and total RNA is isolated and subjected to RNA -seq.


title: Active N6-Methyladenine demethylation by DMAD regulates gene expression by modulating the binding dynamics of Polycomb protein in neurons

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

summary: A Ten-Eleven Translocation (TET) ortholog has been identified as a DNA N6-Methyladenine (6mA) demethylase (DMAD) in Drosophila. However, the molecular roles of 6mA and DMAD remain largely unexplored. Through genome-wide 6mA and transcriptome profiling, we found that 6mA may serve as a repressive epigenetic mark on a group of genes involved in neurodevelopment and neuronal functions. Mechanistically, DMAD coordinates with Trithorax-related complex protein Wds to maintain active transcription by dynamically demethylating intragenic 6mA. Accumulation of 6mA by depleting DMAD recruits Polycomb protein Pc as 6mA reader and contributes to transcriptional repression. Our findings define an epigenetic role for 6mA and suggest that active 6mA demethylation by DMAD plays important roles in fly CNS function by coordinating additional epigenetic mechanisms.

overall_design: Examine the role of DMAD and 6mA DNA modification in Drosophila neuronal functions


title: Single-cell RNA-seq Uncovers Dynamic Processes and Critical Regulators in Mouse Spermatogenesis

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: A systematic interrogation of male germ cells is key to complete understanding of molecular mechanisms governing spermatogenesis and the development of new strategies for infertility therapies and male contraception. Here we develop an approach to purify all types of homogeneous spermatogenic cells by combining transgenic labelling and synchronization of the cycle of the seminiferous epithelium, and subsequent single-cell RNA-sequencing. We reveal extensive and previously uncharacterized dynamic processes and molecular signatures in gene expression, as well as specific patterns of alternative splicing, and novel regulators for specific stages of male germ cell development. Our transcriptomics analyses led us to discover discriminative markers for isolating specific stages of round spermatids, and identify different embryo developmental potential between early and late stage spermatids, providing evidence that maturation of round spermatids impacts on embryo development. This work provides valuable insights into mammalian spermatogenesis, and a comprehensive resource for the complete elucidation of gametogenesis.

overall_design: 2-dpp mice with Lin28-YFP and Vasa-dTomato were pipette fed WIN 18,446 (MP) for 7 consecutive days.  At Day 8 of WIN 18,446 treatments, these animals were received an injection of RA (Sigma), and then left to recover. At the right timepoint,we isolate the Vasa-dTomato positive synchronous spermatogenic cells to perform single-cell RNA-seq. For functional study, we performed Sox30 ChIP-seq.

first: Yao

last: Chen

first: Yun

last: Gao

first: Zhen

last: Lin

first: Suming

last: Yang

first: Tongtong

last: Wang

first: Qiu

first: Nannan

last: Xie

first: Rong

last: Hua

first: Mingxi

last: Liu

first: Jiahao

last: Sha

first: Michael D.

last: Griswold

first: Jinsong

last: Li

first: Fuchou

last: Tang

first: Ming-Han

last: Tong


title: A combination of transcription factors mediates inducible interchromosomal contacts

first: Seungsoo

last: Kim

address: 265 Campus Dr

department: Chemical and Systems Biology

summary: Development of MAP-C (mutation analysis in pools by chromosome conformation capture), which involves performing 3C on a pool of mutants (generated by programmed oligonucleotide pools, error-prone PCR, or existing mutant collections), followed by amplification of 3C DNA using primers specific to a chromosomal contact of interest (with the mutagenized or barcode region included), and as a control, amplifying the mutagenized or barcode region regardless of ligation. The 3C and genomic libraries are amplified with primers that add sequencing and flowcell adapters, and then deep sequenced to quantify the abundance of each mutant/barcode. The ratio of abundance in the 3C compared to the genomic library reflects the extent to which each sequence variant participates in the chromosomal contact of interest.

sample_organism: Saccharomyces cerevisiae x Saccharomyces uvarum

overall_design:
Hi-C on a S. cerevisiae x S. uvarum hybrid yeast strain; cis MAP-C to test 178 bp tiling subsequences of the S. cerevisiae HAS1pr-TDA1pr region, error-prone PCR and programmed 3 bp substitution mutants of a minimal pairing region; trans MAP-C to test knockouts of transcription factor and nucleoporins, interaction partners of Rgt1, 10 amino acid deletions of Rgt1, and domain deletion and phosphorylation site mutants of Rgt1; RNA-seq of S. cerevisiae x S. uvarum hybrids with mutations in binding sites for Leu3 or Rgt1; RNA-seq of S. cerevisiae deletion strains for LEU3, SDD4, and RGT1; ChIP-seq for TAP-tagged Leu3, Sdd4, and Rgt1. Each MAP-C experiment was done in 2 or 3 technical replicates beginning with cell lysis, and the Rgt1 deletions were done in two biological replicates beginning with yeast transformation. RNA-seq and ChIP-seq experiments were done in biological triplicate.

All FASTA files are available on the series record. Gene KO IDs are included in the processed data files *counts.txt.

first: Maitreya

last: Dunham

first: Jay

last: Shendure


title: Characterization of genome-wide DNA binding rhythms of HNF4A

first: Meng

last: Qu

state: California

address: 1002 West Childs Way

department: Keck Medical School

institute: University of Southern California

summary: HNF4A mRNA cycles over the coure of 24 h. To understand whether the chromatin binding of the transcription factor is also rhythmic, we performed ChIP-seq for HNF4A using mouse liver samples of ZT4 and ZT16. By analysing this dataset, we conclude that HNF4A binds chromatin much more robustly during the evening ( at ZT16).

overall_design: Examination of HNF4A genome binding at ZT4 and ZT16 using mouse liver samples, three mice were tested for each time point

first: Steve

last: Kay


title: Functional aspects of meningeal lymphatics in ageing and Alzheimer's disease [2 of 3]

first: Christopher

last: Overall

overall_design: Male C57BL/6J mice (2 months-old) were injected (intra-cisterna magna) with Visudyne (verteporfin for injection), or vehicle as control, and submitted to a step of photoconversion, to induce meningeal lymphatic vessel ablation. This procedure was repeated 2 weeks later to ensure prolonged meningeal lymphatic dysfunction. 2 weeks after the last surgical procedure, mice were subjected to the MWM test. 3 days after, whole hippocampus was macrodissected and total RNA was extracted for sequencing.

first: Sandro

last: Da Mesquita

first: Antoine

last: Louveau

first: Andrea

last: Vaccari

first: Igor

last: Smirnov

first: R

last: Cornelison

first: Kathryn

last: Kingsmore

first: Christian

last: Contarino

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Daniel

last: Raper

first: Kenneth

middle: E

last: Viar

first: Romie

last: Powell

first: Wendy

last: Baker

first: Nisha

last: Dabhi

first: Robin

last: Bai

first: Rui

last: Cao

first: Song

last: Hu

first: Stephen

middle: S

last: Rich

first: Jennifer

last: Munson

first: M

last: Lopes

first: Scott

last: Acton

first: Jonathan

last: Kipnis


title: Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells

first: Colleen

last: Lau

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

overall_design: Refer to individual Series


title: Biphasic polysaccharide metabolism of Alteromonas macleodii 83-1 analyzed by RNA-Seq

city: Oldenburg

first: Hanna

last: Koch

address: Carl-von-Ossietzky-Str. 9-11

institute: Institute for Chemistry and Biology of the Marine Environment

summary: Polysaccharides from macroalgae are important bacterial nutrient source and central biogeochemical component in the oceans. To illuminate the cellular mechanisms of polysaccharide degradation by marine bacteria, growth of Alteromonas macleodii 83-1 on a mix of laminarin, alginate and pectin was characterized using transcriptomics, proteomics and exometabolomics. A. macleodii 83-1 showed two distinct growth stages, with exponential growth during laminarin utilization followed by maintenance during simultaneous alginate/pectin utilization. The biphasic growth coincided with major temporal shifts in gene expression and metabolite secretion, enabling to define major/accessory polysaccharide utilization loci, reconstruct the complete degradation pathways for each polysaccharide, as well as identify temporal phenotypes in other relevant traits. FT-ICR-MS revealed a distinct suite of secreted metabolites for each growth phase, with pyrroloquinoline quinone exclusively produced with alginate/pectin. The finding of substrate-unique phenotypes indicates an exquisite adaptation to polysaccharide utilization with probable relevance for the degradation of macroalgal biomass, which comprises a complex mix of polysaccharides. Moreover, substrate-unique exometabolomes possibly influence metabolic interactions with other community members. Overall, the presence of fine-tuned genetic machineries for polysaccharide degradation and the widespread detection of related CAZymes in global locations indicate an ecological relevance of A. macleodii in marine polysaccharide cycling and bacteria-algae interactions.

overall_design:
Alteromonas macleodii 83-1 cells were grown on a mix of three polysaccharides (laminarin, pectin, alginate) in triplicates (Mix1-3). As control, cells were grown on glucose also in triplicates (Glucose1-3). For both incubations, biomass samples were taken at two time points; T1 (13h) and T2 (21h of incubation) and transcriptomics analyses were performed by doing RNA-Seq.

Please note that the FASTA file contains the nucleotide sequences of all genes of the genome, which were used as a reference to obtain transcript abundance counts by aligning them onto the gene sequences. The genome sequence is deposited in the DOE JGI-IMG/MER database (accession number 2716884210).

first: Alexandra

last: Duerwald

first: Thomas

last: Schweder

first: Beatriz

last: Noriega-Ortega

first: Thorsten

last: Dittmar

first: Heike

last: Freese

first: Meinhard

last: Simon

first: Matthias

last: Wietz


title: RNA Sequencing of Mycobacterium dioxanotrophicus PH-06

city: Houston

first: Ya

last: He

state: Texas

department: Department of Civil and Environmental Engineering

institute: Rice University

summary: Mycobacterium dioxanotrophicus PH-06  can degrade 1,4-dioxane (dioxane), which is a groundwater contaminant of emerging concern. In order to find the genes involved in dioxane degradation. RNA sequencing was first used to investigate gene expression levels of PH-06 during growth on two different carbon sources (dioxane and glucose). The sequencing shows that a monooxygenase gene cluster was upregulated when treated with dioxane relative to glucose.

overall_design: 2 samples, no replicate